Infokiri

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Contents INTRODUCTION .................................................................................................................................................. 2

HOW TO USE THIS DOCUMENT ........................................................................................................................................ 2 FINDING FURTHER INFORMATION .................................................................................................................................... 2 COPYRIGHT ................................................................................................................................................................ 2

REPORTING TO EPIPULSE CASES ......................................................................................................................... 3

CHECKING THE DATA COLLECTION SCHEDULE ..................................................................................................................... 3 PREPARING DATA ......................................................................................................................................................... 3 CHECKING METADATA ................................................................................................................................................... 3 CHECKING YOUR SURVEILLANCE SYSTEM DESCRIPTORS........................................................................................................ 4 UPLOADING YOUR DATA ................................................................................................................................................ 4 FINALISING YOUR SUBMISSION........................................................................................................................................ 5 EPIPULSE CASES HELPDESK ............................................................................................................................................ 9

DIPHTHERIA-SPECIFIC REPORTING ................................................................................................................... 10

MONTHLY AND ANNUAL REPORTING .............................................................................................................................. 10 NARRATIVE INFORMATION ........................................................................................................................................... 10

ANNEX 1. DIPHTHERIA METADATA .................................................................................................................. 12

DIPHTHERIA METADATA SET ......................................................................................................................................... 12 Current record type versions ............................................................................................................................. 12 Case-based reporting ........................................................................................................................................ 12 Aggregated reporting ....................................................................................................................................... 18 Changes to the diphtheria metadata ................................................................................................................ 20

ANNEX 2. CHANGES IN CASE DEFINITION ......................................................................................................... 23

Diphtheria Reporting Protocol 2024

Surveillance data for 2023 - 2024

EpiPulse Cases

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Introduction

This reporting protocol describes the reporting of 2024 measles and rubella cases to EpiPulse Cases, which is replacing TESSy.

Please note:

• Since February 2023, the reporting of diphtheria is described in a separate reporting protocol: Diphtheria, Reporting Protocol 2023, Version 1.0.

• The Vaccine Preventable Diseases (VPD) reporting protocol 2024 describes reporting of: pertussis, mumps, poliomyelitis and tetanus.

• The Invasive Bacteria Diseases (IBD) reporting protocol 2024 describes reporting of: invasive H. influenzae disease, invasive meningococcal disease, Neisseria Meningitidis isolates, and invasive pneumococcal disease.

Reporting protocols are data collection guidelines for the data managers of reporting countries and the protocol design is intended to improve user-friendliness by:

• introducing a uniform structure to make it easier for data managers to find data collection information across different subjects;

• removing information which is not relevant for data managers.

Similarly, the surveillance protocol will contain some of the generic information previously contained in the reporting protocols.

Since the data managers in reporting countries often have multiple roles, subject-specific material is sometimes distributed together with a reporting protocol. To maintain the uniform structure, this type of material is now included in Annex 1 and Annex 2.

How to use this document

This reporting protocol provides information for the data managers of reporting countries in three main sections:

• Reporting to EpiPulse Cases which contains guidelines on how to prepare data for submission to EpiPulse Cases, deadlines, subject-specific information (e.g. new changes to metadata), and links to further information.

• Annex 1 which contains:

− the metadata set for the subject(s) covered by this reporting protocol. − a list of metadata changes for the subject(s) covered by this reporting protocol.

• Annex 2 which contains subject-specific material relevant for distribution with the reporting protocol.

Finding further information Updated links to all the schedules, documentation and training materials mentioned in this reporting protocol are included in the Documentation and Help pages, including links to:

• EpiPulse Cases Metadata

• TESSy Metadata sets and change history • EpiPulse Cases Machine to Machine Technical Documentation • Tutorials for data transformation using respectively Excel and Access

Copyright © European Centre for Disease Prevention and Control, 2024. Reproduction is authorised, provided the source is acknowledged.

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Reporting to EpiPulse Cases

In September 2024 EpiPulse Cases is expected to go live. We have built it as a replacement for TESSy, with the aim of improving the process of reporting, reviewing, and updating surveillance data.

Only Vaccine-Preventable Diseases will be reported to EpiPulse Cases in 2024, all other diseases will continue to be reported to TESSy for now.

This section provides both an overview of the EpiPulse Cases reporting process and tips on where you can find useful information.

The overall process is as follows:

• Familiarise yourself with the data collection deadlines. • Prepare (export and transform) your data. • Check that your data complies with the EpiPulse Cases metadata. • Check that your data sources are up to date. • Submit your file(s) to EpiPulse Cases.

• Finalise and approve your submission.

Checking the data collection schedule

A link to the current data collections schedule can be found in the Communication section of the ‘Documentation and Help’ pages.

Preparing data

After you have exported the data from your national database, you need to ensure that the data are in a format that EpiPulse Cases can accept. EpiPulse Cases accepts only CSV and XML files, optionally ZIP-compressed. The EpiPulse Cases metadata has been developed from the TESSy Metadata, with the aim to make only the minimal number of changes necessary, and to hopefully provide a better experience when reporting your datasets to ECDC.

Specific guidelines for measles and rubella data collection and preparation for EpiPulse Cases are provided in Annex 1 and Annex 2.

Checking metadata

The metadata defines the fields and data formats that are valid as input to EpiPulse Cases for a given subject. The EpiPulse Cases metadata includes a section that compares and highlights the changes between TESSy and EpiPulse Cases, to facilitate the transition.

As the requirements for data to be shared among ECDC Stakeholders can change, the data format changes needed to support the new requirements are identified and agreed upon between the National Surveillance Contact Points, the Network Coordination Groups and ECDC’s Disease Experts. These changes are then implemented to the EpiPulse Cases metadata.

Changes to the metadata for the subject of this reporting protocol are described in Annex 1.

It is especially important to focus on:

• Field formats Many fields require the data to be formatted in a specific way. For example, dates must be in the YYYY-MM- DD format; dates in the DD/MM/YYYY format will be rejected.

• Reference Values (the equivalent of TESSy Coded Values) Some fields only permit the use of specific values (reference values). For example, M, F or OTH are the coded values for ‘Gender’ and any other value in a ‘Gender’ field will be rejected. Please note that UNK is no longer a valid code, you may leave the field empty instead.

The EpiPulse Cases metadata Excel file contains all the definitions and rules necessary to format data correctly. The READ ME sheet of the Excel document explains how to work with the metadata. It can be downloaded from the Technical Guidelines & Tools section of the ‘TESSy Help & Docs’ pages.

Filtering the fields in the file by subject will enable you to see the fields required for your subject and the rules that apply to these fields.

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Checking your Surveillance System Descriptors Before submitting file(s), please review your data source(s) in EpiPulse (in the menu, go to ‘Report’ -> ‘Surveillance systems descriptors’) and update the information as necessary.

Complete and up-to-date data source information for each subject is important for improving the interpretation of data - each surveillance system has different features that need to be taken into account when comparing data European level.

If your data source information is out-of-date and you do not have access rights to update it, please ask your National Focal Point for Surveillance or National Coordinator to do so.

Information on data sources is available in the TESSy User Guide, as this functionality is still only available through TESSy.

Uploading your data Data is submitted through the EpiPulse web interface (in the menu, go to Report -> EpiPulse Cases).

The visual interface for reporting new data and editing existing records has remained very similar to that of TESSy. For those of you that are also responsible for reporting diseases outside of the Vaccine Preventable Diseases group, you will continue to use TESSy (under EpiPulse) in parallel with the new EpiPulse Cases, until all disease groups will have been migrated to the new tool.

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Similar to TESSy, you can Add/Update or Replace data with new uploads, using either CSV or XML files. You can

also manually create records for some diseases, and report zero cases where appropriate.

The functionality for manually editing existing records is also a familiar experience. Search for the record you wish to edit, and modify the existing information as needed.

Finalising your submission The compliance of your data with the validation rules in the metadata is checked automatically during the data upload process. In EpiPulse Cases this process is called “Technical Validation”, and it is the only step where your upload can be rejected, for severe data quality issues, such as the file format not being readable by the system, or

(one of the few) mandatory variables having missing values.

If your file has been rejected, there will be a message explaining each instance of non-compliance with the metadata that needs correcting.

The significant new feature in EpiPulse Cases is the Data Validation Report, which puts your data in the context of the already existing information for the same disease, and provides you with a detailed overview of the new data in the file you have just uploaded, as well as the resulting overall epidemiological situation painted by the existing (past) data together with the newly uploaded file(s). This means much more timely feedback on your uploads, including details on data quality, as well as outputs (graphs, charts, and tables) on some of epidemiological indicators. The Data Validation reports will evolve and grow based on your feedback in collaboration with our Disease Experts. These reports will provide a new and better way of understanding and updating the information collected at European level, and will hopefully increase the quality and timeliness of the data, while reducing workloads.

Below you can find a few screenshots of the Data Validation Report.

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1. Begin by opening the report:

2. View the report in a window, download the list of eventual validation messages, or download the report

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3. Check data completeness; both for the new upload, and in the context of historical data

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4. The downloaded report can be opened full screen for easier viewing and navigation. This is a preview of the currently developed epidemiological indicators/stratifications.

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5. After reviewing the information in the Data Validation Report you can choose to approve or reject it.

If you choose to reject it, no data will be saved in the EpiPulse Cases system, but your file will remain visible should you wish to re-download it, or resubmit it for a new Data Validation at a later date or after further checks. Please check the Epi Validation Report carefully, there might be warnings and remarks relating to possible data quality issues or potential overwriting of existing records that you should consider.

When your file has been validated and you are satisfied that all corrections have been made, please ensure prompt approval or rejection. Unapproved uploads can block the approval of other related uploads.

EpiPulse Cases Helpdesk

Email: [email protected]

Telephone number: +46-(0)8-5860 1601

Availability: 9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC holidays)

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Diphtheria-specific reporting

Monthly and annual reporting

Monthly data collection – deadline last day of each month

Diphtheria data should be uploaded monthly by the last day of the month. Possible, probable and

confirmed cases should be reported.

Annual data collection – deadline 15 October of each year

An annual data call will still be carried out in order to finalise datasets for the previous year for use in

the annual epidemiological report. In the annual data call it will also be necessary to report “zero cases”

if no cases have occurred.

Once the data are validated by the disease experts at ECDC, they are made publicly available on a monthly basis on the Surveillance Atlas of Infectious Diseases with a choice of weekly, monthly and

annual temporal resolution, and through annual surveillance reports on the ECDC website.

Narrative information

Changes over time in the number of cases reported in a surveillance system do not always reflect true

changes in the incidence of disease. New reporting practices, improved laboratory capacities and

changes in legislation are some of the factors that can influence the number of cases reported. It is important to be aware of such “surveillance artefacts” when analysing surveillance data and countries

are encouraged to describe changes in the surveillance environment that may impact on the number of cases reported. It is equally important to report if the surveillance environment has remained the same

from one year to the next. We encourage reporting countries to provide this information at the same

time as data submission to TESSy and to [email protected].

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Case definition

Cases of diphtheria should be reported to TESSy if they meet any of the following criteria:

Clinical Criteria

Any person with at least one of the following clinical forms:

Classic Respiratory Diphtheria:

An upper respiratory tract illness with laryngitis or nasopharyngitis or tonsillitis

AND

an adherent membrane/pseudomembrane

Mild Respiratory Diphtheria:

An upper respiratory tract illness with laryngitis or nasopharyngitis or tonsillitis

WITHOUT

an adherent membrane/pseudomembrane.

Cutaneous Diphtheria:

Skin lesion

Diphtheria of other sites:

Lesion of conjunctiva or mucous membranes

Laboratory Criteria

Isolation of toxin-producing Corynebacterium diphtheriae, Corynebacterium ulcerans or

Corynebacterium pseudotuberculosis from a clinical specimen.

Epidemiological Criteria

At least one of the following epidemiological links:

— Human to human transmission

— Animal to human transmission

Case Classification

A. Possible case

Any person meeting the clinical criteria for classical respiratory diphtheria

B. Probable case

Any person meeting the clinical criteria for diphtheria (Classic Respiratory Diphtheria, Mild

Respiratory Diphtheria, Cutaneous Diphtheria, Diphtheria of other sites) with an epidemiological link to a human confirmed case or with an epidemiological link to animal

to human transmission

C. Confirmed case

Any person meeting the laboratory criteria AND at least one of the clinical forms.

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Annex 1. Diphtheria metadata

This section describes:

• The diphtheria metadata set • Changes to the diphtheria metadata

Diphtheria metadata set

Current record type versions

Table 1 shows the subject codes to be used when reporting diphtheria surveillance data to TESSy. Cases

should be reported according to the EU Case Definition1.

We strongly encourage case-based reporting. If case-based data are not available, aggregated data

may be reported.

Table 1. Diphtheria subject code

Disease Case-based subject code Aggregated subject code

Diphtheria DIPH DIPHAGGR

Case-based reporting

The metadata set has variables that are common across the VPD and disease specific variables. All

variables relevant to the reporting of diphtheria are summarised in alphabetical order in Table 2.

Table 2. Case-based metadata for the reporting of diphtheria (DIPH)

Variable Description Coded value list

Age Age of patient in years as reported in the

national system at the time of disease onset.

AgeMonth Age of patient in months as reported in

the national system for cases < 2 years of age at the time of disease onset.

AntimicrobialAgent Antibiotic tested for susceptibility. CIP = Ciprofloxacin

CLI = Clindamycin

ERY = Erythromycin

LNZ = Linezolid

MEM = Meropenem

PEN = Penicillin

RIF = Rifampin

SXT =

Sulfamethoxazole + trimethoprim

TCY = Tetracyclines

Biotype Biotype of DIP - C. diphtheriae only NST = Not subtypeable

OTH = Other

1 EU case definitions (europa.eu)

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VARBELF = var belfanti

VARGRAV = var gravis

VARINTMED = var intermedius

VARMITIS = var mitis

CaseClassification Case classification according to EU case definition.

CONF = Confirmed

DISCARDED = Discarded

POSS = Possible

PROB = Probable

ClinicalCriteria Clinical presentation (criteria) of the case. CONJ = Conjunctival

presentation

CUTA = Cutaneous

GEN = Genital presentation

NASAL = Uni- or bilateral nasal

discharge intially clear becoming bloody

OTH = Other

RESPCUTA = Respiratory and

cutaneous presentation

RESPMEMBR = Classic Respiratory with membrane

RESPNOMEMBR =

Respiratory with no membrane

ClusterID Unique identifier of the cluster as provided by the country epidemiologist.

ClusterRelated Is the case part of an outbreak/cluster?

ClusterSetting Setting of the cluster (for epidemiologically-linked cases).

CHILDCARE =

Kindergarten or child care

DET = Migrant detention centre

FAM = Family

MIL = Military

NOS = Nosocomial (hospital)

OTH = Other

SCH = School

SPORT = Sports team

UNI = University

ComplicationDiagnosis Any secondary disease that occurs as a consequence of Diphtheria.

CARDIACDIS = Cardiac disorder

NEURO = Neurological complications

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NEUROCARD =

Neurological & Cardiac disorder

OTH = Other

CountryOfBirth Country of birth of the case. Consult the reference values in mdLocation dataset

DataSource The data source (surveillance system) that the record originates from. The

DataSource value must be a special

reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateOfDiagnosis First date of clinical or lab diagnosis. In

case the DateOfOnset is missing this date is used for analysis.

DateOfEntry Date of entry into country where sampling and diagnosis occurred.

DateOfFirstSample The date of the first diagnostic sample that was positive for diphtheria.

DateOfLastVaccination

Date of administration of the last

vaccination dose - indicates the date when the last dose of vaccine was given before

disease onset (if exact date is not known, then provide month or year).

DateOfNotification

Date when the case report is first notified to public health authorities.

DateOfOnset

Date of onset of disease. Leave empty for

asymptomatic cases.

DateUsedForStatistics

The reference date used for standard

reports that is compared to the reporting

period. The date used for statistics can be any date that the reporting country finds

applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being

reported.

DIPH = Diphtheria

EpiLinkCaseId Provide record identifiers

(NationalRecordId) of epilinked cases.

Gender Gender of the reported case. F = Female

M = Male OTH = Other

ImportedStatus Imported: Having been outside the

country of notification during the incubation period of the reported disease,

and no links to local transmisison has been

identified. Import related case: case epidemiologically linked to an imported

case, i.e. cases that acquired the infection locally through a direct link to an imported

case in the first chain (only) of

transmission as supported by

END = Endemic case

IMP = Imported case

IMPREL = Import related case

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epidemiological and/or virological

evidence. Indigenous case: is a case

infected within the country of residence (based on epidemiological and virological

evidence) and that is not import-related, or any case with unknown source of

infection (no epidemiological or virological evidence).

MainPathogenDetectionMethod Pathogen detection method used on

MainSpecimen for confirmation of the case (Isolation of toxin-producing C.

diphtheriae/C. ulcerans/C pseudotuberculosis from a clinical

specimen). More than one method can be reported.

CULT = Culture

ELEK = Elek plate test

OTH = Other

PCR = PCR confirmation

RTPCR = Real time PCR

Main Specimen Main type of specimen with positive result

to be reported (can include material and/or sampling method and/or site).

MEMBR = Membrane

NASALSWAB = Nasal swab

OTH = Other

SKINSWAB = Skin swab

THROATSWAB = Throat swab

NationalRecordId Unique identifier for each record within and across the specified surveillance

system (data source) – selected and

generated by the country reporting the record.

Outcome Information on whether the case is alive or

deceased. The death should be due to the reported disease.

A = Alive

D = Died

Pathogen Species and genus of the pathogen which is the cause of the reported disease.

CORDIP =

Corynebacterium diphtheriae

CORPSE = Corynebacterium pseudotuberculosis

CORSPP =

Corynebacterium species, not specified

CORULC =

Corynebacterum ulcerans

PlaceOfInfection If ImportedStatus = 'IMP': The probable

place of infection should be provided at the country level. One entry for each

country visited before or during the diagnosis of the disease. Note this is a repeatable field.

Consult the reference values in mdLocation dataset

PlaceOfNotification Place of the first notification of the case to

a regional authority. Select the most detailed NUTS level possible.

Consult the reference values in mdLocation dataset

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PlaceOfResidence Place of residence of patient at the time of

disease onset. Select the most detailed NUTS level possible.

Consult the reference values in mdLocation dataset

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

SecondPathogenDetectionMethod Pathogen detection method used on

SecondSpecimen for confirmation of the case (Isolation of toxin-producing C.

diphtheriae/C. ulcerans/C

pseudotuberculosis from a clinical specimen). More than one method can be reported.

CULT = Culture

ELEK = Elek plate test

OTH = Other

PCR = PCR confirmation

RTPCR = Real time PCR

SecondSpecimen Second type of specimen with positive

result to be reported as optional (can include material and/or sampling method and/or site).

MEMBR = Membrane

NASALSWAB = Nasal swab

OTH = Other

SKINSWAB = Skin swab

THROATSWAB = Throat swab

SequenceType Diphtheria sequence type. Obtained by

multi locus sequence typing (MLST) or core genome multi locus sequence typing (cgMLST).

SIR_CIP Susceptibility to Ciprofloxacin as the final

interpretation based on one or more test results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_CLI Susceptibility to Clindamycin as the final

interpretation based on one or more test

results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_ERY Susceptibility to Erythromycin as the final

interpretation based on one or more test

results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_LNZ Susceptibility to Linezolid as the final interpretation based on one or more test

results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_MEM Susceptibility to Meropenem as the final

interpretation based on one or more test results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_PEN Susceptibility to Benzylpenicillin (penicillin

G) as the final interpretation based on one or more test results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_RIF Susceptibility to Rifampicin as the final

interpretation based on one or more test

I = Intermediate

R = Resistant

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results according to clinical breakpoints from EUCAST.

S = Susceptible

SIR_SXT Susceptibility to Trimethoprim-

sulfamethoxazole as the final

interpretation based on one or more test results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_TCY Susceptibility to Tetracycline as the final

interpretation based on one or more test results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

Status The Status value is used to provide the

functionality for a record within EpiPulse

Cases database. Default value: NEW/UPDATE. If set to DELETE, the

record with the specified NationalRecordId is deleted (invalidated) from EpiPulse

Cases database, if it exists. If set to

NEW/UPDATE, the record is inserted into the database: If the same

NationalRecordId already exists for the same data source and subject code, then

the current submitted record updates (replace) the existing one.

DELETE = Delete a

previously reported record

NEW/UPDATE = Update a previously

reported record (default)

SubjectCode SubjectCode is a reporting model for a disease/health topic - identifies the

reporting structure and format of a record (case based or aggregate reporting).

DIPH = Diphtheria

SuspectedVehicle Suspected vehicle or source of infection -

contact within the last 1-7 days (C. ulcerans only).

FARMANIMAL = Farm

animal such as cattle or sheep

OTH = Other

OTHERANIM = Other animal

PET = Pet animal such as dog or cat

RAWMILK = Raw milk/raw milk products

TravelPlaces Only applicabel if case is imported

(ImportedStatus = 'IMP'). The list can be

left empty even if the case is known to be imported. Note that this is a repeatable

field: List each country visited recently before/during diagnosis.

Consult the reference values in mdLocation dataset

VaccinationStatus Indicates if the case is vaccinated and

number of vaccine doses received.

10DOSE = 10 doses

1DOSE = 1 dose

2DOSE = 2 doses

3DOSE = 3 doses

4DOSE = 4 doses

5DOSE = 5 doses

6DOSE = 6 doses

7DOSE = 7 doses

8DOSE = 8 doses

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9DOSE = 9 doses

NOTVACC = Not vaccinated

UNKDOSE = Vaccinated, dose unknown

Wgs Information on whether whole genome

sequencing has been performed on isolates from the case.

WgsAccession Accession number if sequencing data have

already been uploaded to any public repository.

WgsSequenceId Sequence Read Archive (SRA) run

identifier, based on which the sequence read data can be retrieved.

Aggregated reporting

Please refer to Table 3 to see the format for aggregated reporting for diphtheria.

If only a few variables can be reported, it is recommended to give the following priority for reporting:

AgeGroup, CaseClassification, VaccinationStatus, Gender.

Table 3: Aggregate metadata for diphtheria (DIPHAGGR)

Variable Description Coded value list

AgeGroup Age group of the reported record. See Table 4 below.

CaseClassification Case classification according to EU

case definition.

CONF = Confirmed

POSS = Possible

PROB = Probable

DataSource The data source (surveillance system)

that the record originates from. The

DataSource value must be a special reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateUsedForStatistics

The reference date used for standard

reports that is compared to the

reporting period. The date used for statistics can be any date that the

reporting country finds applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being reported.

DIPH = Diphtheria

Gender Gender of the reported case. F = Female

M = Male OTH = Other

NumberOfCases Total number of cases during the reported period for the specified disease.

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

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SubjectCode SubjectCode is a reporting model for

a disease/health topic - identifies the reporting structure and format of a

record (case based or aggregate reporting).

DIPH = Diphtheria

VaccinationStatus Indicates if the case is vaccinated and number of vaccine doses received.

10DOSE = 10 doses

1DOSE = 1 dose

2DOSE = 2 doses

3DOSE = 3 doses

4DOSE = 4 doses

5DOSE = 5 doses

6DOSE = 6 doses

7DOSE = 7 doses

8DOSE = 8 doses

9DOSE = 9 doses

NOTVACC = Not vaccinated

UNKDOSE = Vaccinated, dose unknown

When reporting age, the age groups listed in Table 4 should be used.

Table 4. Age categories compatible with aggregate diphtheria reporting

Variable Narrative description Coded value of the variable AgeGroup

AgeGroup <1 year

1-4 years

5-9 years

10-14 years

15-19 years

20-24 years

25-29 years

30-34 years

35-39 years

40-44 years

45-49 years

50-54 years

55-59 years

60-64 years

65 and over

0

01-04

05-09

10-14

15-19

20-24

25-29

30-34

35-39

40-44

45-49

50-54

55-59

60-64

65+

Diphtheria Reporting Protocol 2024

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Changes to the diphtheria metadata

Metadata changes prior to 2014 can be found on the TESSy documents website. Changes from 2014

onwards have been summarised in Table 5 below.

Table 5. Summary of implemented changes in case-based and aggregated record types for diphtheria from 2014 to current Year of change

Subject Variables Description

2024 DIPH ALL Reporting moved from TESSy to the Epipulse Cases platform. This transition has led to changes in some variable names and categorical values (see below).

DIPH AccNumber Antibiotic Classification ClinicalPresentation ClusterIdentification Complications DateLastVaccDose EpiLinkCaseID Imported ProbablyCountryOfInfection RecordId RecordType ResultBiotype ResultSeqType Specimen1 Specimen2 Subject TestMethod1 TestMethod2 VaccStatus WGS

Variable names changed from (TESSy) → to (Epipulse Cases): AccNumber → WgsAccession Antibiotic → AntimicrobialAgent Classification → CaseClassification ClinicalPresentation → ClinicalCriteria ClusterIdentification → ClusterId Complications → ComplicationDiagnosis DateLastVaccDose → DateOfLastVaccination EpiLinkCaseID → EpiLinkCaseId Imported → ImportedStatus ProbablyCountryOfInfection → PlaceOfInfection RecordId → NationalRecordId RecordType → SubjectCode ResultBiotype → Biotype ResultSeqType → SequenceType Specimen1 → MainSpecimen Specimen2 → SecondSpecimen Subject → Disease TestMethod1 → MainPathogenDetectionMethod TestMethod 2→ SecondPathogenDetectionMethod VaccStatus → VaccinationStatus WGS → Wgs

ResultRibotype RecordTypeVersion

Variable removed

AntimicrobialAgent

SIR_CIP

SIR_CLI

SIR_ERY

SIR_LNZ

SIR_MEM

SIR_PEN

SIR_RIF

SIR_SXT

SIR_TCY

Discontinued values: “NA”, “UNK”

ClinicalCriteria Gender MainSpecimen SecondSpecimen MainPathogenDetectionMethod

SeondPathogenDetectioMethod

Discontinued values: UNK;

Remapping of: “O” to “OTH”

Biotype Discontinued values: “NA”, “NUS”, “UNK”; Remapping of: “O” to “OTH”

CaseClassification Discontinued values: UNK

ClusterRelated Wgs

Discontinued values: UNK; Variable changed from coded value to Boolean (0 = No ; 1 = Yes)

ClusterSetting Discontinued values: “NA”, “UNK”; Remapping of: “HOSP” to “NOS”, “MIGR” to “DET”

ComplicationDiagnosis Discontinued values: UNK; Remapping of: “NEURODIS” to “NEURO”, “O” to “OTH”

ImportedStatus Discontinued values: UNK; Remapping of: ”N” to “END”, “Y” to “IMP”

Outcome Discontinued values: NUS, UNK

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Pathogen Discontinued values: NUS Remapping of: “DIP” to “CORDIP”, “PSEU” to “CORPSE”, “ULC” to “CORULC”, “O” to “CORSPP”, “UNK” to “CORSPP”

SuspectedVehicle Discontinued values: “NA”, “NUS”, “UNK”; Remapping of: “FARMAN” to “FARMANIMAL”, “O” to “OTH”

VaccinationStatus Discontinued values: UNK; Remapping of: ”DOSEUNK” to “UNKDOSE”

Disease Status

Changed “Required” from “Yes” to “No”

DIPHAGGR

AgeClass Classification RecordType Subject

Variable names changed from (TESSy) → to (Epipulse Cases): AgeClass → AgeGroup Classification → CaseClassification RecordType → SubjectCode Subject → Disease

AgeGroup CaseClassification

Discontinued values: “UNK”

Disease Changed “Required” from “Yes” to “No”

Gender Discontinued values: “UNK” Remapping of: “O” to “OTH”

RecordTypeVersion Variable removed

SubjectCode Remapping of: “AGGR” to “DIPHAGGR”

VaccinationStatus New variable

2023 DIPH • The following variables were added:

DateOfEntry

o CountryOfBirth

TravelPlaces

o ClusterIdentification o ClusterRelated o ClusterSetting o EpiLinkCaseId o WGS o WgsSequenceId o AccNumber o DateOfFirstSample o ResultSeqType o Antibiotic o SIR_PEN o SIR_ERY o SIR_CIP o SIR_CLI o SIR_LNZ o SIR_MEM o SIR_RIF o SIR_TCY o SIR_SXT

2017 All VPD DateLastVaccDose • The description of the variable ‘DateLastVaccDose’ was updated to specify that the date given should be the date of last dose before

disease onset.

DIPH Classification

Pathogen

ClinicalPresentation

TestMethod

• The validation rules regarding the variables ‘Classification’ and ‘Pathogen’ were changed to ‘error’ so that cases with Classification==CONF could not be reported with unknown or missing data on Pathogen.

• A validation rule (warning) was added for cases reported as Classification==CONF but ClinicalPresentation==”UNK”.

• A validation rule (warning) for cases of Pathogen==ULC with ClinicalPresentation!=CUTA was removed.

• For the variable ‘ClinicalPresentation’, the coded value ‘NUS’ (not under surveillance) was dropped.

• For the variable ‘ClinicalPresentation’, the coded values ‘CONJ’ (conjunctival) and “GEN” (genital) were added.

• The variable ‘ClinicalPresentation’ was made a mandatory variable.

• The variable ‘TestMethod’ was made a mandatory variable.

22

• A validation rule (warning) was added where, for cases reported

as Classification==CONF, at least one of TestMethod1 or

TestMethod2 must be reported as 'PCR', 'RTPCR' , 'ELEK' or 'O'.

2016 DIPH TestMeth1 TestMeth2 AgeMonth ClinicalPresentation’

• The variables ‘TestMeth1’ and TestMeth2’ were renamed

‘TestMethod1’ and ‘TestMethod2’, in line with other VPDs.

• The variable ‘AgeMonth’ was added.

• The description of the variable ‘ClinicalPresentation’ was edited to match other VPDs.

2015 All VPD EpiLink ClinicalCriteria Labresult

• The variables ‘EpiLink’, ‘ClinicalCriteria’ and ‘Labresult’ were removed.

DIPH Classification

DateLastVaccDose

Pathogen

• The description of the variable ‘Classification’ was edited to ensure consistency with the EU case definition.

• The RecordType ‘HAGGR’ was removed.

• The variable ‘DateLastVaccDose’ was added.

• Two new coded values were added to the variable ‘Pathogen’. The coded value were PSEU=Corynebacterium pseudotuberculosis and NUS = Not under surveillance. This change reflects the update of the case definition in 2012.

2014 All VPD VaccStatus • The description of the coding for DOSEUNK (VaccStatus variable) was changed in the 2014 metadata for Measles, Mumps, Rubella, Pertussis, and Diphtheria. The name of the DOSEUNK coding was changed from “Unknown number of doses” to “Vaccinated with unknown number of doses”. This modification did not imply any operational change during data upload.

All • Update NUTS codes according to the NUTS Codes 2010

classification from EUROSTAT.

Diphtheria Reporting Protocol 2024

23

Annex 2. Changes in case definition

Countries are encouraged to use the 2018 EU case definition for the data collection. In the 2018 definition, no changes are implemented for diphtheria. For the 2018 EU Case Definition, see:

https://eur-lex.europa.eu/legal-content/EN/TXT/PDF/?uri=CELEX:32018D0945&from=EN

or https://ecdc.europa.eu/en/surveillance-and-disease-data/eu-case-definitions

The changes in the 2012 EU case definition as compared to 2008 are indicated in red:

(Corynebacterium diphtheriae, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis)

Clinical Criteria

Any person with at least one of the following clinical forms:

Classic Respiratory Diphtheria:

An upper respiratory tract illness with laryngitis or nasopharyngitis or tonsillitis

AND

an adherent membrane/pseudomembrane

Mild Respiratory Diphtheria:

An upper respiratory tract illness with laryngitis or nasopharyngitis or tonsillitis

WITHOUT

an adherent membrane/pseudomembrane.

Cutaneous Diphtheria:

Skin lesion

Diphtheria of other sites:

Lesion of conjunctiva or mucous membranes

Laboratory Criteria

Isolation of toxin-producing Corynebacterium diphtheriae, Corynebacterium ulcerans or

Corynebacterium pseudotuberculosis from a clinical specimen.

Epidemiological Criteria

At least one of the following epidemiological links:

— Human to human transmission

— Animal to human transmission

Case Classification

A. Possible case

Any person meeting the clinical criteria for classical respiratory diphtheria

B. Probable case

Any person meeting the clinical criteria for diphtheria (Classic Respiratory Diphtheria, Mild Respiratory Diphtheria, Cutaneous Diphtheria, Diphtheria of other sites) with an epidemiological

link to a human confirmed case or with an epidemiological link to animal to human transmission

C. Confirmed case

Any person meeting the laboratory criteria AND at least one of the clinical forms

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Machine to Machine Communication API Specification

EpiPulse Cases

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Document Version Version Date Comments

1.0 2024-07-06 Technical Documentation for Machine to Machine Interconnection

1. Introduction

1.1. Purpose

The Technical Design (TD) document provides an overview of the interfaces that are available for external systems to

interact with EpiPulse Cases.

1.2. Definitions

This table describes terms and abbreviations used in this document. Commonly used IT terms and abbreviations can

be found in ECDC’s IT Glossary Error! Bookmark not defined..

Term/Acronym Definition

JWT JSON Web Token Error! Reference source not found.

OIDC Open ID Connect

FME Feature Manipulation Engine

API Application Programming Interface

DUAPI Data Upload API

TV Technical Validation

EV Epidemiological Validation

WS Web Service

M2M Machine-to-Machine

WGS Whole Genome Sequencing

AWS Amazon Web Services

FMV File Mapping Validation

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1.3. Provide API for machine-to-machine interfacing.

The DUAPI is the externally exposed endpoint of the EpiPulse Cases architecture. It’s utilized by the DUUI to allow

users to access the system and it can also be used by external systems to interface as M2M. The interfaces provided

can be split in 3 major groups and are described in detail in Error! Reference source not found., section Error!

Reference source not found..

• Uploads, which provides functionality related to uploaded files (submitting, searching, retrieving)

• Technical Validation, which provides functionality related to the flow of technical validation (starting, retrieving

status and output, etc)

• Epidemiological Validation, which provides similar functionality to TV for EV

Appendix A – APIs This section describes the various interfaces of the system grouped per component and per area of functionality

provided. Payload or response attributes in grey are optional and may be omitted.

A.1 Authentication

This is the first call we have to do in order to gain access to the EpiPulse Cases. This call ADFS to get a JWT token.

URL: https://zfs.ecdc.europa.eu/adfs/oauth2/token

Authentication:

Authorization:

HTTP Method: POST

Payload as urlencoded:

{

grant_type:password

client_id:f142116f-a5d0-4089-bfaf-46bb0e5dd340

client_secret:a0P5pZqkIJKORIqoLzwoYr_PJDZdpv86nA7k_48u

username:ecdcdmz\EPC_NL_GENERAL-U

password:P@ssw0rd

resource: https://epipulse.ecdc.europa.eu/api/epipulsecases/dataupload

scope:openid

}

Response: {

"access_token": "TOKEN",

"token_type": "bearer",

"expires_in": 3600,

"resource": "https://epipulse.ecdc.europa.eu/api/epipulsecases/dataupload",

"refresh_token": "",

"refresh_token_expires_in": 28800,

"scope": "user_impersonation openid",

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"id_token": ""

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

A.2 Data Upload

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/Uploads

Authentication: JWT Barer Token

Authorization: Environment Access + Upload

HTTP Method: POST

Payload: {

"stream": "BASE64",

"fileName": "STRING",

"start": "DATETIME",

"end": "DATETIME", "ignoreDateStartEnd": "BOOLEAN"

"uploadType": "STRING",

"chunkIdentifier": "GUID"

}

Response: {

"fileName": "STRING",

"uploadGuid": "GUID",

"children": [{

"fileName": "STRING",

"uploadGuid": "GUID"

},...]

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 409 Conflict. If there is an ongoing metadata synchronization

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller • DUUI

Comments: Uploads a file and returns one or more (in case of a zip file containing multiple files) GUID(s). If the file is a zip, then the first entry returned will correspond to the zip file itself and the remaining to each of the children

URL: https://epipulse.ecdc.europa.eu /api/v1/DataUploadAPI/Uploads/UploadSaveStatus

Authentication JWT Barer Token

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Authorization: Environment Access + Upload

HTTP Method: POST

Payload: {

"uploadGuids": [

"GUID", … ],

}

Response: {

"uploadGuids": [

"GUID", … ],

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the content is 0 length or if the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Checks if the save was completed in the database for the given Guids and returns the list of Guids to start the technical validation if the file(s) was successfully saved.

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/Uploads/{uploadGuid}

Authentication JWT Barer Token

Authorization: Environment Access + UploadApprove

HTTP Method: PUT

Payload: {

"reportingPeriodStart": "DATETIME",

"reportingPeriodEnd": "DATETIME"

}

Response: {

"isSuccessful": BOOLEAN,

"taskCorrelationGuid": "GUID"

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the uploadGuid is not provided

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If the provided uploadGuid is not found in the Upload database

• 500 Internal Server Error. If an exception is thrown while servicing the request

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Caller

Comments: Allows the UI to update the reporting period start and end date.

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/Uploads/Search

Authentication JWT Barer Token

Authorization: Environment Access

HTTP Method: GET

Payload: {

"uploadDate": "STRING",

"subjectCode": "STRING",

"diseaseCode": "STRING",

"healthTopicCode": "STRING",

"fileName": "STRING",

"userName": "STRING",

"hasErrors": "BOOLEAN",

"hasWarnings": "BOOLEAN",

"uploadGuids": [

"GUID", …],

"onlySubmittedByMe", "BOOLEAN"

"orderBy": "STRING",

"pageNumber": INTEGER,

"pageSize": INTEGER

"allowedStatuses": ["STRING", …],

"notAllowedStatuses": ["STRING", …]

}

Response: {

"uploads": [ {

"uploadGuid": "GUID",

"technicalValidationJobGroupGuid": "GUID",

"epidemiologicalValidationGuid": "GUID",

"dateUploaded": "DATETIME",

"dateEpiStarted": "DATETIME",

"dateTechnicalValidationStarted": "DATETIME",

"subjectCode": "STRING",

"fileName": "STRING",

"userName": "STRING",

"uploadState": "STRING",

"recordCount": INTEGER,

"deletedRowCount": INTEGER,

"numberOfErrors": INTEGER,

"numberOfWarnings": INTEGER,

"technicalValidationProgressPercentage": INTEGER,

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"epidemiologicalValidationProgressPercentage": INTEGER,

"parentUploadGuid": "GUID",

"parentUploadFileName": "STRING",

"hasComplesSubjectCode": "BOOLEAN", "reportingPeriodStartDate": "DATETIME",

"reportingPeriodEndDate": "DATETIME",

"minDateUsedForStatistics": "DATETIME",

"maxDateUsedForStatistics": "DATETIME",

"uploadType": "STRING",

"uploadTypeName": "STRING",

"hasOngoingEpiValidation": "BOOLEAN",

"diseaceCode": "STRING",

"fileSize": LONG,

"fileTypeID": SHORT,

"reportingCountry": "STRING",

"ignoreDateStartEnd: "BOOLEAN",

"parentComplexUploadGuid": "GUID",

"uiSubjectCodeColumn": "STRING",

"healthTopicCode": "STRING"

}, … ],

"totalUploadsCount": INTEGER

}

HTTP codes: • 200 Success. Response returned as documented above

• 401 Unauthorized. If authorization checks fail

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Performs a query on the uploaded files based on provided filters providing ordering and paging functionality

A.3 Technical validation

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations

Authentication JWT Barer Token

Authorization: Environment Access + UploadApprove

HTTP Method: POST

Payload: {

"uploadGuids": [

"GUID", … ],

"autoStartEpidemiologicalValidation": BOOLEAN

}

Response: {

"technicalValidationJobGroupCount": INTEGER

}

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HTTP codes: • 200 Success. Response returned as documented above

• 401 Unauthorized. If authorization checks fail

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Starts the Technical Validation for an upload.

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations/ {technicalValidationJobGroupGuid}

Authentication JWT Barer Token

Authorization: Environment Access

HTTP Method: GET

Response: {

"startDateTime": "DATETIME",

"currentStep": "STRING",

"progressPercentage": INTEGER

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If technicalValidationJobGroupGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Queries the status/progress of a technical validation job

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations/ {technicalValidationJobGroupGuid}/Results

Authentication JWT Barer Token

Authorization: Environment Access

HTTP Method: GET

Response: {

"messages": [ {

"location": {

"recordIdentifier": "STRING",

"variable": "STRING",

"rowNumber": "STRING",

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"columnIndex": "STRING"

},

"severity": "STRING",

"subjectCode": "STRING",

"validationRuleCode": "STRING",

"validationMessage": "STRING",

"solutionMessage": "STRING"

}, … ],

"identityFieldName": "STRING"

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If technicalValidationJobGroupGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Retrieves the messages generated as a result of the technical validation process directly from the EpiPulseCasesTechnicalValidation database

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations/ {uploadGuid}

Authentication JWT Barer Token

Authorization: Environment Access + UploadApprove

HTTP Method: DELETE

Response: {

"isSuccessful": BOOLEAN,

"taskCorrelationGuid": "GUID"

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the provided uploadGuid is empty

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If uploadGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Cancel a running technical validation

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URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations/ {technicalValidationJobGroupGuid}?Action=Reject

Authentication JWT Barer Token

Authorization: Environment Access + UploadApprove

HTTP Method: PUT

Response: {

"isSuccessful": BOOLEAN,

"taskCorrelationGuid": "GUID"

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the provided technicalValidationJobGroupGuid is empty or the action is not “Reject”

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If technicalValidationJobGroupGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Reject a completed technical validation

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations/ {technicalValidationJobGroupGuid}/Results/csv

Authentication JWT Barer Token

Authorization: Environment Access

HTTP Method: GET

Response: CSV file containing the technical validation messages for a given technicalValidationJobGroupGuid. The MIME types used is "Text/csv" and the file name "TechnicalValidationMessages – {technicalValidationJobGroupGuid}.csv"

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If technicalValidationJobGroupGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller • DUUI

Comments: Retrieves the messages generated as a result of the technical validation process as a CSV file directly from the EpiPulseCasesTechnicalValidation database

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A.4 Data (Epidemiological) Validation

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/EpidemiologicalValidations

Authentication JWT Barer Token

Authorization: Environment Access + Upload

HTTP Method: POST

Payload: {

"uploadGuids": [

"GUID"

]

}

Response: {

"isSuccessful": BOOLEAN,

"taskCorrelationGuid": "GUID"

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 409 Conflict. If there is another running epidemiological validation for the same country and disease

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller • DUUI

Comments: Starts the Epidemiological Validation for an upload.

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/EpidemiologicalValidations/ OngoingStatus/{subjectGuid}

Authentication JWT Barer Token

Authorization: Environment Access

HTTP Method: GET

Response: BOOLEAN

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception) or the provide subjectGuid was not a valid GUID

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If subjectGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

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Caller

Comments: Returns if a particular subject has an ongoing epidemiological validation (for the country of the caller)

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EpiPulse Cases.

Quick guide.

The new design of EpiPulse Cases is the first step of improving user experience during submitting epidemiological surveillance data for the communicable diseases and related special health issues.

A new (single page) EpiPulse Cases application is available for the users. When a nominated user selects to use the new EpiPulse Cases lands in the main page of the application (called “Submissions page”):

This page provides an overview of the current state of the already submitted data, with some useful searching or sorting functionalities:

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Additional functionalities for the way information appears is also available. The user is able to add or remove columns or select to view only files uploaded from the current user:

Multiple options are available for the user to upload data.

Depending on the permissions of the user, all or some of the following options are available:

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The user can upload data (for both “Add/Update” or “Replace” upload action types) by using three different types of files: csv, xml or zip (that contain csv or/and xml files).

The application automatically performs all required checks, so that the user could proceed with the upload:

The user can also create manually the required data submission, using the “Manually create” and/or “Zero reporting” functionalities.

A wizard, using all required fields as specified in metadata, will help user fill the data. Auto-validation functionality during the process helps user avoid errors:

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The user can proceed through the flow by using an emerging floating “actions” bar:

The actions appearing are controlled by configuration related to the combination of rules for each file selected (submission status, subjectcode etc.) and the user’s permissions:

The reporting of molecular surveillance and required WGS data (Raw reads and/or Assembly files) is also a user-friendly process for the user.

Data could be uploaded using some of the options mentioned above and/or as a hierarchy of datasets which is used to submit complex files:

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Or, in case of additional data required, after selecting the related action from the actions bar, a pop- up window guides the user to the next steps.

Uploading the WGS data files, using the related window:

And then, after using the required genomic files naming conventions, proceed to the WGS file validation:

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During the submission flow for both types, epidemiological and molecular surveillance, user can follow up the progress of his submission(s) and view details of the current submission state as well as some useful information about the content of the submitted file and the timeline of the previous steps:

Viewing “Data validation report” is the next-to-last step in order for the user to conclude with the submission of the data:

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The user reviews information included in the report:

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and then decides whether submitted data should be stored (approved) or discarded (rejected):

Given that the user approves data submission, information is updating the ECDC data warehouse.

User is also able to access stored data and edit or delete records:

Page 1 of 30

Contents INTRODUCTION ......................................................................................................................................... 2

HOW TO USE THIS DOCUMENT ............................................................................................................................... 2 FINDING FURTHER INFORMATION ........................................................................................................................... 2 COPYRIGHT ........................................................................................................................................................... 2

REPORTING TO EPIPULSE CASES ......................................................................................................... 3

CHECKING THE DATA COLLECTION SCHEDULE .......................................................................................................... 3 PREPARING DATA ................................................................................................................................................... 3 CHECKING METADATA ............................................................................................................................................ 3 CHECKING YOUR SURVEILLANCE SYSTEM DESCRIPTORS .......................................................................................... 4 UPLOADING YOUR DATA ......................................................................................................................................... 4 FINALISING YOUR SUBMISSION ............................................................................................................................... 5 EPIPULSE CASES HELPDESK ................................................................................................................................... 9

ANNEX 1. IBD METADATA ...................................................................................................................... 10

IBD METADATA SET ............................................................................................................................................. 10 Current subject codes ................................................................................................................................. 10 Case-based reporting.................................................................................................................................. 10 Aggregated reporting ................................................................................................................................. 19

CHANGES TO THE IBD METADATA ........................................................................................................................ 21

ANNEX 2. IBD-SPECIFIC MATERIAL ................................................................................................... 26

IBD DATA REPORTING FREQUENCY ....................................................................................................................... 26 REPORTING OF MENINGOCOCCAL DISEASE ISOLATES (MENIISO) ......................................................................... 26 NARRATIVE INFORMATION ................................................................................................................................... 27 INVASIVE H. INFLUENZAE DISEASE DATA COLLECTION AND CASE DEFINITIONS ....................................................... 28 INVASIVE MENINGOCOCCAL DISEASE DATA COLLECTION AND CASE DEFINITIONS ..................................................... 29 INVASIVE PNEUMOCOCCAL DISEASE DATA COLLECTION AND CASE DEFINITIONS ...................................................... 30

Invasive Bacterial Diseases (IBD) Reporting Protocol 2024

Invasive H. influenzae Disease, Invasive Meningococcal disease, Neisseria Meningitidis Isolate, Invasive Pneumococcal Disease

Surveillance data for 2023

EpiPulse Cases

Page 2 of 30

Introduction

This reporting protocol describes the reporting of 2024 measles and rubella cases to EpiPulse Cases, which is replacing TESSy.

Please note:

• Since February 2023, the reporting of diphtheria is described in a separate reporting protocol: Diphtheria, Reporting Protocol 2023, Version 1.0.

• The Vaccine Preventable Diseases (VPD) reporting protocol 2024 describes reporting of: pertussis, mumps, poliomyelitis and tetanus.

• The Invasive Bacteria Diseases (IBD) reporting protocol 2024 describes reporting of: invasive H. influenzae disease, invasive meningococcal disease, Neisseria Meningitidis isolates, and invasive pneumococcal disease.

Reporting protocols are data collection guidelines for the data managers of reporting countries and the protocol

design is intended to improve user-friendliness by:

• introducing a uniform structure to make it easier for data managers to find data collection information across different subjects;

• removing information which is not relevant for data managers.

Similarly, the surveillance protocol will contain some of the generic information previously contained in the reporting protocols.

Since the data managers in reporting countries often have multiple roles, subject-specific material is sometimes distributed together with a reporting protocol. To maintain the uniform structure, this type of material is now included in Annex 2.

How to use this document

This reporting protocol provides information for the data managers of reporting countries in three main sections:

• Reporting to EpiPulse Cases which contains guidelines on how to prepare data for submission to EpiPulse

Cases, deadlines, subject-specific information (e.g. new changes to metadata), and links to further information.

• Annex 1 which contains:

− the metadata set for the subject(s) covered by this reporting protocol. − a list of metadata changes for the subject(s) covered by this reporting protocol.

• Annex 2 which contains subject-specific material relevant for distribution with the reporting protocol.

Finding further information Updated links to all the schedules, documentation and training materials mentioned in this reporting protocol are included in the Documentation and Help pages, including links to:

• EpiPulse Cases Metadata • TESSy Metadata sets and change history • EpiPulse Cases Machine to Machine Technical Documentation • Tutorials for data transformation using respectively Excel and Access

Copyright

© European Centre for Disease Prevention and Control, 2024. Reproduction is authorised, provided the source is acknowledged.

Page 3 of 30

Reporting to EpiPulse Cases

In September 2024 EpiPulse Cases is expected to go live. We have built it as a replacement for TESSy, with the aim of improving the process of reporting, reviewing, and updating surveillance data.

Only Vaccine-Preventable Diseases will be reported to EpiPulse Cases in 2024, all other diseases will continue to be reported to TESSy for now.

This section provides both an overview of the EpiPulse Cases reporting process and tips on where you can find useful information.

The overall process is as follows:

• Familiarise yourself with the data collection deadlines. • Prepare (export and transform) your data. • Check that your data complies with the EpiPulse Cases metadata. • Check that your data sources are up to date. • Submit your file(s) to EpiPulse Cases. • Finalise and approve your submission.

Checking the data collection schedule

A link to the current data collections schedule can be found in the Communication section of the ‘Documentation and Help’ pages.

Preparing data After you have exported the data from your national database, you need to ensure that the data are in a format that EpiPulse Cases can accept. EpiPulse Cases accepts only CSV and XML files, optionally ZIP-compressed. The EpiPulse Cases metadata has been developed from the TESSy Metadata, with the aim to make only the minimal number of changes necessary, and to hopefully provide a better experience when reporting your datasets to ECDC.

Specific guidelines for measles and rubella data collection and preparation for EpiPulse Cases are provided in Annex 1 and Annex 2.

Checking metadata The metadata defines the fields and data formats that are valid as input to EpiPulse Cases for a given subject. The EpiPulse Cases metadata includes a section that compares and highlights the changes between TESSy and EpiPulse Cases, to facilitate the transition.

As the requirements for data to be shared among ECDC Stakeholders can change, the data format changes needed to support the new requirements are identified and agreed upon between the National Surveillance Contact Points, the Network Coordination Groups and ECDC’s Disease Experts. These changes are then implemented to the EpiPulse Cases metadata.

Changes to the metadata for the subject of this reporting protocol are described in Annex 1.

It is especially important to focus on:

• Field formats Many fields require the data to be formatted in a specific way. For example, dates must be in the YYYY- MM-DD format; dates in the DD/MM/YYYY format will be rejected.

• Reference Values (the equivalent of TESSy Coded Values) Some fields only permit the use of specific values (reference values). For example, M, F or OTH are the coded values for ‘Gender’ and any other value in a ‘Gender’ field will be rejected. Please note that UNK is no longer a valid code, you may leave the field empty instead.

The EpiPulse Cases metadata Excel file contains all the definitions and rules necessary to format data correctly. The READ ME sheet of the Excel document explains how to work with the metadata. It can be downloaded from the Technical Guidelines & Tools section of the ‘TESSy Help & Docs’ pages.

Filtering the fields in the file by subject will enable you to see the fields required for your subject and the rules that apply to these fields.

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Checking your Surveillance System Descriptors Before submitting file(s), please review your data source(s) in EpiPulse (in the menu, go to ‘Report’ -> ‘Surveillance systems descriptors’) and update the information as necessary.

Complete and up-to-date data source information for each subject is important for improving the interpretation of data - each surveillance system has different features that need to be taken into account when comparing data European level.

If your data source information is out-of-date and you do not have access rights to update it, please ask your National Focal Point for Surveillance or National Coordinator to do so.

Information on data sources is available in the TESSy User Guide, as this functionality is still only available through TESSy.

Uploading your data

Data is submitted through the EpiPulse web interface (in the menu, go to Report -> EpiPulse Cases).

The visual interface for reporting new data and editing existing records has remained very similar to that of TESSy. For those of you that are also responsible for reporting diseases outside of the Vaccine Preventable Diseases group, you will continue to use TESSy (under EpiPulse) in parallel with the new EpiPulse Cases, until all disease groups will have been migrated to the new tool.

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Similar to TESSy, you can Add/Update or Replace data with new uploads, using either CSV or XML files. You can

also manually create records for some diseases, and report zero cases where appropriate.

The functionality for manually editing existing records is also a familiar experience. Search for the record you wish to edit, and modify the existing information as needed.

Finalising your submission The compliance of your data with the validation rules in the metadata is checked automatically during the data upload process. In EpiPulse Cases this process is called “Technical Validation”, and it is the only step where your upload can be rejected, for severe data quality issues, such as the file format not being readable by the system, or (one of the few) mandatory variables having missing values.

If your file has been rejected, there will be a message explaining each instance of non-compliance with the metadata that needs correcting.

The significant new feature in EpiPulse Cases is the Data Validation Report, which puts your data in the context of the already existing information for the same disease, and provides you with a detailed overview of the new data in the file you have just uploaded, as well as the resulting overall epidemiological situation painted by the existing (past) data together with the newly uploaded file(s). This means much more timely feedback on your uploads, including details on data quality, as well as outputs (graphs, charts, and tables) on some of epidemiological indicators. The Data Validation reports will evolve and grow based on your feedback in collaboration with our Disease Experts. These reports will provide a new and better way of understanding and updating the information collected at European level, and will hopefully increase the quality and timeliness of the data, while reducing workloads.

Below you can find a few screenshots of the Data Validation Report.

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1. Begin by opening the report:

2. View the report in a window, download the list of eventual validation messages, or download the report

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3. Check data completeness; both for the new upload, and in the context of historical data

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4. The downloaded report can be opened full screen for easier viewing and navigation. This is a preview of the currently developed epidemiological indicators/stratifications.

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5. After reviewing the information in the Data Validation Report you can choose to approve or reject it.

If you choose to reject it, no data will be saved in the EpiPulse Cases system, but your file will remain visible should you wish to re-download it, or resubmit it for a new Data Validation at a later date or after further checks. Please check the Epi Validation Report carefully, there might be warnings and remarks relating to possible data quality issues or potential overwriting of existing records that you should consider.

When your file has been validated and you are satisfied that all corrections have been made, please ensure

prompt approval or rejection. Unapproved uploads can block the approval of other related uploads.

EpiPulse Cases Helpdesk

Email: [email protected]

Telephone number: +46-(0)8-5860 1601

Availability: 9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC holidays)

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Annex 1. IBD metadata

This section describes:

• The IBD metadata set • Changes to the IBD metadata

IBD metadata set

Current subject codes

Table 1 shows the subject codes (formerly ‘record types’) to be used when reporting 2023 VPD surveillance data to Epipulse Cases (EPC). Cases should be reported according to the relevant EU Case

Definition1.

We strongly encourage case-based reporting. If case-based data are not available, aggregated data

may be reported.

Table 1: IBD subject codes

Disease Case-based

subject code

Aggregated

subject code

Invasive Haemophilus influenzae disease HAEINF HAEINFAGGR

Invasive meningococcal disease MENI MENIAGGR

Invasive pneumococcal disease PNEU PNEUAGGR

Neisseria Meningitidis Isolates (Molecular surveillance) MENIISO n/a

Comment: An aggregated format called “AGGR” was previously available. From 2024, with the move

from TESSy reporting to Epipulse Cases, aggregated subject codes HAEINFAGGR, MENIAGGR and

PNEUAGGR have been launched. An aggregated subject code is not available for MENIISO.

Case-based reporting

The metadata set has variables that are common across all the Invasive Bacterial Diseases (IBD): invasive H. influenzae disease (HAEINF), invasive meningococcal disease (MENI), invasive

pneumococcal disease (PNEU), which are summarised in Table 2. Disease-specific variables (in addition to the common variables) are subsequently summarised in Table 3 (HAEINF), Table 4 (MENI)

and Table 5 (PNEU). Case-based variables for the Neisseria meningitidis Isolates (MENIISO) dataset

are summarised in Table 6.

1 EU case definitions (europa.eu)

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Table 2: Case-based metadata common across IBD data (subject codes: HAEINF, MENI, PNEU)

2 For both PNEU and HAEINF: only confirmed cases should be reported according to the EU Case Definition. For MENI: confirmed, probable and possible cases can be reported according to the EU Case Definition. 3 Only reported for HAEINF and MENI - not included in PNEU dataset.

Variable Description Coded value list

Age Age of patient in years as reported in the national system at the time of disease onset.

AgeMonth Age of patient in months as reported in the national system for cases < 2 years of age at the time of disease onset.

CaseClassification 2 Case classification according to EU case definition. CONF = Confirmed POSS = Possible

PROB = Probable

DataSource The data source (surveillance system) that the record originates from. The DataSource value must be a special reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateOfDiagnosis First date of clinical or lab diagnosis. In case the DateOfOnset is missing this date is used for analysis.

DateOfLastVaccination Date of administration of the last vaccination dose - indicates the date when the last dose of vaccine was given before disease onset (if exact date is not known, then provide month or year).

DateOfNotification Date when the case report is first notified to public health authorities.

DateOfOnset 3 Date of onset of disease. Leave empty for asymptomatic cases.

DateUsedForStatistics The reference date used for standard reports that is compared to the reporting period. The date used for statistics can be any date that the reporting country finds applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being reported. HAEINF = Haemophilus infection MENI = Invasive meningococcal disease PNEU = Invasive pneumococcal disease

Gender Gender of the reported case. F = Female M = Male OTH = Other

NationalRecordId Unique identifier for each record within and across the specified surveillance system (data source) – selected and generated by the country reporting the record.

Outcome Information on whether the case is alive or deceased. The death should be due to the reported disease. A = Alive D = Died

PlaceOfNotification Place of the first notification of the case to a regional authority. Select the most detailed NUTS level possible. Consult the reference values in mdLocation dataset

PlaceOfResidence Place of residence of patient at the time of disease onset. Select the most detailed NUTS level possible. Consult the reference values in mdLocation dataset

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

Status The Status value is used to provide the functionality for a record within EpiPulse Cases database. Default value: NEW/UPDATE. If set to DELETE, the record with the specified NationalRecordId is deleted (invalidated) from EpiPulse Cases database, if it exists. If set to NEW/UPDATE, the record is inserted into the database: If

DELETE = Delete a previously reported record. NEW/UPDATE = Update a previously reported record (default).

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Table 3: Case-based metadata – additional HAEINF-specific variables

the same NationalRecordId already exists for the same data source and subject code, then the current submitted record updates (replace) the existing one.

SubjectCode SubjectCode is a reporting model for a disease/health topic - identifies the reporting structure and format of a record (case based or aggregate reporting).

HAEINF = Haemophilus infection MENI = Meningococcal disease PNEU = Pneumococcal infection

Variable Description Coded value list

ClinicalCriteria Clinical presentation of the disease. CELL = Cellulitis EPIG = Epiglottitis MENI = Meningitis/Meningeal/ Meningoencephalitic MENISEPTI = Meningitis and septicaemia OSE = Osteomyelitits/septic arthritis OTH = Other PNEU = Pneumonia

SEPTI = Septicaemia

MainPathogenDetectionMethod Pathogen detection method used on the primary laboratory specimen with a positive result for case confirmation and further characterisation of the disease. More than one method can be reported.

ANTIGEN = Antigen detection CULT = Culture GENOSEQ = Genotyping/Sequencing IMMUNO = Immunodiagnostic tests NUCLACID = Detection of nucleic acid OTH = Other

SecondPathogenDetectionMethod Pathogen detection method used on the second type of laboratory specimen with a positive result (if taken) for diagnosis or further characterisation of the disease. More than one method can be reported.

ANTIGEN = Antigen detection CULT = Culture GENOSEQ = Genotyping/Sequencing

IMMUNO = Immunodiagnostic tests NUCLACID = Detection of nucleic acid OTH = Other

Serotype Serotype of the pathogen which is the cause of the reported disease. HAEINF_A = H. influenzae type a HAEINF_B = H. influenzae type b HAEINF_C = H. influenzae type c HAEINF_D = H. influenzae type d HAEINF_E = H. influenzae type e HAEINF_F = H. influenzae type f HAEINF_NONCAPS = H. influenzae non-capsulated strain

HAEINF_NOT_B = H. influenzae non-b strain HAEINF_UNK = H. influenzae type unknown

VaccinationStatus Indicates if the case is vaccinated against serotype b and number of vaccine doses received.

10DOSE = 10 doses 1DOSE = 1 dose

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Table 4: Case-based metadata – additional MENI-specific variables

2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses 5DOSE = 5 doses 6DOSE = 6 doses 7DOSE = 7 doses 8DOSE = 8 doses 9DOSE = 9 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

Variable Description Coded value list

ClinicalCriteria Clinical presentation of the disease according to the EU case definition. MENI = Meningitis/Meningeal/ Meningoencephalitic MENISEPTI = Meningitis and septicaemia OTH = Other PNEU = Pneumonia SEPTI = Septicaemia

Imported Infection has occurred following exposure outside the reporting country during a time compatible with the incubation period of the infection.

0 = No 1 = Yes

IsolateId Unique identifier for each isolate within the data source/laboratory system related to the case. In option1 in the Reporting Protocol, this variable corresponds to the EMERT II identifier.

MainPathogen DetectionMethod

Pathogen detection method used on the primary laboratory specimen with a positive result for case confirmation and further characterisation of the disease. More than one method can be reported.

ANTIGEN = Antigen detection CULT = Culture GENOSEQ = Genotyping/Sequencing

MICRO = Microscopy NUCLACID = Detection of nucleic acid OTH = Other

MICSign_CIP This field can indicate if a value of the MICValueAST_CIP test is "less than" (<); "equal to or less than" (<=); "equal to" (=); "equal to or greater than"(>=); or "greater than" (>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

MICSign_CTX_CFX This field can indicate if a value of the MICValueAST_CTX_CFX test is "less than"(<); "equal to or less

than"(<=); "equal to"(=); "equal to or greater than"(>=); or "greater than"(>) the value indicated in the following field.

< = Less than

<= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

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MICSign_PEN This field can indicate if a value of the MICValueAST_PEN test is "less than" (<); "equal to or less than" (<=); "equal to" (=); "equal to or greater than"(>=); or "greater than" (>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

MICSign_RIF This field can indicate if a value of the MICValueAST_RIF test is "less than" (<); "equal to or less than" (<=); "equal to" (=); "equal to or greater than"(>=); or "greater than" (>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

MICValueAST_CIP MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

MICValueAST_CTX_CFX MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

MICValueAST_PEN MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

MICValueAST_RIF MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

PlaceOfInfection If Imported = 1 (TRUE): The probable place of infection should be provided at the country level. One entry for each country visited during the incubation period of the disease. Note this is a repeatable field.

Consult the reference values in mdLocation dataset

ReportedEMERTII Describe if the isolate related to the case was reported to EMERT II. 0 = No 1 = Yes

ResultFetVR Serotype Gene FetA VR variable region. Values from http://neisseria.org/nm/typing/tessy/. Consult the reference values for SubjectCode = MENI and Variable = ResultFetVR

ResultMLST Multilocus Sequence Typing clonal complex of strain. Values from http://neisseria.org/nm/typing/tessy/. Consult the reference values for SubjectCode = MENI and Variable = ResultMLST

ResultPorA1 Serotype Gene PorA variable region 1. Values from http://neisseria.org/nm/typing/tessy/. Consult the reference values for SubjectCode = MENI and Variable = ResultPorA1

ResultPorA2 Serotype Gene PorA variable region 2. Values from http://neisseria.org/nm/typing/tessy/. Consult the reference values for SubjectCode = MENI and Variable = ResultPorA2

SecondPathogen DetectionMethod

Pathogen detection method used on the second type of laboratory specimen with a positive result (if taken) for diagnosis or further characterisation of the disease. More than one method can be reported.

ANTIGEN = Antigen detection CULT = Culture GENOSEQ = Genotyping/Sequencing MICRO = Microscopy NUCLACID = Detection of nucleic acid OTH = Other

Serogroup Serogroup will not be known if clinical diagnosis only used to identify disease. NEIMENI_29E = N. meningitidis serogroup 29E NEIMENI_A = N. meningitidis serogroup A NEIMENI_B = N. meningitidis serogroup B NEIMENI_C = N. meningitidis serogroup C NEIMENI_NGA = N. meningitidis not groupable

NEIMENI_OTH = N. meningitidis other serogroup NEIMENI_W = N. meningitidis serogroup W NEIMENI_X = N. meningitidis serogroup X NEIMENI_Y = N. meningitidis serogroup Y

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Table 5: Case-based metadata – additional PNEU-specific variables

NEIMENI_Z = N. meningitidis serogroup Z NEIMENI_Z/29E = N. meningitidis serogroup Z/29E

SIR_CIP Susceptibility to Ciprofloxacin as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

SIR_CTX_CFX Susceptibility to Cefotaxime or Ceftriaxone as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

SIR_PEN Susceptibility to Penicillin as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

SIR_RIF Susceptibility to Rifampicin as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

VaccinationStatus Indicates if the case is vaccinated against the serogroup of meningococcus that was the cause of infection and number of vaccine doses received.

1DOSE = 1 dose 2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

Variable Description Coded value list

ASTMethod Test method(s) used for MIC determination. AGARDIL = Agar dilution AUTOM = Automated instrument method BROTHDIL = Broth microdilution GRAD = Antimicrobial gradient (E-test, etc) OTH = Other

BrandPCV1 Type of PCV at first dose. PCV10 = Pneumococcal conjugate vaccine 10 PCV13 = Pneumococcal conjugate vaccine 13 PCV15 = Pneumococcal conjugate vaccine 15 PCV20 = Pneumococcal conjugate vaccine 20 PCV7 = Pneumococcal conjugate vaccine 7

BrandPCV2 Type of PCV at second dose. PCV10 = Pneumococcal conjugate vaccine 10

PCV13 = Pneumococcal conjugate vaccine 13 PCV15 = Pneumococcal conjugate vaccine 15 PCV20 = Pneumococcal conjugate vaccine 20 PCV7 = Pneumococcal conjugate vaccine 7

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BrandPCV3 Type of PCV at third dose. PCV10 = Pneumococcal conjugate vaccine 10 PCV13 = Pneumococcal conjugate vaccine 13 PCV15 = Pneumococcal conjugate vaccine 15 PCV20 = Pneumococcal conjugate vaccine 20 PCV7 = Pneumococcal conjugate vaccine 7

BrandPCV4 Type of PCV at fourth dose. PCV10 = Pneumococcal conjugate vaccine 10 PCV13 = Pneumococcal conjugate vaccine 13 PCV15 = Pneumococcal conjugate vaccine 15 PCV20 = Pneumococcal conjugate vaccine 20 PCV7 = Pneumococcal conjugate vaccine 7

ClinicalCriteria Clinical presentation of the disease. BACTERPNEUMO = Bacteraemic pneumonia MENI = Meningitis/Meningeal/Meningoencephalitic MENISEPTI = Meningitis and septicaemia OTH = Other SEPTI = Septicaemia

DatePCV1 Date of first dose of PCV.

DatePCV2 Date of second dose of PCV.

DatePCV3 Date of third dose of PCV.

DatePCV4 Date of fourth dose of PCV.

DatePPV Date of PPV.

DosePCV1 First dose of vaccination with a PCV. 0 = No 1 = Yes

DosePCV2 Second dose of vaccination with a PCV. 0 = No 1 = Yes

DosePCV3 Third dose of vaccination with a PCV. 0 = No 1 = Yes

DosePCV4 Fourth dose of vaccination with a PCV. 0 = No

1 = Yes

DosePPV Vaccinated with PPV. 0 = No 1 = Yes

MICSign_CTX_CFX This field can indicate if a value of the MICValueAST_CTX_CFX test is "less than"(<); "equal to or less than"(<=); "equal to"(=); "equal to or greater than"(>=); or "greater than"(>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

MICSign_ERY This field can indicate if a value of the MICValueAST_ERY test is "less than" (<); "equal to or less than" (<=); "equal to" (=); "equal to or greater than"(>=); or "greater than" (>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

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MICSign_PEN This field can indicate if a value of the MICValueAST_PEN test is "less than" (<); "equal to or less than" (<=); "equal to" (=); "equal to or greater than"(>=); or "greater than" (>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

MICValueAST_CTX_CFX MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

MICValueAST_ERY MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

MICValueAST_PEN MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

NRLData If 1 (TRUE) - data is based on data from National Reference laboratory, if 0 (FALSE) - data is based on

clinical and non-reference-laboratory data.

0 = No

1 = Yes

PathogenDetectionMethod Pathogen detection method used for serotyping. More than one method can be reported. COAGG = Coagglutination GDIFF = Gel diffusion MPCR = Multiplex PCR OTH = Other PTEST = Pneumotest QUE = Quellung SLAGG = Slide agglutination

PCVDoses Total number of PCV doses received by case prior to onset.

PPVDoses Total number of PPV doses received by case prior to onset.

Serotype Serotype of the pathogen which is the cause of the reported disease. Consult the reference values for SubjectCode = PNEU and Variable = Serotype

SIR_CTX_CFX Susceptibility to Cefotaxime or Ceftriaxone as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

SIR_ERY Susceptibility to Erythromicin as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

SIR_PEN Susceptibility to Penicillin as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

VaccinationStatus Indicates if the case is vaccinated and number of vaccine doses received. 10DOSE = 10 doses 1DOSE = 1 dose 2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses 5DOSE = 5 doses 6DOSE = 6 doses 7DOSE = 7 doses 8DOSE = 8 doses 9DOSE = 9 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

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Table 6: Case-based metadata – MENIISO-specific variables

Vaccine Type of pneumococcal vaccine; if the last vaccine given in the series was different from the vaccine with which the series was initiated, indicate the last vaccine in the series.

PCV10 = Pneumococcal conjugate vaccine 10 PCV13 = Pneumococcal conjugate vaccine 13 PCV15 = Pneumococcal conjugate vaccine 15 PCV20 = Pneumococcal conjugate vaccine 20 PCV3 = Pneumococcal conjugate vaccine - third dose PCV7 = Pneumococcal conjugate vaccine 7 PPV23 = Pneumococcal polysaccharide vaccine

Variable Description Coded value list

CaseId Unique identifier for each case within the data source / surveillance system related to the isolate, so that isolate records can be linked to case records. This should match the corresponding NationalRecordId of MENI case-based data in option 2, as per Reporting Protocol.

DataSource The data source (laboratory) that the record originates from. Consult the reference values in mdDataSource dataset

DateOfReceiptReferenceLab Date of receipt in reference laboratory or typing laboratory with reference function.

DateOfReceiptSourceLab Date of receipt in source laboratory, i.e. the laboratory the sample was first sent to.

DateOfSampling Date the sample from which the isolate was derived, was taken.

DateUsedForStatistics The most epidemiologically relevant date for the isolate. Equal to the date of sampling if available. If not, equal to the date of receipt in the source lab, and if that is not available, the date of receipt in the reference lab.

Disease The code of the disease that is being reported. MENI = Invasive meningococcal disease

HealthTopic The code of the health topic that is being reported. ISO = Isolate data

ItemCode Item code.

NationalRecordId Unique identifier for each record within and across the specified surveillance system (data source) – selected and generated by the country reporting the record.

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

Status The Status value is used to provide the functionality for a record within EpiPulse Cases database. Default value: NEW/UPDATE. If set to DELETE, the record with the specified NationalRecordId is deleted (invalidated) from EpiPulse Cases database, if it exists. If set to NEW/UPDATE, the record is inserted into the database: If the same NationalRecordId already exists for the same data source and subject code, then the current submitted record updates (replace) the existing one.

DELETE = Delete a previously reported record. NEW/UPDATE = Update a previously reported record (default).

SubjectCode SubjectCode is a reporting model for a disease/health topic - identifies the reporting structure and format of a record (case based or aggregate reporting).

MENIISO = Neisseria meningitidis isolate

WgsAccession European Nucleotide Archive (ENA) run identifier, based on which the sequence read data can be retrieved / Sequence Read Archive (SRA) run identifier, based on which the sequence read data can be retrieved. Starts with ERR or SRR, i.e. not the sample or experiment which ERS/ERX or SRS/SRX.

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Aggregated reporting

Please refer to Table 7 to see the format for aggregated reporting of IBD data. If only a few variables can be reported, it is recommended to give the following priority for

reporting: AgeGroup, Classification, VaccStatus, Gender.

Table 7: Aggregate metadata for reporting of IBD data (record type: AGGR)

WgsAssembler The assembler used for sequencing, optionally including parameter settings. MAP_TO_LOCI1 = Mapping to individual loci, variant 1 for IonTorrent SKESA = SKESA assembler SPADES = SPAdes without read mapping and consensus calling SPADES_READMAP = SPAdes either including or followed by read mapping and consensus calling VELVET = Velvet without read mapping and consensus calling VELVET_READMAP = Velvet using k-mer optimisation, and followed by read mapping and consensus calling

WgsAssembly The assembled genome, as a gzipped FASTA file. The file contents are subsequently converted into a Base64-encoded string for inclusion into either the XML or CSV data for the isolate.

WgsProtocol Protocol used for sequencing, limited to the sequencing technology used (today Illumina or IonTorrent) and the read length.

HISEQ_2X100 = Illumina HiSeq 2x100 IONTORRENT = IonTorrent MINISEQ_2X150 = Illumina MiniSeq 2x150 MISEQ_2X150 = Illumina MiSeq 2x150 MISEQ_2X250 = Illumina MiSeq 2x250 MISEQ_2X300 = Illumina MiSeq 2x300 NEXTSEQ_2X150 = Illumina NextSeq 2x150 PAIRED_END_ILLUMINA = Illumina HiSeq, MiSeq, NextSeq or MiniSeq

WgsRawReads The raw reads obtained from the sequencer stored as FASTQ files. Each FASTQ file is a text file which represents sequence readouts for a sample.

Variable Description Coded value list

AgeGroup Age group of the reported record. 0 = <1 year 01-04 = 1-4 years 05-09 = 5-9 years 10-14 = 10-14 years 15-19 = 15-19 years 20-24 = 20-24 years 25-29 = 25-29 years 30-34 = 30-34 years 35-39 = 35-39 years 40-44 = 40-44 years

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4 For PNEU and HAEINF, only confirmed cases should be reported according to the EU Case Definition. For MENI, confirmed, probable and possible cases can be reported.

45-49 = 45-49 years 50-54 = 50-54 years 55-59 = 55-59 years 60-64 = 60-64 years 65+ = 65 and over

CaseClassification 4 Case classification according to EU case definition. CONF = Confirmed POSS = Possible PROB = Probable

DataSource The data source (surveillance system) that the record originates from. The DataSource value must be a special reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateUsedForStatistics The reference date used for standard reports that is compared to the reporting period. The date used for statistics can be any date that the reporting country finds applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being reported. HAEINF = Haemophilus infection MENI = Invasive meningococcal disease PNEU = Invasive pneumococcal disease

Gender Gender of the reported record. F = Female M = Male OTH = Other

NumberOfCases Total number of cases during the reported period for the specified disease.

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

SubjectCode SubjectCode is a reporting model for a disease/health topic - identifies the reporting structure and format of a record (case based or aggregate reporting).

HAEINFAGGR = Haemophilus infection aggregated MENIAGGR = Meningococcal disease aggregated PNEUAGGR = Pneumococcal infection aggregated

VaccinationStatus Indicates if the case is vaccinated and number of vaccine doses received. 1DOSE = 1 dose 2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

21

Changes to the IBD metadata

Metadata changes prior to 2014 can be found on the TESSy documents website. Changes from 2014 onwards have been summarised in Table 8 below.

Table 8: Summary of implemented changes in case-based and aggregated subject codes (formerly ‘record types’) for IBD from 2014 to current

Year of change

Subject Variables Description

2024 HAEINF MENI PNEU MENIISO HAEINFAGGR MENIAGGR PNEUAGGR

ALL Reporting moved from TESSy to the Epipulse Cases platform. This transition has led to changes in some variable names and categorical values (see below).

RecordTypeVersion Remove variable

MENI ECDCIsolateID Remove variable

PNEU DosePCV1; DatePCV1; BrandPCV1; DosePCV2; DatePCV2; BrandPCV2; DosePCV3; DatePCV3; BrandPCV3; DosePCV4; DatePCV4; BrandPCV4; PCVDoses; DosePPV; DatePPV; PPVDoses

ADD variables: DosePCV1: First dose of vaccination with a PCV DatePCV1: Date of first dose of PCV BrandPCV1: Type of PCV at first dose DosePCV2: Second dose of vaccination with a PCV DatePCV2: Date of second dose of PCV BrandPCV2: Type of PCV at second dose DosePCV3: Third dose of vaccination with a PCV DatePCV3: Date of third dose of PCV BrandPCV3: Type of PCV at third dose DosePCV4: Fourth dose of vaccination with a PCV DatePCV4: Date of fourth dose of PCV BrandPCV4: Type of PCV at fourth dose PCVDoses: Total number of PCV doses received prior to onset DosePPV: Vaccinated with PPV DatePPV: Date of PPV PPVDoses: Total number of PPV doses received prior to onset

HAEINFAGGR MENIAGGR PNEUAGGR

VaccinationStatus ADD Variable

HAEINF MENI PNEU

Classification → CaseClassification; ClinicalPresentation → ClinicalCriteria ; DateLastVaccDose → DateOfLastVaccination; RecordId → NationalRecordId; RecordType → SubjectCode; Subject → Disease; VaccStatus → VaccinationStatus

Variable names changed from (TESSy) → to (Epipulse Cases): Classification → CaseClassification; ClinicalPresentation → ClinicalCriteria; DateLastVaccDose → DateOfLastVaccination; RecordId → NationalRecordId; RecordType → SubjectCode; Subject → Disease; VaccStatus → VaccinationStatus

HAEINF MENI

TestMethod1 → MainPathogenDetectionMethod; TestMethod2 → SecondPathogenDetectionMethod

Variable names changed from (TESSy) → to (Epipulse Cases): TestMethod1 → MainPathogenDetectionMethod; TestMethod2 → SecondPathogenDetectionMethod

MENI ResultMICSign_CTX_CFX → MICSign_CTX_CFX; Variable names changed from (TESSy) → to (Epipulse Cases):

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PNEU ResultMICSign_PEN → MICSign_PEN; ResultMICValueCTX_CFX → MICValueAST_CTX_CFX; ResultMICValuePEN → MICValueAST_PEN

ResultMICSign_CTX_CFX → MICSign_CTX_CFX; ResultMICSign_PEN → MICSign_PEN; ResultMICValueCTX_CFX → MICValueAST_CTX_CFX; ResultMICValuePEN → MICValueAST_PEN

MENI ProbableCountryOfInfection → PlaceOfInfection; ResultMICSign_CIP → MICSign_CIP; ResultMICSign_RIF → MICSign_RIF; ResultMICValueCIP → MICValueAST_CIP; ResultMICValueRIF → MICValueAST_RIF

Variable names changed from (TESSy) → to (Epipulse Cases): ProbableCountryOfInfection → PlaceOfInfection; ResultMICSign_CIP → MICSign_CIP; ResultMICSign_RIF → MICSign_RIF; ResultMICValueCIP → MICValueAST_CIP; ResultMICValueRIF → MICValueAST_RIF

PNEU ResultMICSign_ERY → MICSign_ERY ResultMICValueERY → MICValueAST_ERY TestMethodMIC → ASTMethod; VaccType → Vaccine

Variable names changed from (TESSy) → to (Epipulse Cases): ResultMICSign_ERY → MICSign_ERY ResultMICValueERY → MICValueAST_ERY TestMethodMIC → ASTMethod; VaccType → Vaccine

HAEINFAGGR MENIAGGR PNEUAGGR

AgeClass → AgeGroup; Classification → CaseClassification; RecordType → SubjectCode; Subject → Disease;

Variable names changed from (TESSy) → to (Epipulse Cases): AgeClass → AgeGroup; Classification → CaseClassification; RecordType → SubjectCode; Subject → Disease;

HAEINF MENI PNEU

CaseClassification Discontinued “UNK” categorical value

ClinicalCriteria Discontinued “UNK” and “NUS” categorical values, and “O” remapped to “OTH”

Status Remapping of “NEW/UPDATE” to “ADD/UPDATE”

HAEINF MENI

MainPathogenDetectionMethod; SecondPathogenDetectionMethod Discontinued “UNK” and “NA” categorical values, and “O” remapped to “OTH”

Outcome Discontinued “UNK” and “NUS” categorical values

HAEINF PNEU

VaccinationStatus Discontinued “UNK” categorical value and “DOSEUNK” remapped to “UNKDOSE”

MENI PNEU

SIR_CTX_CFX; SIR_PEN Discontinued “UNK” categorical value

HAEINF Serotype Discontinued “NUS” categorical values and remapping of:

“A” to “HAEINF_A” “B” to “HAEINF_B” “C” to “HAEINF_C” “D” to “HAEINF_D” “E” to “HAEINF_E”

“F” to “HAEINF_F” “UNK” to “HAEINF_UNK” “non-b” to “HAEINF_NOT_B” “non-caps” to “HAEINF_NONCAPS”

MENI Imported; ReportedEMERTII Discontinued “UNK” categorical value and variable changed from coded value to Boolean (0 = No ; 1 = Yes)

ResultFetVR; ResultPorA1; ResultPorA2

Discontinued “UNK” and “NUS” categorical values

ResultMLST; SIR_CIP; SIR_RIF Discontinued “UNK” categorical value

VaccinationStatus Discontinued “UNK”, “5DOSE”, “6DOSE”, “7DOSE”, “8DOSE”, “9DOSE”, “10DOSE” categorical values and “DOSEUNK” remapped to “UNKDOSE”

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Serogroup Discontinued “UNK” and “NUS” categorical values and remapping of:

“29E” to “NEIMENI_29E” “A” to “NEIMENI_A” “B” to “NEIMENI_B” “C” to “NEIMENI_C” “NGA” to “NEIMENI_NGA” “O” to “NEIMENI_OTH”

“W” to “NEIMENI_W” “X” to “NEIMENI_X” “Y” to “NEIMENI_Y” “Z” to “NEIMENI_Z” “Z/29E” to “NEIMENI_Z/29E”

ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST

Update coded values (once a year or upon request) from the following list: http://neisseria.org/nm/typing/tessy/

PNEU ASTMethod Discontinued “UNK” categorical value and “O” remapped to “OTH”

NRLData Variable changed from coded value to Boolean (0 = No ; 1 = Yes)

Outcome; SIR_ERY Discontinued “UNK” categorical value

PathogenDetectionMethod Discontinued “UNK” and “NA” categorical values, and “O” remapped to “OTH”

Vaccine Discontinued “UNK” and “NA” categorical values

Serotype

Discontinued “NT” and “O” categorical values and remapping of:

“1” to “STRPNE_1” “10” to “STRPNE_10” “10A” to “STRPNE_10A” “10B” to “STRPNE_10B” “10C” to “STRPNE_10C” “10F” to “STRPNE_10F” “11” to “STRPNE_11” “11A” to “STRPNE_11A” “11B” to “STRPNE_11B” “11C” to “STRPNE_11C” “11D” to “STRPNE_11D” “11E” to “STRPNE_11E” “11F” to “STRPNE_11F” “12” to “STRPNE_12” “12A” to “STRPNE_12A” “12B” to “STRPNE_12B” “12F” to “STRPNE_12F” “13” to “STRPNE_13” “14” to “STRPNE_14” “15” to “STRPNE_15” “15A” to “STRPNE_15A” “15B” to “STRPNE_15B” “15B/C” to “STRPNE_15B/C” “15C” to “STRPNE_15C” “15F” to “STRPNE_15F” “16” to “STRPNE_16” “16A” to “STRPNE_16A” “16F” to “STRPNE_16F” “17” to “STRPNE_17” “17A” to “STRPNE_17A”

“28” to “STRPNE_28” “28A” to “STRPNE_28A” “28F” to “STRPNE_28F” “29” to “STRPNE_29” “3” to “STRPNE_3” “31” to “STRPNE_31” “32” to “STRPNE_32” “32A” to “STRPNE_32A” “32F” to “STRPNE_32F” “33” to “STRPNE_33” “33A” to “STRPNE_33A” “33B” to “STRPNE_33B” “33C” to “STRPNE_33C” “33D” to “STRPNE_33D” “33F” to “STRPNE_33F” “34” to “STRPNE_34” “35” to “STRPNE_35” “35A” to “STRPNE_35A” “35B” to “STRPNE_35B” “35C” to “STRPNE_35C” “35F” to “STRPNE_35F” “36” to “STRPNE_36” “37” to “STRPNE_37” “38” to “STRPNE_38” “39” to “STRPNE_39” “4” to “STRPNE_4” “40” to “STRPNE_40” “41” to “STRPNE_41” “41A” to “STRPNE_41A” “41F” to “STRPNE_41F”

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“17F” to “STRPNE_17F” “18” to “STRPNE_18” “18A” to “STRPNE_18A” “18B” to “STRPNE_18B” “18C” to “STRPNE_18C” “18F” to “STRPNE_18F” “19” to “STRPNE_19” “19A” to “STRPNE_19A” “19B” to “STRPNE_19B” “19C” to “STRPNE_19C” “19F” to “STRPNE_19F” “2” to “STRPNE_2” “20” to “STRPNE_20” “21” to “STRPNE_21” “22” to “STRPNE_22” “22A” to “STRPNE_22A” “22F” to “STRPNE_22F” “23” to “STRPNE_23” “23A” to “STRPNE_23A” “23B” to “STRPNE_23B” “23F” to “STRPNE_23F” “24” to “STRPNE_24” “24A” to “STRPNE_24A” “24B” to “STRPNE_24B” “24F” to “STRPNE_24F” “25” to “STRPNE_25” “25A” to “STRPNE_25A” “25F” to “STRPNE_25F” “27” to “STRPNE_27”

“42” to “STRPNE_42” “43” to “STRPNE_43” “44” to “STRPNE_44” “45” to “STRPNE_45” “46” to “STRPNE_46” “47” to “STRPNE_47” “47A” to “STRPNE_47A” “47F” to “STRPNE_47F” “48” to “STRPNE_48” “5” to “STRPNE_5” “6” to “STRPNE_6” “6A” to “STRPNE_6A” “6B” to “STRPNE_6B” “6C” to “STRPNE_6C” “6D” to “STRPNE_6D” “7” to “STRPNE_7” “7A” to “STRPNE_7A” “7B” to “STRPNE_7B” “7C” to STRPNE_7C” “7F” to “STRPNE_7F” “8” to “STRPNE_8” “9” to “STRPNE_9” “9A” to “STRPNE_9A” “9L” to “STRPNE_9L” “9N” to “STRPNE_9N” “9V” to “STRPNE_9V” “NTYP” to “STRPNE_NTYP” “UNK” to “STRPNE_UNK”

HAEINF MENI PNEU HAEINFAGGR MENIAGGR PNEUAGGR

Gender Discontinued “UNK” categorical value and “O” remapped to “OTH”

HAEINFAGGR MENIAGGR PNEUAGGR

AgeGroup Discontinued “UNK” categorical value

SubjectCode “AGGRVPD” value remapped to “HAEINFAGGR” / “MENIAGGR” / “PNEUAGGR”

HAEINFAGGR PNEUAGGR

CaseClassification Discontinued “UNK”, “POSS” and “PROB” categorical values

MENIAGGR CaseClassification Discontinued “UNK” categorical value

2023 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

2022 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

2021 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

ReportedEMERTII New variable: Describe if the isolate related to the case was reported to EMERT II

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2020 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

MENIISO DateUsedForStatistics Change to date format to allow other date formats like: yyyy, yyyy-Qq, yyyy-mm, yyyy-Www, yyyy-mm-dd

2019 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

MENIISO New record type added

2018 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

2017 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

2016 HAEINF Specimen1; Specimen2; Pathogen Variables dropped

TestMethod1; TestMethod2; Age; ClinicalPresentation Description changed

DateLastVaccDose Variable added

Classification Coded value ‘PROB’ removed, as EU case definition disease does not include probable cases

MENI TestMethod1; TestMethod2; ResultPorA1; ResultPorA2; ResultMLST Description changed

ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST The available coded values for all fine typing variables were updated from http://neisseria.org/nm/typing/tessy/

DateLastVaccDose Variable added

Pathogen Variable dropped

PNEU Specimen; DateOfSpecimen Variables dropped

TestMethod1; TestMethod2; VaccType Description changed

DateLastVaccDose Variable added

ClinicalPresentation The coded values were edited. ‘Bacteraemia’ was replaced with ‘Septicaemia’, and ‘Meningitis’ was split into ‘Meningitis’ and ‘Meningitis and Septicaemia’.

2015 HAEINF MENI PNEU

EpiLink; ClinicalCriteria; Labresult Variables dropped

HAEINF ClinicalPresentation; VaccinationStatus Description changed

HAGGR All variables Record type removed

MENI ClinicalPresentation; VaccinationStatus Description changed

Specimen1; Specimen2 Variables dropped

Serogroup The coded value W135 was replaced with W

ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST The available coded values for all fine typing variables were updated from http://neisseria.org/nm/typing/tessy/

PNEU ClinicalPresentation; Classification; VaccinationStatus Description changed

2014 MENI MIC_CIP; MIC_CTX; MIC_PEN; MIC_RIF Variables dropped

SIR_CIP; SIR_CTX_CFX; SIR_PEN; SIR_RIF; ResultMICValueCIP; ResultMICValueCTX_CFX; ResultMICValuePEN; ResultMICValueRIF

Variables added

26

Annex 2. IBD-specific material

IBD data reporting frequency

The surveillance data for the IBDs (invasive H. influenzae disease, invasive meningococcal disease and invasive pneumococcal disease) should be uploaded annually. In 2024, uploaded data will relate

to cases with date used for statistics in 2023.

The deadline for uploading all data for invasive H. influenzae disease, invasive

meningococcal disease, and invasive pneumococcal disease is 15 October 2024.

As per the case definition for invasive meningococcal disease: possible, probable and confirmed cases should be reported. For invasive H. influenzae disease and invasive pneumococcal disease, the case

definition requires only confirmed cases to be reported. See below for further details of the case

definition for each disease.

It is also possible to update case information retrospectively, i.e. for cases reported in previous years with a date used for statistics prior to 2023. For all diseases, any update of previously reported cases

should be done before the reporting deadline in order for data to be included in the annual

epidemiological report and surveillance atlas.

Once the data are validated by the disease experts at ECDC, they are then made publicly available on

the Surveillance Atlas of Infectious Diseases and through annual surveillance reports on the ECDC

website.

Reporting of meningococcal disease isolates (MENIISO)

ECDC recently launched a project for genomic-based EU/EEA surveillance for invasive meningococcal

disease, in which Member States submit genomic data from linked N. meningitidis isolates to the

European Meningococcal Epidemiology in Real Time II (EMERT-II), for sequence analysis and definition of sequence-derived isolate characterisation data and nomenclature. Sequence-derived data

are then imported to Epipulse Cases and linked to the case-based epidemiological data for integrated

analysis. Data visualisation and joint interpretation are conducted and presented in EpiPulse.

In preparation of this genomic surveillance, in 2019 a subject called “Neisseria Meningitidis Isolate”

and a new record type (MENIISO) were created to capture information on the WGS (whole genome sequence) typing of Neisseria meningitidis submitted to the EMERT II database. The MENIISO

records hold the sequence-derived data imported from EMERT-II, as well as information on relevant

dates for cases, and country of the submitting user, and the EMERT-II ID.

To facilitate linkage of the MENI and MENIISO datasets, two variables were added to the MENI

subject code: IsolateId and ReportedEMERTII. The IsolateId variable is used in the linking of a MENI record (with epidemiological and microbiological characterisation data) with a MENIISO record (with

genomic data). The variable “ReportedEMERTII” is used to include information on whether the isolate

related to the case has been reported in EMERT-II.

The specificities of MENIISO data collection are included in a separate reporting protocol “Protocol for genomic-based EU/EEA surveillance of invasive meningococcal disease” which is available in the

Epipulse platform.

During the pilot phase, ECDC encourages data submission as close to real time as possible, for both the genomic and epidemiological data. If epidemiological data aimed to be submitted directly to

Epipulse Cases is not available, genomic data could be reported to EMERT-II and epidemiological data

submitted at the earliest convenience.

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In the event of an investigation of a signal detected from molecular typing data, Member States may be asked to submit relevant and selected epidemiological information to EpiPulse or Epipulse Cases

for the cases included in the signal to ECDC for EU-level analysis.

Starting in September 2023, a monthly cluster analysis will be done at the end of each month, with

the clusters being refreshed in the EpiPulse molecular typing tool.

Narrative information

Changes over time in the number of cases reported in a surveillance system do not always reflect true

changes in the incidence of disease. New reporting practices, improved laboratory capacities and changes in legislation are some of the factors that can influence the number of cases reported. It is

important to be aware of such “surveillance artefacts” when analysing surveillance data and countries are encouraged to describe changes in the surveillance environment that may impact on the number

of cases reported. It is equally important to report if the surveillance environment has remained the same from one year to the next. We encourage reporting countries to provide this information at the

same time as data submission to TESSy and to [email protected].

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Invasive H. influenzae disease data collection and case definitions

Prior to 2007, data on invasive disease caused by H. influenzae were collected by The European Union Invasive

Bacterial Infections Surveillance Network (EU-IBIS) and subsequently transferred to The European Surveillance

System (TESSy).

From 2018, confirmed cases should be reported according to the following 2018 EU case definition5:

Previous versions of the case definition were published in 2012, 2008 and 2002. The 2018, 2012 and 2008 EU case definitions are identical and differ from the 2002 case definition in (i) their specification of invasive H. influenzae type b (Hib), and (ii) definition of possible and probable cases.

5Commission Implementing Decision 2018/945/EU of 22 June 2018 on the communicable diseases and related special health issues to be covered by epidemiological surveillance as well as relevant case definitions.

Clinical criteria

Not relevant for surveillance purposes

Laboratory criteria

At least one of the following two:

— Isolation of Haemophilus influenzae from a normally sterile site

— Detection of Haemophilus influenzae nucleic acid from a normally sterile site

Epidemiological criteria

Not applicable

Case classification

A. Confirmed case: Any person meeting the laboratory criteria

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Invasive meningococcal disease data collection and case definitions Prior to 2007, data on IMD were collected by The European Union Invasive Bacterial Infections Surveillance Network (EU-IBIS) and subsequently imported into The European Surveillance System database (TESSy).

From 2018, cases (possible, probable and confirmed) should be reported according to the following 2018 case definition6:

Previous versions of the case definition were published in 2002, 2008 and 2012. The EU case definitions of 2018 and 2012 differ in the clinical criteria; in 2018 fever was removed, and petechial rash was replaced with haemorrhagic rash. In 2008, the case definition removed (from the 2002 definition) reporting of a probable case when N. meningitidis was identified from a non-sterile site. From 2008 onwards, only isolations from sterile sites are to be considered for reporting.

6Commission Implementing Decision 2018/945/EU of 22 June 2018 on the communicable diseases and related

special health issues to be covered by epidemiological surveillance as well as relevant case definitions.

Clinical criteria

Any person with at least one of the following symptoms:

— Meningeal signs

— Haemorrhagic rash

— Septic shock

— Septic arthritis

Laboratory criteria

At least one of the following four:

— Isolation of Neisseria meningitidis from a normally sterile site, or from purpuric skin lesions

— Detection of Neisseria meningitidis nucleic acid from a normally sterile site, or from purpuric skin lesions

— Detection of Neisseria meningitidis antigen in CSF

— Detection of gram-negative stained diplococcus in CSF

Epidemiological criteria

An epidemiological link by human-to-human transmission

Case classification

A. Possible case: Any person meeting the clinical criteria

B. Probable case: Any person meeting the clinical criteria and with an epidemiological link

C. Confirmed case: Any person meeting the laboratory criteria

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Invasive pneumococcal disease data collection and case definitions

Data on IPD have been reported by the EU/EEA Member States from 2010, when enhanced surveillance of IPD was first implemented on a European level and the majority of Member States began reporting case-based data from national reference laboratories.

From 2018, confirmed cases should be reported according to the following 2018 EU case definition7:

* The criteria for reporting are published each year as part of the Antimicrobial resistance (AMR) reporting protocol. See: TESSy Antimicrobial resistance (AMR) reporting protocol 2023. European Antimicrobial Resistance Surveillance Network (EARS-Net).

Previous versions of the case definition were published in 2002, 2008 and 2012. The 2018 and 2012 case definitions do not differ with the exception of the note on antimicrobial resistance, which was added to the 2018

case definition. The 2012 and 2008 case definitions were identical but differed from the 2002 EU case definition.

The 2002 EU case definition included possible and probable cases, and considered detection of S. pneumoniae

antigen from a normally sterile site a probable case.

7 Commission Implementing Decision 2018/945/EU of 22 June 2018 on the communicable diseases and related special health issues to be covered by epidemiological surveillance as well as relevant case definitions.

Clinical criteria

Not relevant for surveillance purposes.

Laboratory criteria

At least one of the following three:

— Isolation of Streptococcus pneumoniae from a normally sterile site

— Detection of Streptococcus pneumoniae nucleic acid from a normally sterile site

— Detection of Streptococcus pneumoniae antigen from a normally sterile site

Epidemiological criteria

Not applicable

Case classification

A. Possible case – Not applicable

B. Probable case – Not applicable

C. Confirmed case – Any person meeting the laboratory criteria

Antimicrobial resistance

The results of antimicrobial susceptibility tests must be reported according to the methods and criteria* agreed between ECDC and Member States as specified by ECDC's European Antimicrobial Resistance Surveillance Network (EARS-Net)

ECDC NORMAL

To: National Focal Points for Surveillance Cc: National Coordinators

Dear National Focal Points for Surveillance, We are pleased to announce the upcoming launch of EpiPulse Cases in September 2024. This will be the new platform for reporting indicator-based surveillance data according to the list of EU/EEA notifiable diseases and their case definitions. EpiPulse Cases will be deployed progressively during the course of 2024 and 2025 to include all diseases, health issues, and reporting of isolates for molecular surveillance, according to the two timelines below:

ECDC NORMAL

Around two months prior to any group of diseases being included in EpiPulse Cases, you will receive a notification listing the metadata changes that come with it. Given the staggered deployment of the platform, there will exceptionally be several new metadata releases to review before the end of 2025. With the current communication you are receiving for approval the metadata changes for VPI diseases and most molecular surveillance subjects. Please provide your feedback by 9th August 2024. The metadata is being shared by ECDC VPI colleagues to the NFPs for VPI simultaneously. The deadline for reporting VPI diseases will be postponed to late November. The launch of EpiPulse Cases marks the beginning of the end of TESSy which is planned to be fully decommissioned by the end of 2025. Compared to TESSy, EpiPulse Cases offers the following advantages:

▪ It has been designed to handle large (e.g. pandemic) data volumes and will be cloud- based, which will make for faster processing and allow to scale up capacity as required.

▪ We have substantially reduced the number of mandatory variables. This will lower the threshold for the system accepting your data and will leave it to you to decide if your data quality is sufficient for approval of submission.

▪ EpiPulse Cases will offer an automated technical and epidemiological validation of your data directly upon upload. The epidemiological validation will be based on a combination of the previous TESSy-inbuilt validation rules, completeness checks for key variables and a comparison with historical data of yours to detect any unexplained aberrations. Instead of TESSy error and warning messages, you will receive a graphic online validation report, the content and format of which will be targeted at epidemiologists and data managers and will point you to possible data quality issues. The first release of this automated validation in EpiPulse Cases will not yet completely replace the expert-driven validation currently following the automated validation in TESSy, but over time, we do expect to fully integrate this second step in the system.

▪ EpiPulse Cases and the underlying data warehouse are set up in a way that will markedly facilitate its technical maintenance and hence render the platform more robust also from a user perspective.

In addition, national data providers should expect the following main changes:

▪ Metadata: ECDC has taken the opportunity of the new surveillance platform to increase consistency by harmonising variable names and reference values (formerly known as ‘coded values’) across diseases where previous differences were not needed from an

ECDC NORMAL

epidemiological perspective. The formerly mandatory nature of many variables has been removed as it only hampered data submission and resulted in many ‘Unknown’ values without truly improving overall data quality. Finally, the metadata will no longer be versioned. This means that only the latest metadata will be valid for reporting to EpiPulse Cases. For many diseases, these changes may exceed the scope of the annual routine metadata changes and may therefore require a greater one-off effort when implementing them at the national level. For your convenience, we have attached the updated VPI reporting protocols and the relevant metadata including the changes compared to the current TESSy metadata, which should facilitate the necessary mapping and conversion at national level.

▪ User experience: While the automated validation report in EpiPulse Cases does represent a new feature, the overall logic and steps of reporting national surveillance data to ECDC remain largely the same. However, the user interface will be different from TESSy, and users will need to learn how to navigate a familiar workflow that now comes with a new look and feel.

We believe that EpiPulse Cases will bring palpable improvements and convince users eventually, but we are also aware that the new system may initially pose certain challenges in some Member States. ECDC is committed to easing the transition as much as possible and actively supporting data providers whenever necessary. From September 2024, we will offer online training demos, video tutorials and platform-embedded contextual help for the relevant networks as well as individual hands-on data managerial assistance. Any questions in this context or user feedback may be directed to [email protected]. We would also be happy to receive any suggestions for improvement at future disease network meetings, and this year’s annual meeting of the National Focal Points for Surveillance may already offer an opportunity for a debrief on first user experiences with the new platform. We wish to thank you for your cooperation in advance and hope to be able to make EpiPulse Cases a success jointly with you. Kind regards, Bruno Ciancio on behalf of the TESSy and EpiPulse Cases teams1 In attachment

1. EpiPulse Cases metadata for VPI and most molecular surveillance (including the changes)

2. PDF extract highlighting the metadata changes (from the file above) 3. EpiPulse Cases quick guide 4. VPI reporting protocols 5. Machine to Machine Communication - API Specification

1Catalin Albu, Konstantinos Anthis, Zsolt Bartha, Bruno Ciancio, Emiliano Farinella, Erik Halm, Vicky Lefevre, Georgios Margaronis, Adrian Prodan, and Phillip Zucs.

1

Contents INTRODUCTION .................................................................................................................................................. 2

HOW TO USE THIS DOCUMENT ........................................................................................................................................ 2 FINDING FURTHER INFORMATION .................................................................................................................................... 2 COPYRIGHT ................................................................................................................................................................ 2

REPORTING TO EPIPULSE CASES ......................................................................................................................... 3

CHECKING THE DATA COLLECTION SCHEDULE ..................................................................................................................... 3 PREPARING DATA ......................................................................................................................................................... 3 CHECKING METADATA ................................................................................................................................................... 3 CHECKING YOUR SURVEILLANCE SYSTEM DESCRIPTORS........................................................................................................ 4 UPLOADING YOUR DATA ................................................................................................................................................ 4 FINALISING YOUR SUBMISSION........................................................................................................................................ 5 EPIPULSE CASES HELPDESK ............................................................................................................................................ 9

ANNEX 1: MEASLES AND RUBELLA METADATA ................................................................................................ 10

MEASLES AND RUBELLA METADATA ............................................................................................................................... 10 Current subject codes ........................................................................................................................................ 10 Case-based reporting ........................................................................................................................................ 10 Aggregated reporting ....................................................................................................................................... 16 Changes to the measles and rubella metadata ................................................................................................. 18

ANNEX 2. MEASLES & RUBELLA-SPECIFIC MATERIAL ........................................................................................ 21

MONTHLY REPORTING ................................................................................................................................................ 21 NARRATIVE INFORMATION ........................................................................................................................................... 21 MEASLES DATA COLLECTION AND CASE DEFINITIONS ......................................................................................................... 21 RUBELLA DATA COLLECTION AND CASE DEFINITIONS .......................................................................................................... 23 REFERENCES ............................................................................................................................................................. 24

Measles & Rubella Reporting Protocol 2024

Surveillance data for 2024

EpiPulse Cases

Measles & Rubella Reporting Protocol 2024

2

Introduction

This reporting protocol describes the reporting of 2024 measles and rubella cases to EpiPulse Cases, which is replacing TESSy.

Please note:

• Since February 2023, the reporting of diphtheria is described in a separate reporting protocol: Diphtheria, Reporting Protocol 2023, Version 1.0.

• The Vaccine Preventable Diseases (VPD) reporting protocol 2024 describes reporting of: pertussis, mumps, poliomyelitis and tetanus.

• The Invasive Bacteria Diseases (IBD) reporting protocol 2024 describes reporting of: invasive H. influenzae disease, invasive meningococcal disease, Neisseria Meningitidis isolates, and invasive pneumococcal disease.

Reporting protocols are data collection guidelines for the data managers of reporting countries and the protocol design is intended to improve user-friendliness by:

• introducing a uniform structure to make it easier for data managers to find data collection information across different subjects;

• removing information which is not relevant for data managers.

Similarly, the surveillance protocol will contain some of the generic information previously contained in the reporting protocols.

Since the data managers in reporting countries often have multiple roles, subject-specific material is sometimes distributed together with a reporting protocol. To maintain the uniform structure, this type of material is now included in Annex 2.

How to use this document

This reporting protocol provides information for the data managers of reporting countries in three main sections:

• Reporting to EpiPulse Cases which contains guidelines on how to prepare data for submission to EpiPulse Cases, deadlines, subject-specific information (e.g. new changes to metadata), and links to further information.

• Annex 1 which contains:

− the metadata set for the subject(s) covered by this reporting protocol. − a list of metadata changes for the subject(s) covered by this reporting protocol.

• Annex 2 which contains subject-specific material relevant for distribution with the reporting protocol.

Finding further information Updated links to all the schedules, documentation and training materials mentioned in this reporting protocol are included in the Documentation and Help pages, including links to:

• EpiPulse Cases Metadata

• TESSy Metadata sets and change history • EpiPulse Cases Machine to Machine Technical Documentation • Tutorials for data transformation using respectively Excel and Access

Copyright © European Centre for Disease Prevention and Control, 2024. Reproduction is authorised, provided the source is acknowledged.

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Reporting to EpiPulse Cases

In September 2024 EpiPulse Cases is expected to go live. We have built it as a replacement for TESSy, with the aim of improving the process of reporting, reviewing, and updating surveillance data.

Only Vaccine-Preventable Diseases will be reported to EpiPulse Cases in 2024, all other diseases will continue to be reported to TESSy for now.

This section provides both an overview of the EpiPulse Cases reporting process and tips on where you can find useful information.

The overall process is as follows:

• Familiarise yourself with the data collection deadlines. • Prepare (export and transform) your data. • Check that your data complies with the EpiPulse Cases metadata. • Check that your data sources are up to date. • Submit your file(s) to EpiPulse Cases.

• Finalise and approve your submission.

Checking the data collection schedule

A link to the current data collections schedule can be found in the Communication section of the ‘Documentation and Help’ pages.

Preparing data

After you have exported the data from your national database, you need to ensure that the data are in a format that EpiPulse Cases can accept. EpiPulse Cases accepts only CSV and XML files, optionally ZIP-compressed. The EpiPulse Cases metadata has been developed from the TESSy Metadata, with the aim to make only the minimal number of changes necessary, and to hopefully provide a better experience when reporting your datasets to ECDC.

Specific guidelines for measles and rubella data collection and preparation for EpiPulse Cases are provided in Annex 1 and Annex 2.

Checking metadata

The metadata defines the fields and data formats that are valid as input to EpiPulse Cases for a given subject. The EpiPulse Cases metadata includes a section that compares and highlights the changes between TESSy and EpiPulse Cases, to facilitate the transition.

As the requirements for data to be shared among ECDC Stakeholders can change, the data format changes needed to support the new requirements are identified and agreed upon between the National Surveillance Contact Points, the Network Coordination Groups and ECDC’s Disease Experts. These changes are then implemented to the EpiPulse Cases metadata.

Changes to the metadata for the subject of this reporting protocol are described in Annex 1.

It is especially important to focus on:

• Field formats Many fields require the data to be formatted in a specific way. For example, dates must be in the YYYY-MM- DD format; dates in the DD/MM/YYYY format will be rejected.

• Reference Values (the equivalent of TESSy Coded Values) Some fields only permit the use of specific values (reference values). For example, M, F or OTH are the coded values for ‘Gender’ and any other value in a ‘Gender’ field will be rejected. Please note that UNK is no longer a valid code, you may leave the field empty instead.

The EpiPulse Cases metadata Excel file contains all the definitions and rules necessary to format data correctly. The READ ME sheet of the Excel document explains how to work with the metadata. It can be downloaded from the Technical Guidelines & Tools section of the ‘TESSy Help & Docs’ pages.

Filtering the fields in the file by subject will enable you to see the fields required for your subject and the rules that apply to these fields.

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Checking your Surveillance System Descriptors Before submitting file(s), please review your data source(s) in EpiPulse (in the menu, go to ‘Report’ -> ‘Surveillance systems descriptors’) and update the information as necessary.

Complete and up-to-date data source information for each subject is important for improving the interpretation of data - each surveillance system has different features that need to be taken into account when comparing data European level.

If your data source information is out-of-date and you do not have access rights to update it, please ask your National Focal Point for Surveillance or National Coordinator to do so.

Information on data sources is available in the TESSy User Guide, as this functionality is still only available through TESSy.

Uploading your data Data is submitted through the EpiPulse web interface (in the menu, go to Report -> EpiPulse Cases).

The visual interface for reporting new data and editing existing records has remained very similar to that of TESSy. For those of you that are also responsible for reporting diseases outside of the Vaccine Preventable Diseases group, you will continue to use TESSy (under EpiPulse) in parallel with the new EpiPulse Cases, until all disease groups will have been migrated to the new tool.

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Similar to TESSy, you can Add/Update or Replace data with new uploads, using either CSV or XML files. You can

also manually create records for some diseases, and report zero cases where appropriate.

The functionality for manually editing existing records is also a familiar experience. Search for the record you wish to edit, and modify the existing information as needed.

Finalising your submission The compliance of your data with the validation rules in the metadata is checked automatically during the data upload process. In EpiPulse Cases this process is called “Technical Validation”, and it is the only step where your upload can be rejected, for severe data quality issues, such as the file format not being readable by the system, or

(one of the few) mandatory variables having missing values.

If your file has been rejected, there will be a message explaining each instance of non-compliance with the metadata that needs correcting.

The significant new feature in EpiPulse Cases is the Data Validation Report, which puts your data in the context of the already existing information for the same disease, and provides you with a detailed overview of the new data in the file you have just uploaded, as well as the resulting overall epidemiological situation painted by the existing (past) data together with the newly uploaded file(s). This means much more timely feedback on your uploads, including details on data quality, as well as outputs (graphs, charts, and tables) on some of epidemiological indicators. The Data Validation reports will evolve and grow based on your feedback in collaboration with our Disease Experts. These reports will provide a new and better way of understanding and updating the information collected at European level, and will hopefully increase the quality and timeliness of the data, while reducing workloads.

Below you can find a few screenshots of the Data Validation Report.

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1. Begin by opening the report:

2. View the report in a window, download the list of eventual validation messages, or download the report

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3. Check data completeness; both for the new upload, and in the context of historical data

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4. The downloaded report can be opened full screen for easier viewing and navigation. This is a preview of the currently developed epidemiological indicators/stratifications.

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5. After reviewing the information in the Data Validation Report you can choose to approve or reject it.

If you choose to reject it, no data will be saved in the EpiPulse Cases system, but your file will remain visible should you wish to re-download it, or resubmit it for a new Data Validation at a later date or after further checks. Please check the Epi Validation Report carefully, there might be warnings and remarks relating to possible data quality issues or potential overwriting of existing records that you should consider.

When your file has been validated and you are satisfied that all corrections have been made, please ensure prompt approval or rejection. Unapproved uploads can block the approval of other related uploads.

EpiPulse Cases Helpdesk

Email: [email protected]

Telephone number: +46-(0)8-5860 1601

Availability: 9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC holidays)

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Annex 1: Measles and Rubella metadata

This section describes:

• The measles and rubella metadata set • Changes to the measles and rubella metadata

Measles and rubella metadata

Current subject codes

Table 1 shows the subject codes (formerly ‘record types’) to be used when reporting measles and rubella

surveillance data to Epipulse Cases (EPC). Cases should be reported according to the EU Case Definition1.

We strongly encourage case-based reporting. If case-based data are not available, aggregated data

may be reported.

Table 1: Measles and rubella subject codes

Disease Case-based subject code Aggregated subject code

Measles MEAS MEASAGGR

Rubella RUBE RUBEAGGR

Comment: An aggregated format called “AGGRVPD” was available for measles and rubella since 2013. This format was the same as the “AGGR” format, but with “Vaccination Status” as an additional variable. From 2024, with the move from TESSy reporting to Epipulse Cases, aggregated subject codes MEASAGGR and RUBEAGGR have been launched.

Case-based reporting

The metadata set has variables that are common for both measles (MEAS) and rubella (RUBE), which

are summarised in Table 2. Disease-specific variables (in addition to the common variables) are

subsequently summarised in Table 3 (measles) and Table 4 (rubella).

Table 2: Case-based metadata common for both measles (MEAS) and rubella (RUBE)

Variable Description Coded value list

Age Age of patient in years as reported in the national system at the time of disease

onset.

AgeMonth Age of patient in months as reported in the national system for cases < 2 years

of age at the time of disease onset.

CaseClassification Case classification according to EU case

definition.

CONF = Confirmed

PROB = Probable POSS = Possible

DISCARDED = Discarded

ClinicalCriteriaStatus The clinical criteria are met. 0 = No 1 = Yes

ClusterID Unique identifier of the cluster as provided by the country epidemiologist.

ClusterRelated Is the case part of an outbreak/cluster? 0 = No 1 = Yes

1 EU case definitions (europa.eu)

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ClusterSetting Setting of the cluster (for

epidemiologically-linked cases).

CHILDCARE = Kindergarten or

childcare

FAM = Family MIL = Military

NOS = Nosocomial (hospital) OTH = Other

SCH = School

SPORT = Sports team UNI = University

DataSource The data source (surveillance system)

that the record originates from. The DataSource value must be a special

reference value from EpiPulse Cases

metadata.

Consult the reference values in mdDataSource dataset

DateOfInvestigation Date of start of epidemiological investigation of case by public health

authorities.

DateOfLabResult

Date when laboratory results become

available (first validated result to confirm or invalidate the case).

DateOfLastVaccination

Date of administration of the last vaccination dose - indicates the date

when the last dose of vaccine was given

before disease onset (if exact date is not known, then provide month or year).

DateOfNotification

Date when the case report is first

notified to public health authorities.

DateOfOnset

Date of onset of disease. Leave empty for asymptomatic cases.

DateOfSpecimen

Date when first specimen was collected from patient regardless of test results.

DateUsedForStatistics

The reference date used for standard

reports that is compared to the reporting period. The date used for statistics can

be any date that the reporting country

finds applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being

reported.

MEAS = Measles

RUBE = Rubella

Gender Gender of the reported case. F = Female M = Male

OTH = Other

Hospitalisation History of hospitalisation due to the

disease or related complications. Hospitalisation defined as at least one

overnight stay.

0 = No 1 = Yes

ImportedStatus Definition of the origin of infection as per

Surveillance Guidelines for Measles Rubella and Congenital Rubella

Syndrome in the WHO European region.

END = Endemic case

IMP = Imported case IMPREL = Import related case

NationalRecordId Unique identifier for each record within and across the specified surveillance

system (data source) – selected and

generated by the country reporting the record.

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Outcome Information on whether the case is alive

or deceased. The death should be due to

the reported disease.

A = Alive

D = Died

PlaceOfInfection If ImportedStatus = 'IMP': The probable place of infection should be provided at

the country level. One entry for each country visited during the incubation

period of the disease. Note this is a

repeatable field.

Consult the reference values in mdLocation dataset

PlaceOfNotification Place of the first notification of the case to a regional authority. Select the most

detailed NUTS level possible.

Consult the reference values in mdLocation dataset

PlaceOfResidence Place of residence of patient at the time

of disease onset. Select the most detailed NUTS level possible.

Consult the reference values in mdLocation dataset

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

ResultIgG Result of serologic test for IgG (at least

a fourfold rise in specific antibodies titre or seroconversion in paired serum

samples).

EQUI = Equivocal

NEG = Negative NOTEST = Not tested

POS = Positive

ResultIgM Result of serologic test for IgM. EQUI = Equivocal NEG = Negative

NOTEST = Not tested

POS = Positive

ResultVirDetect Validated result of virus detection or isolation, by for example RT-PCR or

culture.

EQUI = Equivocal NEG = Negative

NOTEST = Not tested POS = Positive

SpecimenSero Type of specimen(s) collected for

serological analysis.

DRYBLOSP = Dry blood spot

EDTA = EDTA whole blood

NASALSWAB = Nasal swab OTH = Other

SALOR = Saliva/oral fluid SER = Serum

URINE = Urine

SpecimenVirDetect Type of specimen(s) collected. DRYBLOSP = Dry blood spot

EDTA = EDTA whole blood NASALSWAB = Nasal swab

OTH = Other SALOR = Saliva/oral fluid

SER = Serum

URINE = Urine

Status The Status value is used to provide the functionality for a record within EpiPulse

Cases database. Default value: NEW/UPDATE. If set to DELETE, the

record with the specified

NationalRecordId is deleted (invalidated) from EpiPulse Cases database, if it

exists. If set to NEW/UPDATE, the record is inserted into the database: If

the same NationalRecordId already

exists for the same data source and subject code, then the current submitted

record updates (replace) the existing one.

DELETE = Delete a previously reported record.

NEW/UPDATE = Update a previously reported record (default).

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SubjectCode SubjectCode is a reporting model for a

disease/health topic - identifies the

reporting structure and format of a record (case based or aggregate

reporting).

MEAS = Measles

RUBE = Rubella

VaccinationStatus Indicates if the case is vaccinated and number of vaccine doses received.

10DOSE = 10 doses 1DOSE = 1 dose

2DOSE = 2 doses

3DOSE = 3 doses 4DOSE = 4 doses

5DOSE = 5 doses 6DOSE = 6 doses

7DOSE = 7 doses

8DOSE = 8 doses 9DOSE = 9 doses

NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose

unknown

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Table 3: Case-based metadata – additional measles-specific variables

Variable Description Coded value list

CauseOfDeath If death related to the measles

episode, short description of the event leading to death.

ComplicationDiagnosis Complications of measles. Can

be repeated if several

complications have occurred.

ACENCE = Acute encephalitis

DIARR = Diarrhoea

NONE = None OME = Otitis Media

OTH = Other PNEU = Bacterial pneumonia

Genotype Measles virus genotype. MEASV_A = Measles virus Genotype A

MEASV_B1 = Measles virus Genotype B1

MEASV_B2 = Measles virus Genotype B2 MEASV_B3 = Measles virus Genotype B3

MEASV_C1 = Measles virus Genotype C1 MEASV_C2 = Measles virus Genotype C2

MEASV_D1 = Measles virus Genotype D1

MEASV_D10 = Measles virus Genotype D10 MEASV_D11 = Measles virus Genotype D11

MEASV_D2 = Measles virus Genotype D2 MEASV_D3 = Measles virus Genotype D3

MEASV_D4 = Measles virus Genotype D4

MEASV_D5 = Measles virus Genotype D5 MEASV_D6 = Measles virus Genotype D6

MEASV_D7 = Measles virus Genotype D7 MEASV_D8 = Measles virus Genotype D8

MEASV_D9 = Measles virus Genotype D9 MEASV_E = Measles virus Genotype E

MEASV_F = Measles virus Genotype F

MEASV_G1 = Measles virus Genotype G1 MEASV_G2 = Measles virus Genotype G2

MEASV_G3 = Measles virus Genotype G3 MEASV_H1 = Measles virus Genotype H1

MEASV_H2 = Measles virus Genotype H2

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Table 4: Case-based metadata – additional rubella-specific variables

Variable Description Coded value list

ComplicationDiagnosis Complications of rubella. Can be

repeated if several complications have occurred.

ARTH = Rubella arthritis

NEURO = Neurological complications NONE = None

OTH = Other

Genotype Rubella virus genotype. RUBEV_1A = Rubella virus Genotype 1A

RUBEV_1B = Rubella virus Genotype 1B RUBEV_1C = Rubella virus Genotype 1C

RUBEV_1D = Rubella virus Genotype 1D RUBEV_1E = Rubella virus Genotype 1E

RUBEV_1F = Rubella virus Genotype 1F

RUBEV_1G = Rubella virus Genotype 1G RUBEV_1H = Rubella virus Genotype 1H

RUBEV_1I = Rubella virus Genotype 1I RUBEV_1J = Rubella virus Genotype 1J

RUBEV_2A = Rubella virus Genotype 2A RUBEV_2B = Rubella virus Genotype 2B

RUBEV_2C = Rubella virus Genotype 2C

IgGAvidityTest IgG avidity test method performed

for confirmation of the case according to EU case definition.

0 = No 1 = Yes

Pregnancy Pregnancy at the time of infection. 0 = No 1 = Yes

WeekOfGestation Gestational age (weeks) at time of

infection.

W1-12 = 1 to 12 weeks

W13-20 = 13 to 20 weeks W20+ = More than 20 weeks

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Aggregated reporting

Please refer to Table 5 to see the format for aggregated reporting for measles and rubella.

If only a few variables can be reported, it is recommended to give the following priority for reporting:

AgeGroup, Classification, VaccStatus, Gender.

Table 5: Aggregate metadata for measles (MEASAGGR) and rubella (RUBEAGGR)

Variable Description Coded value list

AgeGroup Age group of the reported record. See Table 6 below.

CaseClassification Case classification according to EU case definition.

CONF = Confirmed

POSS = Possible

PROB = Probable

DISCARDED = Discarded

DataSource The data source (surveillance system)

that the record originates from. The DataSource value must be a special

reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateUsedForStatistics The reference date used for standard

reports that is compared to the reporting period. The date used for

statistics can be any date that the reporting country finds applicable,

e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being reported.

MEAS = Measles

RUBE = Rubella

Gender Gender of the reported record. F = Female

M = Male

OTH = Other

NumberOfCases Total number of cases during the

reported period for the specified disease.

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

SubjectCode SubjectCode is a reporting model for

a disease/health topic - identifies the reporting structure and format of a

record (case based or aggregate reporting).

MEASAGGR = Measles aggregated

RUBEAGGR = Rubella aggregated

VaccinationStatus Indicates if the case is vaccinated and number of vaccine doses received.

1DOSE = 1 dose

2DOSE = 2 doses

3DOSE = 3 doses

4DOSE = 4 doses

NOTVACC = Not vaccinated

UNKDOSE = Vaccinated, dose unknown

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When reporting age, the age classes listed in Table 6 should be used. The age groups listed in Option 1

are the preferred categories for aggregate measles and rubella reporting.

Table 6: Age categories compatible with aggregate measles and rubella reporting

Option Variable Narrative description Coded value of the variable AgeGroup

1 (preferred) AgeGroup <1 year

1-4 years

5-9 years

10-14 years

15-19 years

20-24 years

25-29 years

30-34 years

35-39 years

40-44 years

45-49 years

50-54 years

55-59 years

60-64 years

65 and over

0

01-04

05-09

10-14

15-19

20-24

25-29

30-34

35-39

40-44

45-49

50-54

55-59

60-64

65+

2 AgeGroup <1 year

1-4 years

5-9 years

10-14 years

15-19 years

20-24 years

25-29 years

30 and over

0

01-04

05-09

10-14

15-19

20-24

25-29

30+

3 AgeGroup <1 year

1-4 years

5-9 years

10-14 years

15-19 years

20-29 years

30 and over

0

01-04

05-09

10-14

15-19

20-29

30+

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Changes to the measles and rubella metadata

Metadata changes prior to 2014 can be found on the TESSy documents website. Changes from 2015 onwards have been summarised in Table 7 below.

Table 7: Summary of implemented changes in case-based and aggregated subject codes (formerly ‘record types’) for measles and rubella from 2015 to current

Year of change

Subject Variables Description Validation rule

2024 MEAS RUBE MEASAGGR RUBEAGGR

ALL Reporting moved from TESSy to the Epipulse Cases platform. This transition has led to changes in some variable names and categorical values (see below).

MEAS RUBE

Classification → CaseClassification; ClusterIdentification → ClusterId; Complications → ComplicationDiagnosis; DateLastVaccDose → DateOfLastVaccination; Imported → ImportedStatus; ProbablyCountryOfInfection → PlaceOfInfection; RecordType → SubjectCode; RecordId → NationalRecordId; Subject → Disease; VaccStatus → VaccinationStatus

Variable names changed from (TESSy) → to (Epipulse Cases): Classification → CaseClassification; ClusterIdentification → ClusterId; Complications → ComplicationDiagnosis; DateLastVaccDose → DateOfLastVaccination; Imported → ImportedStatus; ProbablyCountryOfInfection → PlaceOfInfection; RecordType → SubjectCode; RecordId → NationalRecordId; Subject → Disease; VaccStatus → VaccinationStatus

RecordTypeVersion Remove variable

CaseClassification; Outcome

Discontinued “UNK” categorical value

ResultIgG; ResultIgM; ResultVirDetect Discontinued “UNK” and “NA” categorical values

ClusterRelated; Hospitalisation Discontinued “UNK” categorical value and variable changed from coded value to Boolean (0 = No ; 1 = Yes)

ClusterSetting Discontinued “UNK” and “NA” categorical values and “HOSP” remapped to “NOS”

ComplicationDiagnosis Discontinued “UNK” categorical value and remapping of: “NOCOMP” to “NONE” “O” to “OTH”

Gender Discontinued “UNK” categorical value and “O” remapped to “OTH”

ImportedStatus Discontinued “UNK” categorical value and remapping of: “N” to “END” “Y” to “IMP”

SpecimenSero Discontinued “UNK” and “NA” categorical values and “O” remapped to “OTH”

SpecimenVirDetect Discontinued “UNK” and “NA” categorical values and remapping of: “O” to “OTH” “URI” to “URINE”

Status Remapping of “NEW/UPDATE” to “ADD/UPDATE”

VaccinationStatus Discontinued “UNK” and “NA” categorical values and “DOSEUNK” remapped to “UNKDOSE”

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MEAS

CauseOfDeathText → CauseOfDeath; ClinicalCriteria → ClinicalCriteriaStatus

Variable names changed from (TESSy) → to (Epipulse Cases): CauseOfDeathText → CauseOfDeath; ClinicalCriteria → ClinicalCriteriaStatus

CauseOfDeath Variable name changed from CauseOfDeathText to CauseOfDeath

ClinicalCriteriaStatus Discontinued “UNK” and “NA” categorical values and variable changed from coded value to Boolean (0 = No ; 1 = Yes)

Genotype Discontinued “UNK” and “NA” categorical values and remapping of:

“A” to “MEASV_A” “B1” to “MEASV_B1” “B2” to “MEASV_B2” “B3” to “MEASV_B3” “C1” to “MEASV_C1” “C2” to “MEASV_C2” “D1” to “MEASV_D1” “D10” to “MEASV_D10” “D11” to “MEASV_D11” “D2” to “MEASV_D2” “D3” to “MEASV_D3” “D4” to “MEASV_D4”

“D5” to “MEASV_D5” “D6” to “MEASV_D6” “D7” to “MEASV_D7” “D8” to “MEASV_D8” “D9” to “MEASV_D9” “E” to “MEASV_E” “F” to “MEASV_F” “G1” to “MEASV_G1” “G2” to “MEASV_G2” “G3” to “MEASV_G3” “H1” to “MEASV_H1” “H2 to “MEASV_H2”

RUBE Genotype Discontinued “UNK” and “NA” categorical values and remapping of:

“1A” to “RUBEV_1A” “1B” to “RUBEV_1B” ”1C” to “RUBEV_1C” ”1D” to “RUBEV_1D” ”1E” to “RUBEV_1E” ”1F” to “RUBEV_1F” ”1G” to “RUBEV_1G”

”1H” to “RUBEV_1H” ”1I” to “RUBEV_1I” ”1J” to “RUBEV_1J” “2A” to “RUBEV_2A” “2B” to “RUBEV_2B” “2C” to “RUBEV_2C”

IgGAvidityTest; Pregnancy

Discontinued “UNK” and “NA” categorical values and variable changed from coded value to Boolean (0 = No ; 1 = Yes)

WeekOfGestation Discontinued “UNK” and “NA” categorical values

MEASAGGR RUBEAGGR

AgeClass → AgeGroup; Classification → CaseClassification; RecordType → SubjectCode; Subject → Disease; VaccStatus → VaccinationStatus

Variable names changed from (TESSy) → to (Epipulse Cases): AgeClass → AgeGroup; Classification → CaseClassification; RecordType → SubjectCode; Subject → Disease; VaccStatus → VaccinationStatus

AgeGroup; CaseClassification

Discontinued “UNK” categorical value

Gender Discontinued “UNK” categorical value and “O” remapped to “OTH”

SubjectCode “AGGRVPD” value remapped to “MEASAGGR” and “RUBEAGGR”

VaccinationStatus Discontinued “UNK” and “NA” categorical values and “DOSEUNK” remapped to “UNKDOSE”

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2 Note: the addition of the ClinicalCriteria variable was implemented following discussion at the Advisory Forum in September 2018 about modified measles. Vaccinated, laboratory confirmed cases must have the

Clinicalcriteria field completed. The intention is to be able to identify modified measles cases, i.e. that are vaccinated and laboratory confirmed but don’t meet the entire clinical criteria of the EU case definition.

2019 MEAS ClinicalCriteria 2 Add variable (Error) if not completed when Classification is 'CONF' and VaccStatus’ is not 'NOTVACC' and ‘VaccStatus’ is not 'UNK'

2019 MEAS ClinicalCriteria; Classification; VaccStatus

Add validation rule (Error) if ClinicalCriteria is not ‘Yes’, ‘No’ or ‘UNK’, if Classification is 'CONF' and VaccStatus’ is not 'NOTVACC' and ‘VaccStatus’ is not 'UNK'

2018 MEAS ClinicalCriteria Variable reactivated for use in the event of vaccinated cases with classification ‘CONF’; whether these cases met the clinical criteria of the EU case definition should be recorded using this variable.

2018 MEAS Classification; ResultIgG; ResultIgM; ResultVirDetect

Add validation rule (Error) If Classification is 'CONF' and (ResultVirDetect is not 'POS' or ResultIgM is not 'POS' or ResultIgG is not 'POS') Validation message: Confirmed cases should have evidence of laboratory confirmation, so should be 'POS' for at least one of ResultVirDetect, ResultIgM or ResultIgG

2017 MEAS RUBE

DateLastVacc Dose The description of the variable updated to specify that the date given should be the date of last dose before disease onset.

2017 MEAS Add validation rule A validation rule was changed, so that cases reported with ResultVirDetect==POS, must have Classification==CONF or DISCARDED. Previously, these cases could only be reported as Classification==CONF.

2017 RUBE Add validation rule A validation rule was changed, so that cases reported with ResultVirDetect==POS, must have Classification==CONF or DISCARDED. Previously, these cases could only be reported as Classification==CONF.

2015 MEAS RUBE

Imported Description and coded values for the variable ‘Imported’ were edited to ensure consistency with the Surveillance Guidelines for measles, rubella and congenital rubella syndrome in the WHO European Region.

2015 MEAS RUBE

Classification The description of the variable was edited to ensure consistency with the EU case definition.

21

Annex 2. Measles & rubella-specific material

Monthly reporting

Measles and Rubella - deadline 25th of each month

Measles and rubella data should be uploaded monthly. The deadline for upload is the 25th of each

calendar month, and the data to be uploaded is up to the end of the previous calendar month. On the

morning of the 26th of each month, the dataset available in TESSy is validated by disease experts at

ECDC and forwarded to the WHO Regional Office for Europe.

Once the data are validated by the disease experts at ECDC, they are then made publicly available on the Surveillance Atlas of Infectious Diseases. Subsequently, monthly and annual surveillance reports are made available on the ECDC website.

Collection of discarded measles cases

Possible, probable, confirmed and discarded cases of measles and rubella should be reported to ECDC.

The collection of discarded cases is important to monitor progress towards the measles and rubella elimination goal [1]. The metadata variable “Classification” for measles and rubella includes five

different values (possible, probable, confirmed, discarded and unknown).

Discarded cases are defined according to WHO guidelines [2] as suspected cases which were

investigated and discarded either through negative results of adequate laboratory testing for

measles/rubella or by an epidemiological link to a laboratory-confirmed case of another disease. Suspected cases are defined as cases with signs and symptoms consistent with the clinical criteria of

measles.

Collection of modified measles cases that don’t fully meet the clinical criteria

Vaccinated, laboratory confirmed cases must have the Clinicalcriteria field completed. Please see

comments from the paragraph “2019 metadata changes”.

Narrative information

Changes over time in the number of cases reported in a surveillance system do not always reflect true

changes in the incidence of disease. New reporting practices, improved laboratory capacities and changes in legislation are some of the factors that can influence the number of cases reported. It is

important to be aware of such “surveillance artefacts” when analysing surveillance data and countries are encouraged to describe changes in the surveillance environment that may impact on the number of

cases reported. It is equally important to report if the surveillance environment has remained the same

from one year to the next. We encourage reporting countries to provide this information at the same

time as data submission to TESSy and to [email protected].

Measles data collection and case definitions

From 1999, data on cases of measles were collected by the European surveillance network for selected vaccine-preventable diseases (EUVAC.NET), hosted at the Statens Serum Institute (SSI) in Denmark3. In

2011, the coordination of this network was transferred to ECDC, which closely collaborates with WHO

and the Member States.

3 Information about EUVAC.NET is available here: EUVAC.Net (europa.eu)

Measles & Rubella Reporting Protocol 2024

22

Cases are reported according to the following 2018 EU case definition for measles [3]:

Previous versions of the EU case definition were published in 2012, 2008 and 2002. There were no

differences between the 2018, 2012 and 2008 EU case definitions.

In the 2002 EU case definition, the clinical criteria were defined as “a clinical picture compatible with measles, i.e. a generalised rash lasting >3 days and a temperature >38.0°C and one or more of the

following: cough, coryza, Koplik's spots, conjunctivitis”. The laboratory criteria excluded the detection of

measles antigen by DFA and did not stipulate the need to investigate for wild virus in recently vaccinated

cases.

In the 2002 EU case definition, the case classifications were also defined differently, and as such, a laboratory-confirmed case did not need to meet the clinical case definition to be classified as confirmed.

The 2002 EU case definition included the following case classifications:

- possible, a case diagnosed by a physician as measles (no classification in 2008 or 2012);

- probable, a clinically compatible case (possible in 2008 or 2012);

- confirmed, a case that is laboratory confirmed (confirmed in 2008 or 2012, if clinical criteria are

met) or a clinically compatible case with an epidemiological link (probable in 2008 or 2012).

Clinical criteria

Any person with fever;

AND

Maculo-papular rash;

AND at least one of the following three:

— Cough;

— Coryza;

— Conjunctivitis.

Laboratory criteria

At least one of the following four:

— Isolation of measles virus from a clinical specimen;

— Detection of measles virus nucleic acid in a clinical specimen;

— Measles virus specific antibody response characteristic for acute infection in serum or saliva;

— Detection of measles virus antigen by DFA in a clinical specimen using measles specific monoclonal antibodies.

Laboratory results need to be interpreted according to the vaccination status. If recently vaccinated, investigate for wild

virus.

Epidemiological criteria

An epidemiological link by human to human transmission

Case classification

A. Possible case: any person meeting the clinical criteria

B. Probable case: any person meeting the clinical criteria and with an epidemiological link

C. Confirmed case: any person not recently vaccinated and meeting the clinical and the laboratory criteria

Measles & Rubella Reporting Protocol 2024

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Rubella data collection and case definitions

From 2002, data on cases of rubella were collected by a European surveillance network for selected vaccine-preventable diseases (EUVAC.NET), hosted at the Statens Serum Institute (SSI) in Denmark. In

2011, the coordination of this network was transferred to ECDC, which closely collaborates with WHO and the Member States.

Cases are reported according to the following 2018 EU case definition for rubella [3]:

Previous versions of the case definition were published in 2012, 2008 and 2002.

In the 2018 EU case definition, compared with the 2012 and 2008 EU case definitions, the laboratory

criteria and probable case classification were amended as below.

Clinical criteria

Any person with sudden onset of generalised maculo-papular rash;

AND at least one of the following five:

— Clinical adenopathy;

— Sub-occupital adenopathy;

— Post-auricular adenopathy;

— Arthralgia;

— Arthritis.

Laboratory criteria

At least one of the following four:

— Isolation of rubella virus from a clinical specimen;

— Detection of rubella virus nucleic acid in a clinical specimen;

— Rubella IgM antibody detection (*);

— Rubella IgG seroconversion or significant rise in rubella IgG antibody titre in paired specimens tested in parallel.

Laboratory results need to be interpreted according to the vaccination status (possible persistence of IgM antibodies upon

vaccination).

Epidemiological criteria

An epidemiological link to a confirmed case

Case classification

A. Possible case: any person meeting the clinical criteria

B. Probable case: any person meeting the clinical criteria and with an epidemiological link

C. Confirmed case: any person meeting the clinical and the laboratory criteria who has not been recently vaccinated.

In case of recent vaccination, a person meeting the clinical criteria with detection of wild-type rubella virus strain is considered as a confirmed case.

Note: When rubella in pregnancy is suspected, further confirmation of a positive rubella IgM result is required for case management (for example, a rubella specific IgG avidity test, rubella IgM and comparison of rubella IgG levels on paired

sera conducted in a reference laboratory).

(*) In elimination settings, additional testing may be considered in certain situations to exclude false-positive IgM results (WHO Manual for the Laboratory Surveillance of Measles and Rubella Viruses, 2018).

Measles & Rubella Reporting Protocol 2024

24

2018 EU Case Definition 2008 & 2012 EU Case Definitions

Laboratory criteria

At least one of the following four:

— Isolation of rubella virus from a clinical specimen;

— Detection of rubella virus nucleic acid in a clinical

specimen;

— Rubella IgM antibody detection (*)

— Rubella IgG seroconversion or significant rise in rubella

IgG antibody titre in paired specimens tested in parallel.

Laboratory results need to be interpreted according to the

vaccination status (possible persistence of IgM antibodies

upon vaccination).

(*) In elimination settings, additional testing may be

considered in certain situations to exclude false-positive IgM

results (WHO Manual for the Laboratory Surveillance of

Measles and Rubella Viruses, 2018).

Laboratory criteria

Laboratory criteria for case confirmation

At least one of the following three:

— Isolation of rubella virus from a clinical specimen;

— Detection of rubella virus nucleic acid in a clinical specimen;

— Rubella virus specific antibody response (IgG) in serum or

saliva.

Laboratory criteria for probable case

— Rubella virus specific antibody response (IgM).

Laboratory results need to be interpreted according to the

vaccination status.

Probable case: any person meeting the clinical criteria and

with an epidemiological link

Probable case: any person meeting the clinical criteria and with

at least one of the following two:

— An epidemiological link

— Meeting the laboratory criteria for a probable case

There were no differences between the 2012 and 2008 EU case definitions.

In 2002, the clinical criteria were defined as a ‘clinical picture compatible with rubella, e.g. acute onset

of generalized maculopapular rash and arthralgia/arthritis, lymphadenopathy, or conjunctivitis’. Among the laboratory criteria, the detection of IgM was included in the criteria for case confirmation. No

laboratory criteria were defined for a probable case. Confirmed cases also had to meet the clinical

criteria.

References

1. World Health Organization Regional Office for Europe. Eliminating measles and rubella – Framework for the verification process in the WHO European Region. Copenhagen: WHO Regional Office for Europe; 2014. Available from: https://iris.who.int/handle/10665/350499?show=full

2. World Health Organization. Regional Office for Europe. (2024). Eliminating measles and rubella in the

WHO European Region: integrated guidance for surveillance, outbreak response and verification of

elimination. World Health Organization. Regional Office for Europe. https://iris.who.int/handle/10665/375923

3. European Centre for Disease Prevention and Control. EU case definitions [Internet]. Stockholm: ECDC; 2024. Available from: https://www.ecdc.europa.eu/en/all-topics/eu-case-definitions

ECDC NORMAL#

SubjectCode UI Page

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TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

AMRISO Subject HealthTopic Name change AMRISO ReportingCountry ReportingCountry No change AMRISO Status Status Content change NEW/UPDATE -> ADD/UPDATE AMRISO RecordType SubjectCode Name change AMRISO RecordTypeVersion Remove variable! AMRISO 1 1 RecordId NationalRecordId Name change AMRISO 1 2 DataSource DataSource No change AMRISO 1 3 DateUsedForStatistics DateUsedForStatistics No change AMRISO 2 1 Age Age No change AMRISO 2 2 Gender Gender Content change UNK O -> OTH AMRISO 2 3 ItemCode New variable No No AMRISO 2 4 DateOfSampling DateOfSampling No change AMRISO 2 5 SampleOrigin SampleOrigin No change AMRISO 2 6 Pathogen Pathogen Content change AMRISO 2 7 SpecimenSite SpecimenSource Name change

Content change NA, UNK

AMRISO 2 8 SpecimenType Specimen Name change Content change

UNK

AMRISO 2 9 Travel Travel Content change UNK AMRISO 2 10 TravelDestination TravelLocation Name change

Content change UNK

AMRISO 2 11 AdmissionCategory PatientType Name change Content change

UNK

AMRISO 2 12 HospitalId HospitalId No change AMRISO 2 13 DateOfHospitalisation DateOfHospitalisation No change AMRISO 2 14 HospNUTS2 HospitalLocation Name change AMRISO 2 15 HospitalLatitude New variable No No AMRISO 2 16 HospitalLongitude New variable No No AMRISO 2 17 HospitalUnitType HospitalUnitType Content change UNK O -> OTH AMRISO 2 18 ClinSig ClinicalSignificance Name change

Content change NA, UNK

AMRISO 2 19 SiteInfcol SiteOfInfection Name change Content change

UNK

AMRISO 2 20 HospComOnset HospitalAcquiredSample Name change Content change

UNK Column changed from CODED VALUE to BOOLEAN! HOSPAC -> 1 (TRUE) COMAC -> 0 (FALSE)

AMRISO 2 21 HospitalTransfer New variable No No AMRISO 2 22 HospTransfCountry CountryOfHospitalTransfer Name change

Content change UNK

AMRISO 2 23 PriorHospitalTransfer New variable No No AMRISO 2 24 PriorHospCountry CountryOfPriorHospitalisation Name change

Content change UNK

AMRISO 2 25 PriorResidenceInLTCF New variable No No AMRISO 2 26 PriorLTCFCountry CountryOfPriorResidenceInLTCF Name change

Content change UNK

AMRISO 3 1 DateOfReceiptReferenceLab DateOfReceiptReferenceLab No change AMRISO 3 2 DateOfReceiptSourceLab DateOfReceiptSourceLab No change AMRISO 3 3 IsolateId SampleId Name change AMRISO 4 1 WgsProtocol WgsProtocol No change AMRISO 4 2 WgsEnaId / WgsSequenceId WgsAccession Name change AMRISO 4 3 WgsAssembler WgsAssembler No change AMRISO 4 4 WgsAssembly WgsAssembly No change AMRISO 4 5 WgsRawReads WgsRawReads No change AMRISO$AST RecordType SubjectCode Name change

Variables Changes

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Variable Status

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Variables Changes

AMRISO$AST 1 1 RecordId NationalRecordId Name change AMRISO$AST 1 2 ParentId ParentNationalRecordId Name change AMRISO$AST 1 3 PhenoAST AntimicrobialAgent Name change AMRISO$AST 1 4 ASTMethod ASTMethod No change AMRISO$AST 1 5 ResultMICSign MICSusceptibilitySign Name change AMRISO$AST 1 6 resultMICValue MICValueAST Name change AMRISO$AST 1 7 ResultDDZDSign DDZDSusceptibilitySign Name change AMRISO$AST 1 8 ResultDDZDValue DDZDValueAST Name change DIPH Subject Disease Name change

Content change Yes -> No

DIPH ReportingCountry ReportingCountry No change DIPH Status Status Content change Yes -> No NEW/UPDATE -> ADD/UPDATE DIPH RecordType SubjectCode Name change DIPH RecordTypeVersion Remove variable! DIPH ResultRibotype Remove variable! DIPH 1 1 RecordId NationalRecordId Name change DIPH 1 2 DataSource DataSource No change DIPH 1 3 DateUsedForStatistics DateUsedForStatistics No change DIPH 2 1 Age Age No change DIPH 2 2 AgeMonth AgeMonth No change DIPH 2 3 Gender Gender Content change UNK O -> OTH DIPH 2 4 CountryOfBirth CountryOfBirth No change DIPH 3 1 Classification CaseClassification Name change

Content change UNK

DIPH 3 2 DateOfOnset DateOfOnset No change DIPH 3 3 DateOfDiagnosis DateOfDiagnosis No change DIPH 3 4 DateOfNotification DateOfNotification No change DIPH 3 5 Outcome Outcome Content change NUS, UNK DIPH 3 6 ClinicalPresentation ClinicalCriteria Name change

Content change UNK O -> OTH

DIPH 3 7 Complications ComplicationDiagnosis Name change Content change

UNK NEURODIS -> NEURO O -> OTH

DIPH 3 8 SuspectedVehicle SuspectedVehicle Content change NA, NUS, UNK FARMAN -> FARMANIMAL O -> OTH

DIPH 3 9 ClusterRelated ClusterRelated Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

DIPH 3 10 ClusterIdentification ClusterId Name change DIPH 3 11 ClusterSetting ClusterSetting Content change NA, UNK HOSP -> NOS

MIGR ->DET DIPH 3 12 EpiLinkCaseID EpiLinkCaseId Name change DIPH 3 13 DateOfFirstSample DateOfFirstSample No change DIPH 3 14 DateLastVaccDose DateOfLastVaccination Name change DIPH 3 15 VaccStatus VaccinationStatus Name change

Content change UNK DOSEUNK -> UNKDOSE

DIPH 4 1 Imported ImportedStatus Name change Content change

UNK N -> END Y -> IMP

DIPH 4 2 ProbableCountryOfInfection PlaceOfInfection Name change DIPH 4 3 PlaceOfNotification PlaceOfNotification No change DIPH 4 4 PlaceOfResidence PlaceOfResidence No change DIPH 4 5 TravelPlaces TravelPlaces No change DIPH 4 6 DateOfEntry DateOfEntry No change DIPH 5 1 Specimen1 MainSpecimen Name change

Content change UNK O -> OTH

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Variables Changes

DIPH 5 2 TestMethod1 MainPathogenDetectionMethod Name change Content change

UNK O -> OTH

DIPH 5 3 Specimen2 SecondSpecimen Name change Content change

UNK O -> OTH

DIPH 5 4 TestMethod2 SecondPathogenDetectionMethod Name change Content change

UNK O -> OTH

DIPH 5 5 Pathogen Pathogen Content change NUS DIP -> CORDIP PSEU -> CORPSE ULC -> CORULC O -> CORSPP UNK -> CORSPP

DIPH 5 6 ResultBiotype Biotype Name change Content change

NA, NUS, UNK O -> OTH

DIPH 5 7 WGS Wgs Name change Content change

UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

DIPH 5 8 WgsSequenceId WgsSequenceId No change DIPH 5 9 AccNumber WgsAccession Name change DIPH 5 10 ResultSeqType SequenceType Name change DIPH 6 1 Antibiotic AntimicrobialAgent Name change

Content change NA, UNK

DIPH 6 2 SIR_CIP SIR_CIP Content change NA, UNK DIPH 6 3 SIR_CLI SIR_CLI Content change NA, UNK DIPH 6 4 SIR_ERY SIR_ERY Content change NA, UNK DIPH 6 5 SIR_LNZ SIR_LNZ Content change NA, UNK DIPH 6 6 SIR_MEM SIR_MEM Content change NA, UNK DIPH 6 7 SIR_PEN SIR_PEN Content change NA, UNK DIPH 6 8 SIR_RIF SIR_RIF Content change NA, UNK DIPH 6 9 SIR_SXT SIR_SXT Content change NA, UNK DIPH 6 10 SIR_TCY SIR_TCY Content change NA, UNK DIPHAGGR Subject Disease Name change

Content change Yes -> No

DIPHAGGR ReportingCountry ReportingCountry No change DIPHAGGR RecordType SubjectCode Name change

Content change AGGR -> DIPHAGGR

DIPHAGGR RecordTypeVersion Remove variable! DIPHAGGR 1 1 DataSource DataSource No change DIPHAGGR 1 2 DateUsedForStatistics DateUsedForStatistics No change DIPHAGGR 1 3 AgeClass AgeGroup Name change

Content change UNK Please check the updated list of AgeGroup reference values for

this SubjectCode! DIPHAGGR 1 4 Gender Gender Content change UNK O -> OTH DIPHAGGR 1 5 Classification CaseClassification Name change

Content change UNK

DIPHAGGR 1 6 VaccinationStatus New variable No No DIPHAGGR 1 7 NumberOfCases NumberOfCases No change ECOLIISO Subject HealthTopic Name change

Content change Yes -> No

ECOLIISO ReportingCountry ReportingCountry No change ECOLIISO Status Status Content change NEW/UPDATE -> ADD/UPDATE ECOLIISO RecordType SubjectCode Name change ECOLIISO ECDCCaseId Remove variable! ECOLIISO RecordTypeVersion Remove variable! ECOLIISO 1 1 RecordId NationalRecordId Name change ECOLIISO 1 2 DataSource DataSource No change

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Variables Changes

ECOLIISO 1 3 DateUsedForStatistics DateUsedForStatistics No change ECOLIISO 1 4 CaseId CaseId No change ECOLIISO 2 1 Age Age No change ECOLIISO 2 2 AgeMonth AgeMonth No change ECOLIISO 2 3 Gender Gender Content change UNK O -> OTH ECOLIISO 2 4 Imported New variable No No ECOLIISO 2 5 PlaceOfInfection New variable No Yes ECOLIISO 2 6 PlaceOfResidence PlaceOfResidence No change ECOLIISO 2 7 ItemCode New variable No No ECOLIISO 3 1 DateOfSampling DateOfSampling No change ECOLIISO 3 2 DateOfReceiptSourceLab DateOfReceiptSourceLab No change ECOLIISO 3 3 DateOfReceiptReferenceLab DateOfReceiptReferenceLab No change ECOLIISO 3 4 SampleId SampleId No change ECOLIISO 3 5 SampleOrigin SampleOrigin No change ECOLIISO 3 6 Specimen Specimen Content change NA, UNK OTHER -> OTH ECOLIISO 3 7 Verotoxin1 Shigatoxin1 Name change

Content change UNK Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

ECOLIISO 3 8 Verotoxin1Subtype Shigatoxin1Subtype Name change Content change

No -> Yes NA, UNK O -> OTH VT1a -> Stx1a VT1a_VT1c -> Stx1a_Stx1c VT1a_VT1d -> Stx1a_Stx1d VT1c -> Stx1c VT1c_VT1d -> Stx1c_Stx1d VT1d -> Stx1d

ECOLIISO 3 9 Verotoxin2 Shigatoxin2 Name change Content change

UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

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Variable Status

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Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

ECOLIISO 3 10 Verotoxin2Subtype Shigatoxin2Subtype Name change Content change

No -> Yes NA, UNK OTHER -> OTH VT2a -> Stx2a VT2a_VT2c -> Stx2a_Stx2c VT2a_VT2d -> Stx2a_Stx2d VT2a_VT2e -> Stx2a_Stx2e VT2a_VT2f -> Stx2a_Stx2f VT2a_VT2g -> Stx2a_Stx2g VT2b -> Stx2b VT2b_VT2c -> Stx2b_Stx2c VT2b_VT2d -> Stx2b_Stx2d VT2b_VT2e -> Stx2b_Stx2e VT2b_VT2f -> Stx2b_Stx2f VT2b_VT2g -> Stx2b_Stx2g VT 2c -> Stx2c VT2c_VT2d -> Stx2c_Stx2d VT2c_VT2e -> Stx2c_Stx2e VT2c_VT2f -> Stx2c_Stx2f VT2c_VT2g -> Stx2c_Stx2g VT2d -> Stx2d VT2d_VT2e -> Stx2d_Stx2e VT2d_VT2f -> Stx2d_Stx2f VT2d_VT2g -> Stx2d_Stx2g VT 2e -> Stx2e VT2e_VT2f -> Stx2e_Stx2f VT2e_VT2g -> Stx2e_Stx2g VT2f -> Stx2f VVT2f_VT2g -> Stx2f_Stx2g

ECOLIISO 3 11 VerotoxinProduction ShigatoxinProduction Name change Content change

UNK

ECOLIISO 3 12 AntigenO AntigenO Content change UNK ECOLIISO 3 13 AntigenH AntigenH Content change UNK ECOLIISO 3 14 IntiminEaeGene IntiminEaeGene Content change UNK Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

ECOLIISO 3 15 aaiCGene aaiCGene Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

ECOLIISO 3 16 aggRGene aggRGene Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

ECOLIISO 3 17 ESBLProduction ESBLProduction Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

ECOLIISO 3 18 SorbitolFermenting SorbitolFermenting Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

ECOLIISO 3 19 SpecificAntibodyResponse SpecificAntibodyResponse Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

ECOLIISO 3 20 Enterohaemolysis Enterohaemolysis Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

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Variable Status

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Reference Value CHANGES (to remap)

Variables Changes

ECOLIISO 3 21 BetaGlucoronidaseActivity BetaGlucoronidaseActivity Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

ECOLIISO 4 1 WgsProtocol WgsProtocol No change ECOLIISO 4 2 WgsEnaId / WgsSequenceId WgsAccession Name change ECOLIISO 4 3 WgsAssembler WgsAssembler No change ECOLIISO 4 4 WgsAssembly WgsAssembly No change ECOLIISO 4 5 WgsRawReads WgsRawReads No change ECOLIISO$AST RecordType SubjectCode Name change ECOLIISO$AST 1 1 RecordId NationalRecordId Name change ECOLIISO$AST 1 2 ParentId ParentNationalRecordId Name change ECOLIISO$AST 1 3 Antibiotic AntimicrobialAgent Name change ECOLIISO$AST 1 4 TestMethod ASTMethod Name change ECOLIISO$AST 1 5 TestValue ValueAST Name change ECOLIISO$AST 1 6 ResultSign SusceptibilitySign Name change ECOLIISO$AST 1 7 SIR ASTInterpretation Name change HAEINF Subject Disease Name change

Content change Yes -> No

HAEINF ReportingCountry ReportingCountry No change HAEINF Status Status Content change NEW/UPDATE -> ADD/UPDATE HAEINF RecordType SubjectCode Name change HAEINF RecordTypeVersion Remove variable! HAEINF 1 1 RecordId NationalRecordId Name change HAEINF 1 2 DataSource DataSource No change HAEINF 1 3 DateUsedForStatistics DateUsedForStatistics No change HAEINF 2 1 Age Age No change HAEINF 2 2 AgeMonth AgeMonth No change HAEINF 2 3 Gender Gender Content change UNK O -> OTH HAEINF 2 4 PlaceOfResidence PlaceOfResidence No change HAEINF 2 5 PlaceOfNotification PlaceOfNotification No change HAEINF 3 1 Classification CaseClassification Name change

Content change UNK

HAEINF 3 2 DateOfOnset DateOfOnset No change HAEINF 3 3 DateOfDiagnosis DateOfDiagnosis No change HAEINF 3 4 DateOfNotification DateOfNotification No change HAEINF 3 5 Outcome Outcome Content change NUS, UNK HAEINF 3 6 ClinicalPresentation ClinicalCriteria Name change

Content change NUS, UNK O -> OTH

HAEINF 3 7 DateLastVaccDose DateOfLastVaccination Name change HAEINF 3 8 VaccStatus VaccinationStatus Name change

Content change UNK DOSEUNK -> UNKDOSE

HAEINF 4 1 TestMethod1 MainPathogenDetectionMethod Name change Content change

NA, UNK O -> OTH

HAEINF 4 2 TestMethod2 SecondPathogenDetectionMethod Name change Content change

NA, UNK O -> OTH

HAEINF 4 3 Serotype Serotype Content change NUS A -> HAEINF_A B -> HAEINF_B C -> HAEINF_C D -> HAEINF_D E -> HAEINF_E F -> HAEINF_F UNK -> HAEINF_UNK non-b -> HAEINF_NOT_B non-caps -> HAEINF_NONCAPS

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Variables Changes

HAEINFAGGR Subject Disease Name change Content change

Yes -> No

HAEINFAGGR ReportingCountry ReportingCountry No change HAEINFAGGR RecordType SubjectCode Name change

Content change AGGR -> HAEINFAGGR

HAEINFAGGR RecordTypeVersion Remove variable! HAEINFAGGR 1 1 DataSource DataSource No change HAEINFAGGR 1 2 DateUsedForStatistics DateUsedForStatistics No change HAEINFAGGR 1 3 AgeClass AgeGroup Name change

Content change UNK Please check the updated list of AgeGroup reference values for

this SubjectCode! HAEINFAGGR 1 4 Gender Gender Content change UNK O -> OTH HAEINFAGGR 1 5 Classification CaseClassification Name change

Content change POSS, PROB, UNK

HAEINFAGGR 1 6 VaccinationStatus New variable No No HAEINFAGGR 1 7 NumberOfCases NumberOfCases No change LISTISO Subject Disease Name change

Content change Yes -> No LISTISO -> LIST

LISTISO Subject HealthTopic Name change Content change

Yes -> No LISTISO -> ISO

LISTISO ReportingCountry ReportingCountry No change LISTISO Status Status Content change NEW/UPDATE -> ADD/UPDATE LISTISO RecordType SubjectCode Name change LISTISO RecordTypeVersion Remove variable! LISTISO 1 1 RecordId NationalRecordId Name change LISTISO 1 2 DataSource DataSource No change LISTISO 1 3 DateUsedForStatistics DateUsedForStatistics No change LISTISO 1 4 CaseId CaseId No change LISTISO 2 1 Age Age No change LISTISO 2 2 AgeMonth AgeMonth No change LISTISO 2 3 Gender Gender Content change UNK O -> OTH LISTISO 2 4 Imported New variable No No LISTISO 2 5 PlaceOfInfection New variable No Yes LISTISO 2 6 PlaceOfResidence PlaceOfResidence No change LISTISO 2 7 ItemCode New variable No No LISTISO 3 1 DateOfSampling DateOfSampling No change LISTISO 3 2 DateOfReceiptSourceLab DateOfReceiptSourceLab No change LISTISO 3 3 DateOfReceiptReferenceLab DateOfReceiptReferenceLab No change LISTISO 3 4 SampleId SampleId No change LISTISO 3 5 SampleOrigin SampleOrigin No change LISTISO 3 6 Serotype Serotype Content change UNK 1/2a -> LISTMON_1/2a

1/2b -> LISTMON_1/2b 1/2c -> LISTMON_1/2c 3a -> LISTMON_3a 3b -> LISTMON_3b 3c -> LISTMON_3c 4a -> LISTMON_4a 4ab -> LISTMON_4ab 4b -> LISTMON_4b 4c -> LISTMON_4c 4d -> LISTMON_4d 4e -> LISTMON_4e 7 -> LISTMON_7

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LISTISO 3 7 PCRserogroup PCRSerogroup Name change Content change

NA IIa -> LISTMON_SGIIa IIb -> LISTMON_SGIIb IIc -> LISTMON_SGIIc IVb -> LISTMON_SGIVb L -> LISTMON_SGL UNK -> LISTMON_SGUNK

LISTISO 4 1 WgsProtocol WgsProtocol No change LISTISO 4 2 WgsEnaId / WgsSequenceId WgsAccession Name change LISTISO 4 3 WgsAssembler WgsAssembler No change LISTISO 4 4 WgsAssembly WgsAssembly No change LISTISO 4 5 WgsRawReads WgsRawReads No change LISTISO 4 6 SequenceType SequenceType No change MEAS Subject Disease Name change

Content change Yes -> No

MEAS ReportingCountry ReportingCountry No change MEAS Status Status Content change NEW/UPDATE -> ADD/UPDATE MEAS RecordType SubjectCode Name change MEAS RecordTypeVersion Remove variable! MEAS 1 1 RecordId NationalRecordId Name change MEAS 1 2 DataSource DataSource No change MEAS 1 3 DateUsedForStatistics DateUsedForStatistics No change MEAS 2 1 Age Age No change MEAS 2 2 AgeMonth AgeMonth No change MEAS 2 3 Gender Gender Content change UNK O -> OTH MEAS 3 1 Classification CaseClassification Name change

Content change UNK

MEAS 3 2 DateOfOnset DateOfOnset No change MEAS 3 3 DateOfInvestigation DateOfInvestigation No change MEAS 3 4 DateOfNotification DateOfNotification No change MEAS 3 5 Hospitalisation Hospitalisation Content change UNK Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

MEAS 3 6 Outcome Outcome Content change UNK MEAS 3 7 CauseOfDeathText CauseOfDeath Name change MEAS 3 8 ClinicalCriteria ClinicalCriteriaStatus Name change

Content change NA, UNK Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

MEAS 3 9 Complications ComplicationDiagnosis Name change Content change

UNK NOCOMP -> NONE O -> OTH

MEAS 3 10 ClusterRelated ClusterRelated Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

MEAS 3 11 ClusterIdentification ClusterId Name change MEAS 3 12 ClusterSetting ClusterSetting Content change NA, UNK HOSP -> NOS MEAS 3 13 DateLastVaccDose DateOfLastVaccination Name change MEAS 3 14 VaccStatus VaccinationStatus Name change

Content change UNK DOSEUNK -> UNKDOSE

MEAS 4 1 Imported ImportedStatus Name change Content change

UNK N -> END Y -> IMP

MEAS 4 2 ProbableCountryOfInfection PlaceOfInfection Name change MEAS 4 3 PlaceOfNotification PlaceOfNotification No change MEAS 4 4 PlaceOfResidence PlaceOfResidence No change MEAS 5 1 DateOfSpecimen DateOfSpecimen No change MEAS 5 2 DateOfLabResult DateOfLabResult No change

ECDC NORMAL#

SubjectCode UI Page

UI Position

TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

MEAS 5 3 SpecimenVirDetect SpecimenVirDetect Content change NA, UNK O -> OTH URI -> URINE

MEAS 5 4 ResultVirDetect ResultVirDetect Content change NA, UNK MEAS 5 5 Genotype Genotype Content change NA, UNK A -> MEASV_A

B1 -> MEASV_B1 B2 -> MEASV_B2 B3 -> MEASV_B3 C1 -> MEASV_C1 C2 -> MEASV_C2 D1 -> MEASV_D1 D10 -> MEASV_D10 D11 -> MEASV_D11 D2 -> MEASV_D2 D3 -> MEASV_D3 D4 -> MEASV_D4 D5 -> MEASV_D5 D6 -> MEASV_D6 D7 -> MEASV_D7 D8 -> MEASV_D8 D9 -> MEASV_D9 E -> MEASV_E F -> MEASV_F G1 -> MEASV_G1 G2 -> MEASV_G2 G3 -> MEASV_G3 H1 -> MEASV_H1 H2 -> MEASV_H2

MEAS 5 6 SpecimenSero SpecimenSero Content change NA, UNK O -> OTH MEAS 5 7 ResultIgG ResultIgG Content change NA, UNK MEAS 5 8 ResultIgM ResultIgM Content change NA, UNK MEASAGGR Subject Disease Name change

Content change Yes -> No

MEASAGGR ReportingCountry ReportingCountry No change MEASAGGR RecordType SubjectCode Name change

Content change AGGRVPD -> MEASAGGR

MEASAGGR RecordTypeVersion Remove variable! MEASAGGR 1 1 DataSource DataSource No change MEASAGGR 1 2 DateUsedForStatistics DateUsedForStatistics No change MEASAGGR 1 3 AgeClass AgeGroup Name change

Content change UNK Please check the updated list of AgeGroup reference values for

this SubjectCode! MEASAGGR 1 4 Gender Gender Content change UNK O -> OTH MEASAGGR 1 5 Classification CaseClassification Name change

Content change UNK

MEASAGGR 1 6 VaccStatus VaccinationStatus Name change Content change

NA, UNK DOSEUNK -> UNKDOSE

MEASAGGR 1 7 NumberOfCases NumberOfCases No change MENI Subject Disease Name change

Content change Yes -> No

MENI ReportingCountry ReportingCountry No change MENI Status Status Content change NEW/UPDATE -> ADD/UPDATE MENI RecordType SubjectCode Name change MENI ECDCIsolateID Remove variable! MENI RecordTypeVersion Remove variable! MENI 1 1 RecordId NationalRecordId Name change

ECDC NORMAL#

SubjectCode UI Page

UI Position

TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

MENI 1 2 DataSource DataSource No change MENI 1 3 DateUsedForStatistics DateUsedForStatistics No change MENI 2 1 Age Age No change MENI 2 2 AgeMonth AgeMonth No change MENI 2 3 Gender Gender Content change UNK O -> OTH MENI 3 1 Classification CaseClassification Name change

Content change UNK

MENI 3 2 DateOfOnset DateOfOnset No change MENI 3 3 DateOfDiagnosis DateOfDiagnosis No change MENI 3 4 DateOfNotification DateOfNotification No change MENI 3 5 Outcome Outcome Content change NUS, UNK MENI 3 6 ClinicalPresentation ClinicalCriteria Name change

Content change NUS, UNK O -> OTH

MENI 3 7 DateLastVaccDose DateOfLastVaccination Name change MENI 3 8 VaccStatus VaccinationStatus Name change

Content change 10DOSE, 5DOSE, 6DOSE, 7DOSE, 8DOSE, 9DOSE, UNK

DOSEUNK -> UNKDOSE

MENI 4 1 Imported Imported Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

MENI 4 2 ProbableCountryOfInfection PlaceOfInfection Name change MENI 4 3 PlaceOfNotification PlaceOfNotification No change MENI 4 4 PlaceOfResidence PlaceOfResidence No change MENI 5 1 ReportedEMERTII ReportedEMERTII Content change UNK Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

MENI 5 2 IsolateId IsolateId No change MENI 5 3 TestMethod1 MainPathogenDetectionMethod Name change

Content change NA, UNK O -> OTH

MENI 5 4 TestMethod2 SecondPathogenDetectionMethod Name change Content change

NA, UNK O -> OTH

MENI 5 5 Serogroup Serogroup Content change NUS, UNK 29E -> NEIMENI_29E A -> NEIMENI_A B -> NEIMENI_B C -> NEIMENI_C NGA -> NEIMENI_NGA O -> NEIMENI_OTH W -> NEIMENI_W X -> NEIMENI_X Y -> NEIMENI_Y Z -> NEIMENI_Z Z/29E -> NEIMENI_Z/29E

MENI 5 6 ResultMLST ResultMLST Content change UNK MENI 5 7 ResultPorA1 ResultPorA1 Content change NUS, UNK MENI 5 8 ResultPorA2 ResultPorA2 Content change NUS, UNK MENI 5 9 ResultFetVR ResultFetVR Content change NUS, UNK MENI 6 1 ResultMICSign_CIP MICSign_CIP Name change MENI 6 2 ResultMICValueCIP MICValueAST_CIP Name change MENI 6 3 SIR_CIP SIR_CIP Content change UNK MENI 6 4 ResultMICSign_CTX_CFX MICSign_CTX_CFX Name change MENI 6 5 ResultMICValueCTX_CFX MICValueAST_CTX_CFX Name change MENI 6 6 SIR_CTX_CFX SIR_CTX_CFX Content change UNK MENI 6 7 ResultMICSign_PEN MICSign_PEN Name change MENI 6 8 ResultMICValuePEN MICValueAST_PEN Name change

ECDC NORMAL#

SubjectCode UI Page

UI Position

TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

MENI 6 9 SIR_PEN SIR_PEN Content change UNK MENI 6 10 ResultMICSign_RIF MICSign_RIF Name change MENI 6 11 ResultMICValueRIF MICValueAST_RIF Name change MENI 6 12 SIR_RIF SIR_RIF Content change UNK MENIAGGR Subject Disease Name change

Content change Yes -> No

MENIAGGR ReportingCountry ReportingCountry No change MENIAGGR RecordType SubjectCode Name change

Content change AGGR -> MENIAGGR

MENIAGGR RecordTypeVersion Remove variable! MENIAGGR 1 1 DataSource DataSource No change MENIAGGR 1 2 DateUsedForStatistics DateUsedForStatistics No change MENIAGGR 1 3 AgeClass AgeGroup Name change

Content change UNK Please check the updated list of AgeGroup reference values for

this SubjectCode! MENIAGGR 1 4 Gender Gender Content change UNK O -> OTH MENIAGGR 1 5 Classification CaseClassification Name change

Content change UNK

MENIAGGR 1 6 VaccinationStatus New variable No No MENIAGGR 1 7 NumberOfCases NumberOfCases No change MUMP Subject Disease Name change

Content change Yes -> No

MUMP ReportingCountry ReportingCountry No change MUMP Status Status Content change NEW/UPDATE -> ADD/UPDATE MUMP RecordType SubjectCode Name change MUMP RecordTypeVersion Remove variable! MUMP 1 1 RecordId NationalRecordId Name change MUMP 1 2 DataSource DataSource No change MUMP 1 3 DateUsedForStatistics DateUsedForStatistics No change MUMP 2 1 Age Age No change MUMP 2 2 AgeMonth AgeMonth No change MUMP 2 3 Gender Gender Content change UNK O -> OTH MUMP 2 4 PlaceOfResidence PlaceOfResidence No change MUMP 2 5 PlaceOfNotification PlaceOfNotification No change MUMP 3 1 Classification CaseClassification Name change

Content change UNK

MUMP 3 2 DateOfOnset DateOfOnset No change MUMP 3 3 DateOfNotification DateOfNotification No change MUMP 3 4 Hospitalisation Hospitalisation Content change UNK Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

MUMP 3 5 Outcome Outcome Content change UNK MUMP 3 6 ClinicalPresentation ClinicalCriteria Name change

Content change UNK O -> OTH

MUMP 3 7 Complications ComplicationDiagnosis Name change Content change

UNK ENC -> ENCEPH NOCOMP -> NONE O -> OTH

ECDC NORMAL#

SubjectCode UI Page

UI Position

TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

MUMP 3 8 Genotype Genotype Content change NA, UNK A -> MUMPV_A B -> MUMPV_B C -> MUMPV_C D -> MUMPV_D F -> MUMPV_F G -> MUMPV_G H -> MUMPV_H I -> MUMPV_I J -> MUMPV_J K -> MUMPV_K L -> MUMPV_L N -> MUMPV_N

MUMP 3 9 ClusterRelated ClusterRelated Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

MUMP 3 10 ClusterIdentification ClusterId Name change MUMP 3 11 ClusterSetting ClusterSetting Content change NA, UNK HOSP -> NOS MUMP 3 12 DateLastVaccDose DateOfLastVaccination Name change MUMP 3 13 VaccStatus VaccinationStatus Name change

Content change UNK DOSEUNK -> UNKDOSE

MUMPAGGR Subject Disease Name change Content change

Yes -> No

MUMPAGGR ReportingCountry ReportingCountry No change MUMPAGGR RecordType SubjectCode Name change

Content change AGGRVPD -> MUMPAGGR

MUMPAGGR RecordTypeVersion Remove variable! MUMPAGGR 1 1 DataSource DataSource No change MUMPAGGR 1 2 DateUsedForStatistics DateUsedForStatistics No change MUMPAGGR 1 3 AgeClass AgeGroup Name change

Content change UNK Please check the updated list of AgeGroup reference values for

this SubjectCode! MUMPAGGR 1 4 Gender Gender Content change UNK O -> OTH MUMPAGGR 1 5 Classification CaseClassification Name change

Content change DISCARDED, UNK

MUMPAGGR 1 6 VaccStatus VaccinationStatus Name change Content change

NA, UNK DOSEUNK -> UNKDOSE

MUMPAGGR 1 7 NumberOfCases NumberOfCases No change PERT Subject Disease Name change

Content change Yes -> No

PERT ReportingCountry ReportingCountry No change PERT Status Status Content change NEW/UPDATE -> ADD/UPDATE PERT RecordType SubjectCode Name change PERT RecordTypeVersion Remove variable! PERT 1 1 RecordId NationalRecordId Name change PERT 1 2 DataSource DataSource No change PERT 1 3 DateUsedForStatistics DateUsedForStatistics No change PERT 2 1 Age Age No change PERT 2 2 AgeMonth AgeMonth No change PERT 2 3 Gender Gender Content change UNK O -> OTH PERT 2 4 PlaceOfResidence PlaceOfResidence No change PERT 2 5 PlaceOfNotification PlaceOfNotification No change PERT 3 1 Classification CaseClassification Name change

Content change UNK

PERT 3 2 DateOfOnset DateOfOnset No change PERT 3 3 DateOfNotification DateOfNotification No change

ECDC NORMAL#

SubjectCode UI Page

UI Position

TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

PERT 3 4 Hospitalisation Hospitalisation Content change UNK Column changed from CODED VALUE to BOOLEAN! N -> 0 (FALSE) Y -> 1 (TRUE)

PERT 3 5 Outcome Outcome Content change UNK PERT 3 6 TestMethod PathogenDetectionMethod Name change

Content change NA, UNK ORALFLUIDIgG -> ORALIgG

PERT 3 7 DateLastVaccDose DateOfLastVaccination Name change PERT 3 8 VaccStatus VaccinationStatus Name change

Content change UNK DOSEUNK -> UNKDOSE

PERT 3 9 VaccinationStatusMaternal New variable No No PERT 3 10 GestationalAgeAtVaccination New variable No No PERTAGGR Subject Disease Name change

Content change Yes -> No

PERTAGGR ReportingCountry ReportingCountry No change PERTAGGR RecordType SubjectCode Name change

Content change AGGRVPD -> PERTAGGR

PERTAGGR RecordTypeVersion Remove variable! PERTAGGR 1 1 DataSource DataSource No change PERTAGGR 1 2 DateUsedForStatistics DateUsedForStatistics No change PERTAGGR 1 3 AgeClass AgeGroup Name change

Content change UNK Please check the updated list of AgeGroup reference values for

this SubjectCode! PERTAGGR 1 4 Gender Gender Content change UNK O -> OTH PERTAGGR 1 5 Classification CaseClassification Name change

Content change DISCARDED, UNK

PERTAGGR 1 6 VaccStatus VaccinationStatus Name change Content change

NA, UNK DOSEUNK -> UNKDOSE

PERTAGGR 1 7 NumberOfCases NumberOfCases No change PNEU Subject Disease Name change

Content change Yes -> No

PNEU ReportingCountry ReportingCountry No change PNEU Status Status Content change NEW/UPDATE -> ADD/UPDATE PNEU RecordType SubjectCode Name change PNEU RecordTypeVersion Remove variable! PNEU 1 1 RecordId NationalRecordId Name change PNEU 1 2 DataSource DataSource No change PNEU 1 3 DateUsedForStatistics DateUsedForStatistics No change PNEU 1 4 NRLData NRLData Content change Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

PNEU 2 1 Age Age No change PNEU 2 2 AgeMonth AgeMonth No change PNEU 2 3 Gender Gender Content change UNK O -> OTH PNEU 2 4 PlaceOfResidence PlaceOfResidence No change PNEU 2 5 PlaceOfNotification PlaceOfNotification No change PNEU 3 1 Classification CaseClassification Name change

Content change UNK

PNEU 3 2 DateOfDiagnosis DateOfDiagnosis No change PNEU 3 3 DateOfNotification DateOfNotification No change PNEU 3 4 Outcome Outcome Content change UNK PNEU 3 5 ClinicalPresentation ClinicalCriteria Name change

Content change UNK O -> OTH

PNEU 3 6 TestMethodTyping PathogenDetectionMethod Name change Content change

NA, UNK O -> OTH

ECDC NORMAL#

SubjectCode UI Page

UI Position

TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

PNEU 3 7 Serotype Serotype Content change NT, O 1 -> STRPNE_1 10 -> STRPNE_10 10A -> STRPNE_10A 10B -> STRPNE_10B 10C -> STRPNE_10C 10F -> STRPNE_10F 11 -> STRPNE_11 11A -> STRPNE_11A 11B -> STRPNE_11B 11C -> STRPNE_11C 11D -> STRPNE_11D 11E -> STRPNE_11E 11F -> STRPNE_11F 12 -> STRPNE_12 12A -> STRPNE_12A 12B -> STRPNE_12B 12F -> STRPNE_12F 13 -> STRPNE_13 14 -> STRPNE_14 15 -> STRPNE_15 15A -> STRPNE_15A 15B -> STRPNE_15B 15B/C -> STRPNE_15B/C 15C -> STRPNE_15C 15F -> STRPNE_15F 16 -> STRPNE_16 16A -> STRPNE_16A 16F -> STRPNE_16FPNEU 4 1 DateLastVaccDose DateOfLastVaccination Name change

PNEU 4 2 VaccType Vaccine Name change Content change

NA, UNK

PNEU 4 3 VaccStatus VaccinationStatus Name change Content change

UNK DOSEUNK -> UNKDOSE

PNEU 4 4 DosePCV1 New variable No No PNEU 4 5 DatePCV1 New variable No No PNEU 4 6 BrandPCV1 New variable No No PNEU 4 7 DosePCV2 New variable No No PNEU 4 8 DatePCV2 New variable No No PNEU 4 9 BrandPCV2 New variable No No PNEU 4 10 DosePCV3 New variable No No PNEU 4 11 DatePCV3 New variable No No PNEU 4 12 BrandPCV3 New variable No No PNEU 4 13 DosePCV4 New variable No No PNEU 4 14 DatePCV4 New variable No No PNEU 4 15 BrandPCV4 New variable No No PNEU 4 16 PCVDoses New variable No No PNEU 4 17 DosePPV New variable No No PNEU 4 18 DatePPV New variable No No PNEU 4 19 PPVDoses New variable No No PNEU 5 1 TestMethodMIC ASTMethod Name change

Content change UNK O -> OTH

PNEU 5 2 ResultMICSign_CTX_CFX MICSign_CTX_CFX Name change PNEU 5 3 ResultMICValueCTX_CFX MICValueAST_CTX_CFX Name change PNEU 5 4 SIR_CTX_CFX SIR_CTX_CFX Content change UNK PNEU 5 5 ResultMICSign_ERY MICSign_ERY Name change

ECDC NORMAL#

SubjectCode UI Page

UI Position

TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

PNEU 5 6 ResultMICValueERY MICValueAST_ERY Name change PNEU 5 7 SIR_ERY SIR_ERY Content change UNK PNEU 5 8 ResultMICSign_PEN MICSign_PEN Name change PNEU 5 9 ResultMICValuePEN MICValueAST_PEN Name change PNEU 5 10 SIR_PEN SIR_PEN Content change UNK PNEUAGGR Subject Disease Name change

Content change Yes -> No

PNEUAGGR ReportingCountry ReportingCountry No change PNEUAGGR RecordType SubjectCode Name change

Content change AGGR -> PNEUAGGR

PNEUAGGR RecordTypeVersion Remove variable! PNEUAGGR 1 1 DataSource DataSource No change PNEUAGGR 1 2 DateUsedForStatistics DateUsedForStatistics No change PNEUAGGR 1 3 AgeClass AgeGroup Name change

Content change UNK Please check the updated list of AgeGroup reference values for

this SubjectCode! PNEUAGGR 1 4 Gender Gender Content change UNK O -> OTH PNEUAGGR 1 5 Classification CaseClassification Name change

Content change POSS, PROB, UNK

PNEUAGGR 1 6 VaccinationStatus New variable No No PNEUAGGR 1 7 NumberOfCases NumberOfCases No change POLI Subject Disease Name change

Content change Yes -> No

POLI ReportingCountry ReportingCountry No change POLI Status Status Content change NEW/UPDATE -> ADD/UPDATE POLI RecordType SubjectCode Name change POLI RecordTypeVersion Remove variable! POLI 1 1 RecordId NationalRecordId Name change POLI 1 2 DataSource DataSource No change POLI 1 3 DateUsedForStatistics DateUsedForStatistics No change POLI 2 1 Age Age No change POLI 2 2 Gender Gender Content change UNK O -> OTH POLI 2 3 PlaceOfResidence PlaceOfResidence No change POLI 2 4 PlaceOfNotification PlaceOfNotification No change POLI 3 1 Classification CaseClassification Name change

Content change UNK

POLI 3 2 DateOfOnset DateOfOnset No change POLI 3 3 DateOfDiagnosis DateOfDiagnosis No change POLI 3 4 DateOfNotification DateOfNotification No change POLI 3 5 Outcome Outcome Content change UNK POLI 3 6 DateLastVaccDose DateOfLastVaccination Name change POLI 3 7 VaccinationStatus New variable No No POLIAGGR Subject Disease Name change

Content change Yes -> No

POLIAGGR ReportingCountry ReportingCountry No change POLIAGGR RecordType SubjectCode Name change

Content change AGGR -> POLIAGGR

POLIAGGR Classification Remove variable! POLIAGGR RecordTypeVersion Remove variable! POLIAGGR 1 1 DataSource DataSource No change POLIAGGR 1 2 DateUsedForStatistics DateUsedForStatistics No change POLIAGGR 1 3 AgeClass AgeGroup Name change

Content change UNK Please check the updated list of AgeGroup reference values for

this SubjectCode! POLIAGGR 1 4 Gender Gender Content change UNK O -> OTH POLIAGGR 1 5 CaseClassification New variable No No

ECDC NORMAL#

SubjectCode UI Page

UI Position

TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

POLIAGGR 1 6 VaccinationStatus New variable No No POLIAGGR 1 7 NumberOfCases NumberOfCases No change RUBE Subject Disease Name change

Content change Yes -> No

RUBE ReportingCountry ReportingCountry No change RUBE Status Status Content change NEW/UPDATE -> ADD/UPDATE RUBE RecordType SubjectCode Name change RUBE RecordTypeVersion Remove variable! RUBE 1 1 RecordId NationalRecordId Name change RUBE 1 2 DataSource DataSource No change RUBE 1 3 DateUsedForStatistics DateUsedForStatistics No change RUBE 2 1 Age Age No change RUBE 2 2 AgeMonth AgeMonth No change RUBE 2 3 Gender Gender Content change UNK O -> OTH RUBE 2 4 Pregnancy Pregnancy Content change NA, UNK Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

RUBE 2 5 WeekOfGestation WeekOfGestation Content change NA, UNK RUBE 3 1 Classification CaseClassification Name change

Content change UNK

RUBE 3 2 DateOfOnset DateOfOnset No change RUBE 3 3 DateOfInvestigation DateOfInvestigation No change RUBE 3 4 DateOfNotification DateOfNotification No change RUBE 3 5 Hospitalisation Hospitalisation Content change UNK Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

RUBE 3 6 Outcome Outcome Content change UNK RUBE 3 7 ClinicalCriteriaStatus New variable No No RUBE 3 8 Complications ComplicationDiagnosis Name change

Content change UNK NOCOMP -> NONE

O -> OTH RUBE 3 9 ClusterRelated ClusterRelated Content change UNK Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

RUBE 3 10 ClusterIdentification ClusterId Name change RUBE 3 11 ClusterSetting ClusterSetting Content change NA, UNK HOSP -> NOS RUBE 3 12 DateLastVaccDose DateOfLastVaccination Name change RUBE 3 13 VaccStatus VaccinationStatus Name change

Content change UNK DOSEUNK -> UNKDOSE

RUBE 4 1 Imported ImportedStatus Name change Content change

UNK N -> END Y -> IMP

RUBE 4 2 ProbableCountryOfInfection PlaceOfInfection Name change RUBE 4 3 PlaceOfNotification PlaceOfNotification No change RUBE 4 4 PlaceOfResidence PlaceOfResidence No change RUBE 5 1 DateOfSpecimen DateOfSpecimen No change RUBE 5 2 DateOfLabResult DateOfLabResult No change RUBE 5 3 SpecimenVirDetect SpecimenVirDetect Content change NA, UNK O -> OTH

URI -> URINE RUBE 5 4 ResultVirDetect ResultVirDetect Content change NA, UNK

ECDC NORMAL#

SubjectCode UI Page

UI Position

TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

RUBE 5 5 Genotype Genotype Content change NA, UNK 1A -> RUBEV_1A 1B -> RUBEV_1B 1C -> RUBEV_1C 1D -> RUBEV_1D 1E -> RUBEV_1E 1F -> RUBEV_1F 1G -> RUBEV_1G 1H -> RUBEV_1H 1I -> RUBEV_1I 1J -> RUBEV_1J 2A -> RUBEV_2A 2B -> RUBEV_2B 2C -> RUBEV_2C

RUBE 5 6 SpecimenSero SpecimenSero Content change NA, UNK O -> OTH RUBE 5 7 IgGAvidityTest IgGAvidityTest Content change NA, UNK Column changed from CODED VALUE to BOOLEAN!

N -> 0 (FALSE) Y -> 1 (TRUE)

RUBE 5 8 ResultIgG ResultIgG Content change NA, UNK RUBE 5 9 ResultIgM ResultIgM Content change NA, UNK RUBEAGGR Subject Disease Name change

Content change Yes -> No

RUBEAGGR ReportingCountry ReportingCountry No change RUBEAGGR RecordType SubjectCode Name change

Content change AGGRVPD -> RUBEAGGR

RUBEAGGR RecordTypeVersion Remove variable! RUBEAGGR 1 1 DataSource DataSource No change RUBEAGGR 1 2 DateUsedForStatistics DateUsedForStatistics No change RUBEAGGR 1 3 AgeClass AgeGroup Name change

Content change UNK Please check the updated list of AgeGroup reference values for

this SubjectCode! RUBEAGGR 1 4 Gender Gender Content change UNK O -> OTH RUBEAGGR 1 5 Classification CaseClassification Name change

Content change UNK

RUBEAGGR 1 6 VaccStatus VaccinationStatus Name change Content change

NA, UNK DOSEUNK -> UNKDOSE

RUBEAGGR 1 7 NumberOfCases NumberOfCases No change TETA Subject Disease Name change

Content change Yes -> No

TETA ReportingCountry ReportingCountry No change TETA Status Status Content change NEW/UPDATE -> ADD/UPDATE TETA RecordType SubjectCode Name change TETA RecordTypeVersion Remove variable! TETA 1 1 RecordId NationalRecordId Name change TETA 1 2 DataSource DataSource No change TETA 1 3 DateUsedForStatistics DateUsedForStatistics No change TETA 2 1 Age Age No change TETA 2 2 Gender Gender Content change UNK O -> OTH TETA 2 3 PlaceOfResidence PlaceOfResidence No change TETA 2 4 PlaceOfNotification PlaceOfNotification No change TETA 3 1 Classification CaseClassification Name change

Content change UNK

TETA 3 2 DateOfOnset DateOfOnset No change TETA 3 3 DateOfDiagnosis DateOfDiagnosis No change TETA 3 4 DateOfNotification DateOfNotification No change TETA 3 5 Outcome Outcome Content change UNK

ECDC NORMAL#

SubjectCode UI Page

UI Position

TESSY Metadata

EpiPulse Cases Metadata

Variable Status

Required (changes)

Repeatable (changes)

Discontinued values

Reference Value CHANGES (to remap)

Variables Changes

TETA 3 6 DateLastVaccDose DateOfLastVaccination Name change TETA 3 7 VaccStatus VaccinationStatus Name change

Content change UNK DOSEUNK -> UNKDOSE

TETAAGGR Subject Disease Name change Content change

Yes -> No

TETAAGGR ReportingCountry ReportingCountry No change TETAAGGR RecordType SubjectCode Name change

Content change AGGR -> TETAAGGR

TETAAGGR RecordTypeVersion Remove variable! TETAAGGR 1 1 DataSource DataSource No change TETAAGGR 1 2 DateUsedForStatistics DateUsedForStatistics No change TETAAGGR 1 3 AgeClass AgeGroup Name change

Content change UNK Please check the updated list of AgeGroup reference values for

this SubjectCode! TETAAGGR 1 4 Gender Gender Content change UNK O -> OTH TETAAGGR 1 5 Classification CaseClassification Name change

Content change UNK

TETAAGGR 1 6 VaccinationStatus New variable No No TETAAGGR 1 7 NumberOfCases NumberOfCases No change

Page 1 of 23

Contents INTRODUCTION ......................................................................................................................................... 2

HOW TO USE THIS DOCUMENT ............................................................................................................................... 2 FINDING FURTHER INFORMATION ........................................................................................................................... 2 COPYRIGHT ........................................................................................................................................................... 2

REPORTING TO EPIPULSE CASES ......................................................................................................... 3

CHECKING THE DATA COLLECTION SCHEDULE .......................................................................................................... 3 PREPARING DATA ................................................................................................................................................... 3 CHECKING METADATA ............................................................................................................................................ 3 CHECKING YOUR SURVEILLANCE SYSTEM DESCRIPTORS .......................................................................................... 3 UPLOADING YOUR DATA ......................................................................................................................................... 4 FINALISING YOUR SUBMISSION ............................................................................................................................... 5 EPIPULSE CASES HELPDESK ................................................................................................................................... 9

ANNEX 1. VPD METADATA ..................................................................................................................... 10

VPD METADATA SET ............................................................................................................................................ 10 Current subject codes ................................................................................................................................. 10 Case-based reporting.................................................................................................................................. 10 Aggregated reporting ................................................................................................................................. 13

CHANGES TO THE VPD METADATA ....................................................................................................................... 16

ANNEX 2. VPD-SPECIFIC MATERIAL .................................................................................................. 19

VPD DATA REPORTING FREQUENCY ...................................................................................................................... 19 NARRATIVE INFORMATION ................................................................................................................................... 19 MUMPS DATA COLLECTION AND CASE DEFINITIONS ............................................................................................... 20 PERTUSSIS DATA COLLECTION AND CASE DEFINITIONS .......................................................................................... 21 POLIOMYELITIS DATA COLLECTION AND CASE DEFINITIONS ................................................................................... 22 TETANUS DATA COLLECTION AND CASE DEFINITIONS ............................................................................................. 23

Vaccine Preventable Diseases (VPD) Reporting Protocol 2024

Mumps, Pertussis, Poliomyelitis and Tetanus

Surveillance data for 2023

EpiPulse Cases

Page 2 of 23

Introduction

This reporting protocol describes the reporting of 2024 measles and rubella cases to EpiPulse Cases, which is replacing TESSy.

Please note:

• Since February 2023, the reporting of diphtheria is described in a separate reporting protocol: Diphtheria, Reporting Protocol 2023, Version 1.0.

• The Vaccine Preventable Diseases (VPD) reporting protocol 2024 describes reporting of: pertussis, mumps, poliomyelitis and tetanus.

• The Invasive Bacteria Diseases (IBD) reporting protocol 2024 describes reporting of: invasive H. influenzae disease, invasive meningococcal disease, Neisseria Meningitidis isolates, and invasive pneumococcal disease.

Reporting protocols are data collection guidelines for the data managers of reporting countries and the protocol

design is intended to improve user-friendliness by:

• introducing a uniform structure to make it easier for data managers to find data collection information across different subjects;

• removing information which is not relevant for data managers.

Similarly, the surveillance protocol will contain some of the generic information previously contained in the reporting protocols.

Since the data managers in reporting countries often have multiple roles, subject-specific material is sometimes distributed together with a reporting protocol. To maintain the uniform structure, this type of material is now included in Annex 2.

How to use this document

This reporting protocol provides information for the data managers of reporting countries in three main sections:

• Reporting to EpiPulse Cases which contains guidelines on how to prepare data for submission to EpiPulse

Cases, deadlines, subject-specific information (e.g. new changes to metadata), and links to further information.

• Annex 1 which contains:

− the metadata set for the subject(s) covered by this reporting protocol. − a list of metadata changes for the subject(s) covered by this reporting protocol.

• Annex 2 which contains subject-specific material relevant for distribution with the reporting protocol.

Finding further information Updated links to all the schedules, documentation and training materials mentioned in this reporting protocol are included in the Documentation and Help pages, including links to:

• EpiPulse Cases Metadata • TESSy Metadata sets and change history • EpiPulse Cases Machine to Machine Technical Documentation • Tutorials for data transformation using respectively Excel and Access

Copyright

© European Centre for Disease Prevention and Control, 2024. Reproduction is authorised, provided the source is acknowledged.

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Reporting to EpiPulse Cases

In September 2024 EpiPulse Cases is expected to go live. We have built it as a replacement for TESSy, with the aim of improving the process of reporting, reviewing, and updating surveillance data.

Only Vaccine-Preventable Diseases will be reported to EpiPulse Cases in 2024, all other diseases will continue to be reported to TESSy for now.

This section provides both an overview of the EpiPulse Cases reporting process and tips on where you can find useful information.

The overall process is as follows:

• Familiarise yourself with the data collection deadlines. • Prepare (export and transform) your data. • Check that your data complies with the EpiPulse Cases metadata. • Check that your data sources are up to date. • Submit your file(s) to EpiPulse Cases. • Finalise and approve your submission.

Checking the data collection schedule

A link to the current data collections schedule can be found in the Communication section of the ‘Documentation and Help’ pages.

Preparing data After you have exported the data from your national database, you need to ensure that the data are in a format that EpiPulse Cases can accept. EpiPulse Cases accepts only CSV and XML files, optionally ZIP-compressed. The EpiPulse Cases metadata has been developed from the TESSy Metadata, with the aim to make only the minimal number of changes necessary, and to hopefully provide a better experience when reporting your datasets to ECDC.

Specific guidelines for measles and rubella data collection and preparation for EpiPulse Cases are provided in Annex 1 and Annex 2.

Checking metadata The metadata defines the fields and data formats that are valid as input to EpiPulse Cases for a given subject. The EpiPulse Cases metadata includes a section that compares and highlights the changes between TESSy and EpiPulse Cases, to facilitate the transition.

As the requirements for data to be shared among ECDC Stakeholders can change, the data format changes needed to support the new requirements are identified and agreed upon between the National Surveillance Contact Points, the Network Coordination Groups and ECDC’s Disease Experts. These changes are then implemented to the EpiPulse Cases metadata.

Changes to the metadata for the subject of this reporting protocol are described in Annex 1.

It is especially important to focus on:

• Field formats Many fields require the data to be formatted in a specific way. For example, dates must be in the YYYY- MM-DD format; dates in the DD/MM/YYYY format will be rejected.

• Reference Values (the equivalent of TESSy Coded Values) Some fields only permit the use of specific values (reference values). For example, M, F or OTH are the coded values for ‘Gender’ and any other value in a ‘Gender’ field will be rejected. Please note that UNK is no longer a valid code, you may leave the field empty instead.

The EpiPulse Cases metadata Excel file contains all the definitions and rules necessary to format data correctly. The READ ME sheet of the Excel document explains how to work with the metadata. It can be downloaded from the Technical Guidelines & Tools section of the ‘TESSy Help & Docs’ pages.

Filtering the fields in the file by subject will enable you to see the fields required for your subject and the rules that apply to these fields.

Checking your Surveillance System Descriptors

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Before submitting file(s), please review your data source(s) in EpiPulse (in the menu, go to ‘Report’ -> ‘Surveillance systems descriptors’) and update the information as necessary.

Complete and up-to-date data source information for each subject is important for improving the interpretation of data - each surveillance system has different features that need to be taken into account when comparing data European level.

If your data source information is out-of-date and you do not have access rights to update it, please ask your National Focal Point for Surveillance or National Coordinator to do so.

Information on data sources is available in the TESSy User Guide, as this functionality is still only available through TESSy.

Uploading your data Data is submitted through the EpiPulse web interface (in the menu, go to Report -> EpiPulse Cases).

The visual interface for reporting new data and editing existing records has remained very similar to that of TESSy. For those of you that are also responsible for reporting diseases outside of the Vaccine Preventable Diseases group, you will continue to use TESSy (under EpiPulse) in parallel with the new EpiPulse Cases, until all disease groups will have been migrated to the new tool.

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Similar to TESSy, you can Add/Update or Replace data with new uploads, using either CSV or XML files. You can

also manually create records for some diseases, and report zero cases where appropriate.

The functionality for manually editing existing records is also a familiar experience. Search for the record you wish to edit, and modify the existing information as needed.

Finalising your submission The compliance of your data with the validation rules in the metadata is checked automatically during the data upload process. In EpiPulse Cases this process is called “Technical Validation”, and it is the only step where your upload can be rejected, for severe data quality issues, such as the file format not being readable by the system, or (one of the few) mandatory variables having missing values.

If your file has been rejected, there will be a message explaining each instance of non-compliance with the metadata that needs correcting.

The significant new feature in EpiPulse Cases is the Data Validation Report, which puts your data in the context of the already existing information for the same disease, and provides you with a detailed overview of the new data in the file you have just uploaded, as well as the resulting overall epidemiological situation painted by the existing (past) data together with the newly uploaded file(s). This means much more timely feedback on your uploads, including details on data quality, as well as outputs (graphs, charts, and tables) on some of epidemiological indicators. The Data Validation reports will evolve and grow based on your feedback in collaboration with our Disease Experts. These reports will provide a new and better way of understanding and updating the information collected at European level, and will hopefully increase the quality and timeliness of the data, while reducing workloads.

Below you can find a few screenshots of the Data Validation Report.

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1. Begin by opening the report:

2. View the report in a window, download the list of eventual validation messages, or download the report

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3. Check data completeness; both for the new upload, and in the context of historical data

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4. The downloaded report can be opened full screen for easier viewing and navigation. This is a preview of the currently developed epidemiological indicators/stratifications.

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5. After reviewing the information in the Data Validation Report you can choose to approve or reject it.

If you choose to reject it, no data will be saved in the EpiPulse Cases system, but your file will remain visible should you wish to re-download it, or resubmit it for a new Data Validation at a later date or after further checks. Please check the Epi Validation Report carefully, there might be warnings and remarks relating to possible data quality issues or potential overwriting of existing records that you should consider.

When your file has been validated and you are satisfied that all corrections have been made, please ensure

prompt approval or rejection. Unapproved uploads can block the approval of other related uploads.

EpiPulse Cases Helpdesk

Email: [email protected]

Telephone number: +46-(0)8-5860 1601

Availability: 9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC holidays)

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Annex 1. VPD metadata

This section describes:

• The VPD metadata set • Changes to the VPD metadata

VPD metadata set

Current subject codes

Table 1 shows the subject codes (formerly ‘record types’) to be used when reporting 2023 VPD surveillance data to Epipulse Cases (EPC). Cases should be reported according to the relevant EU Case

Definition1.

We strongly encourage case-based reporting. If case-based data are not available, aggregated data

may be reported.

Table 1: VPD subject codes

Disease Case-based subject code Aggregated subject code

Mumps MUMP MUMPAGGR

Pertussis PERT PERTAGGR

Poliomyelitis POLI POLIAGGR

Tetanus TETA TETAAGGR

Comment: An aggregated format called “AGGRVPD” was available for mumps and pertussis since 2013. This format was the same as the “AGGR” format, but with “Vaccination Status” as an additional

variable. From 2024, with the move from TESSy reporting to Epipulse Cases, aggregated subject

codes MUMPAGGR, PERTAGGR, POLIAGGR and TETAAGGR have been launched.

Case-based reporting

The metadata set has variables that are common across all the Vaccine Preventable Diseases (VPD):

mumps (MUMP), pertussis (PERT), poliomyelitis (POLI) and tetanus (TETA), which are summarised in

Table 2. Disease-specific variables (in addition to the common variables) are subsequently

summarised in Table 3 (MUMP), Table 4 (PERT), Table 5 (POLI) and Table 6 (TETA).

1 EU case definitions (europa.eu)

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Table 2: Case-based metadata common across VPD data (subject codes: MUMP, PERT, POLI, TETA)

Variable Description Coded value list

Age Age of patient in years as reported in the national system at the time of disease onset.

CaseClassification Case classification according to EU case definition. CONF = Confirmed POSS = Possible

PROB = Probable

DataSource The data source (surveillance system) that the record originates from. The DataSource value must be a special reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateOfLastVaccination Date of administration of the last vaccination dose - indicates the date when the last dose of vaccine was given before disease onset (if exact date is not known, then provide month or year).

DateOfNotification Date when the case report is first notified to public health authorities.

DateOfOnset Date of onset of disease. Leave empty for asymptomatic cases.

DateUsedForStatistics The reference date used for standard reports that is compared to the reporting period. The date used for statistics can be any date that the reporting country finds applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being reported. MUMP = Mumps PERT = Pertussis POLI = Poliomyelitis TETA = Tetanus

Gender Gender of the reported case. F = Female M = Male OTH = Other

NationalRecordId Unique identifier for each record within and across the specified surveillance system (data source) – selected and generated by the country reporting the record.

Outcome Information on whether the case is alive or deceased. The death should be due to the reported disease.

A = Alive D = Died

PlaceOfNotification Place of the first notification of the case to a regional authority. Select the most detailed NUTS level possible.

Consult the reference values in mdLocation dataset

PlaceOfResidence Place of residence of patient at the time of disease onset. Select the most detailed NUTS level possible.

Consult the reference values in mdLocation dataset

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

Status The Status value is used to provide the functionality for a record within EpiPulse Cases database. Default value: NEW/UPDATE. If set to DELETE, the record with the specified NationalRecordId is deleted (invalidated) from EpiPulse Cases database, if it exists. If set to NEW/UPDATE, the record is inserted into the database: If the same NationalRecordId already exists for the same data source and subject code, then the current submitted record updates (replace) the existing one.

DELETE = Delete a previously reported record. NEW/UPDATE = Update a previously reported record (default).

SubjectCode SubjectCode is a reporting model for a disease/health topic - identifies the reporting structure and format of a record (case based or aggregate reporting).

MUMP = Mumps PERT = Pertussis POLI = Poliomyelitis TETA = Tetanus

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Table 3: Case-based metadata – additional MUMP-specific variables

VaccinationStatus Indicates if the case is vaccinated and number of vaccine doses received.

10DOSE = 10 doses 1DOSE = 1 dose 2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses 5DOSE = 5 doses 6DOSE = 6 doses 7DOSE = 7 doses 8DOSE = 8 doses 9DOSE = 9 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

Variable Description Coded value list

AgeMonth Age of patient in months as reported in the national system for cases < 2 years of age at the time of disease onset.

ClinicalCriteria Clinical presentation of the disease according to EU case definition.

MENI = Meningitis/Meningeal/ Meningoencephalitic ORCH = Orchitis OTH = Other PAROT = Swelling of the parotid gland

ClusterId Unique identifier of the cluster as provided by the country epidemiologist.

ClusterRelated Is the case part of an outbreak/cluster? 0 = No 1 = Yes

ClusterSetting Setting of the cluster (for epidemiologically-linked cases).

CHILDCARE = Kindergarten or child care FAM = Family MIL = Military NOS = Nosocomial (hospital) OTH = Other SCH = School SPORT = Sports team UNI = University

ComplicationDiagnosis Complications of mumps. Can be repeated if several complications have occurred.

ENCEPH = Encephalitis MENI = Meningitis NONE = None ORCH = Orchitis OTH = Other PANC = Pancreatitis

Genotype Mumps virus genotype. MUMPV_A = Mumps virusGenotype A MUMPV_B = Mumps virusGenotype B MUMPV_C = Mumps virusGenotype C MUMPV_D = Mumps virusGenotype D MUMPV_F = Mumps virusGenotype F MUMPV_G = Mumps virusGenotype G MUMPV_H = Mumps

virusGenotype H

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Table 4: Case-based metadata – additional PERT-specific variables

Table 5: Case-based metadata – additional POLI-specific variables

Table 6: Case-based metadata – additional TETA-specific variables

Aggregated reporting

Please refer to Table 7 to see the format for aggregated reporting of VPD data. If only a few variables

can be reported, it is recommended to give the following priority for reporting: AgeGroup,

Classification, VaccStatus, Gender.

Table 7: Aggregate metadata for reporting of VPD data (subject codes: MUMPAGGR, PERTAGGR, POLIAGGR, TETAAGGR)

MUMPV_I = Mumps virusGenotype I MUMPV_J = Mumps virusGenotype J MUMPV_K = Mumps virusGenotype K MUMPV_L = Mumps virusGenotype L MUMPV_N = Mumps virusGenotype N

Hospitalisation History of hospitalisation due to the disease or related complications. Hospitalisation defined as at least one overnight stay.

0 = No 1 = Yes

Variable Description Coded value list

AgeMonth Age of patient in months as reported in the national system for cases < 2 years of age at the time of disease onset.

GestationalAgeAtVaccination If mother vaccinated during pregnancy, at what gestational age (in weeks).

Hospitalisation History of hospitalisation due to the disease or related complications. Hospitalisation defined as at least one overnight stay.

0 = No 1 = Yes

PathogenDetectionMethod Pathogen detection method used to diagnose the case. More than one method can be reported.

CULT = Culture ORALIgG = IgG in oral fluid PCR = PCR

confirmation SERO = Serology

VaccinationStatusMaternal Vaccination status of mother during pregnancy for cases < 2 years of age at the time of disease onset.

0 = No 1 = Yes

Variable Description Coded value list

DateOfDiagnosis First date of clinical or lab diagnosis. In case the DateOfOnset is missing this date is used for analysis.

Variable Description Coded value list

DateOfDiagnosis First date of clinical or lab diagnosis. In case the DateOfOnset is missing this date is used for analysis.

Variable Description Coded value list

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AgeGroup Age group of the reported record. See Table 8 below.

CaseClassification Case classification according to EU case definition. CONF = Confirmed POSS = Possible PROB = Probable

DataSource The data source (surveillance system) that the record originates from. The DataSource value must be a special reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateUsedForStatistics The reference date used for standard reports that is compared to the reporting period. The date used for statistics can be any date that the reporting country finds applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being reported. MUMP = Mumps

PERT = Pertussis POLI = Poliomyelitis TETA = Tetanus

Gender Gender of the reported record. F = Female M = Male OTH = Other

NumberOfCases Total number of cases during the reported period for the specified disease.

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

SubjectCode SubjectCode is a reporting model for a disease/health topic - identifies the reporting structure and format of a record (case based or aggregate reporting).

MUMP = Mumps PERT = Pertussis POLI = Poliomyelitis TETA = Tetanus

VaccinationStatus (MUMPAGGR / POLIAGGR)

Indicates if the case is vaccinated and number of vaccine doses received.

1DOSE = 1 dose 2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

VaccinationStatus (PERTAGGR / TETAAGGR)

Indicates if the case is vaccinated and number of vaccine doses received.

1DOSE = 1 dose 2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses 5DOSE = 5 doses 6DOSE = 6 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

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Table 8: Age categories compatible with aggregate VPD reporting *

Option Variable Narrative description Coded value in TESSy of the variable AgeClass

1 (preferred) AgeGroup <1 year

1-4 years

5-9 years

10-14 years

15-19 years

20-24 years

25-29 years

30-34 years

35-39 years

40-44 years

45-49 years

50-54 years

55-59 years

60-64 years

65 and over

0

01-04

05-09

10-14

15-19

20-24

25-29

30-34

35-39

40-44

45-49

50-54

55-59

60-64

65+

2 * AgeGroup <1 year

1-4 years

5-9 years

10-14 years

15-19 years

20-24 years

25-29 years

30 and over

0

01-04

05-09

10-14

15-19

20-24

25-29

30+

3 * AgeGroup <1 year

1-4 years

5-9 years

10-14 years

15-19 years

20-29 years

30 and over

0

01-04

05-09

10-14

15-19

20-29

30+

* Options 2 and 3 above can be used for reporting aggregate mumps and/or pertussis

data but should NOT be used for aggregate reporting of poliomyelitis or tetanus data.

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Changes to the VPD metadata

Metadata changes prior to 2014 can be found on the TESSy documents website. Changes from 2014 onwards have been summarised in Table 9 below.

Table 9: Summary of implemented changes in case-based and aggregated subject codes (formerly ‘record types’) for VPD from 2014 to current

Year of change

Subject Variables Description

2024 MUMP PERT POLI TETA MUMPAGGR PERTAGGR POLIAGGR TETAAGGR

ALL

Reporting moved from TESSy to the Epipulse Cases platform. This transition has led to changes in some variable names and categorical values (see below).

RecordTypeVersion Remove variable

MUMP PERT POLI TETA

Classification → CaseClassification; DateLastVaccDose → DateOfLastVaccination; RecordId → NationalRecordId; RecordType → SubjectCode; Subject → Disease;

Variable names changed from (TESSy) → to (Epipulse Cases): Classification → CaseClassification; DateLastVaccDose → DateOfLastVaccination; RecordId → NationalRecordId; RecordType → SubjectCode; Subject → Disease;

MUMP PERT TETA

VaccStatus → VaccinationStatus Variable name changed from (TESSy) → to (Epipulse Cases): VaccStatus → VaccinationStatus

MUMP ClusterIdentification → ClusterId; ClinicalPresentation → ClinicalCriteria; Complications → ComplicationDiagnosis

Variable names changed from (TESSy) → to (Epipulse Cases): ClusterIdentification → ClusterId; ClinicalPresentation → ClinicalCriteria Complications → ComplicationDiagnosis

PERT TestMethod → PathogenDetectionMethod Variable name changed from (TESSy) → to (Epipulse Cases): TestMethod → PathogenDetectionMethod

MUMPAGGR PERTAGGR POLIAGGR TETAAGGR

AgeClass → AgeGroup; RecordType → SubjectCode; Subject → Disease;

Variable names changed from (TESSy) → to (Epipulse Cases): AgeClass → AgeGroup; RecordType → SubjectCode; Subject → Disease; VaccStatus → VaccinationStatus

MUMPAGGR PERTAGGR TETAAGGR

Classification → CaseClassification;

Variable names changed from (TESSy) → to (Epipulse Cases): Classification → CaseClassification;

MUMPAGGR PERTAGGR

VaccStatus → VaccinationStatus Variable names changed from (TESSy) → to (Epipulse Cases): VaccStatus → VaccinationStatus

PERT VaccMaternal ADD variable: Vaccination status of mother during pregnancy for cases < 2 years of age at the time of disease onset New validation rule: If Age is less than 2 years, then vaccination status of mother during pregnancy (VaccinationStatusMaternal) should be reported.

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VaccMaternal_GestAge ADD variable: If mother vaccinated during pregnancy, at what gestational age (in weeks) New validation rule: If Age is less than 2 years, then vaccination status of mother during pregnancy (VaccinationStatusMaternal) should be reported.

POLIAGGR TETAAGGR

VaccinationStatus ADD variable

MUMP PERT POLI TETA

CaseClassification; Outcome

Discontinued “UNK” categorical value

Status Remapping of “NEW/UPDATE” to “ADD/UPDATE”

MUMP PERT POLI TETA MUMPAGGR PERTAGGR POLIAGGR TETAAGGR

Gender Discontinued “UNK” categorical value and “O” remapped to “OTH”

MUMP

ClinicalCriteria Discontinued “UNK” categorical value and “O” remapped to “OTH”

ClusterRelated Discontinued “UNK” categorical value and variable changed from coded value to Boolean (0 = No ; 1 = Yes)

ClusterSetting Discontinued “UNK” and “NA” categorical values and “HOSP” remapped to “NOS” = Nosocomial (hospital)

ComplicationDiagnosis Discontinued “UNK” categorical value and remapping of: “ENC” to “ENCEPH” “NOCOMP” to “NONEIMP” “O” to “OTH”

Genotype Discontinued “UNK” and “NA” categorical values and remapping of:

“A” to “MUMPV_A” “B” to “MUMPV_B” “C” to “MUMPV_C” “D” to “MUMPV_D” “F” to “MUMPV_F” “G” to “MUMPV_G”

“H” to “MUMPV_H” “I” to “MUMPV_I” “J” to “MUMPV_J” “K” to “MUMPV_K” “L” to “MUMPV_L” “N” to “MUMPV_N”

MUMP PERT

Hospitalisation Discontinued “UNK” categorical value and variable changed from coded value to Boolean (0 = No ; 1 = Yes)

PERT PathogenDetectionMethod Discontinued “UNK” and “NA” categorical values and “ORALFLUIDIgG” remapped to “ORALIgG”

MUMP PERT TETA MUMPAGGR PERTAGGR

VaccinationStatus Discontinued “UNK” and “NA” categorical values and “DOSEUNK” remapped to “UNKDOSE”

MUMPAGGR PERTAGGR POLIAGGR TETAAGGR

AgeGroup Discontinued “UNK” categorical value

SubjectCode “AGGRVPD” value remapped to “MUMPAGGR” / “PERTAGGR” / “POLIAGGR” / “TETAAGGR”

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MUMPAGGR PERTAGGR

CaseClassification Discontinued “UNK” and “DISCARDED” categorical values

TETAAGGR CaseClassification Discontinued “UNK” categorical value

2021 TETA VaccStatus Variable added

2017 MUMP PERT POLI TETA

DateLastVaccDose The description updated to specify that the date given should be the date of last dose before disease onset.

MUMP Genotype The coded value ‘NA’ (not applicable) was added.

PERT TestMethod The coded value ‘ORALFLUIDIgG’ (IgG in oral fluid) was added.

2016 MUMP ClinicalPresentation The description of the variable was edited to match other VPDs

POLI TETA

DateLastVaccDose Variable added

2015 MUMP PERT POLI TETA

EpiLink ClinicalCriteria Labresult

Variables dropped

MUMP Classification The description of the variable was edited to ensure consistency with the EU case definition

Genotype Variable added.

PERT Classification The description of the variable was edited to ensure consistency with the EU case definition

2014 MUMP PERT POLI

VaccStatus Improve description of coded value list

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Annex 2. VPD-specific material

VPD data reporting frequency

The surveillance data for the VPDs (mumps, pertussis, poliomyelitis and tetanus) should be uploaded

annually. In 2024, uploaded data will relate to cases with date used for statistics in 2023.

The deadline for uploading all VPD data is 15 October 2024.

As per the case definitions:

• Mumps – possible, probable and confirmed cases should be reported.

• Pertussis – possible, probable and confirmed cases should be reported.

• Poliomyelitis - confirmed cases should be reported. It is also necessary to report “zero cases”

if no cases have occurred.

• Tetanus – probable and confirmed cases should be reported.

See below for further details of the case definition for each disease.

It is possible to update case information retrospectively, i.e. for cases reported in previous years with

a date used for statistics prior to 2023. For all diseases, any update of previously reported cases should be done before the reporting deadline for data to be included in the annual epidemiological

report and surveillance atlas.

Once the data are validated by the disease experts at ECDC, they are then made publicly available on

the Surveillance Atlas of Infectious Diseases and through annual surveillance reports on the ECDC

website.

ECDC also presents worldwide polio cases, reported by the Global Polio Eradication Initiative (GPEI),

on a monthly basis on a dedicated Polio dashboard.

Narrative information

Changes over time in the number of cases reported in a surveillance system do not always reflect true changes in the incidence of disease. New reporting practices, improved laboratory capacities and

changes in legislation are some of the factors that can influence the number of cases reported. It is

important to be aware of such “surveillance artefacts” when analysing surveillance data and countries are encouraged to describe changes in the surveillance environment that may impact on the number

of cases reported. It is equally important to report if the surveillance environment has remained the same from one year to the next. We encourage reporting countries to provide this information at the

same time as data submission to TESSy and to [email protected].

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Mumps data collection and case definitions Until 2011, data on cases of mumps were collected by the European surveillance network for selected vaccine- preventable diseases (EUVAC.NET), hosted at the Statens Serum Institute (SSI) in Denmark. The coordination of this network and data collection was transferred to ECDC in 2011.

Possible, probable and confirmed cases should be reported according to the 2018 EU case definition for Mumps2:

The 2018 case definition is the same as of 2012, while the 2008 case definition differs from the 2012 case definition with regard to the clinical criteria. In the 2008 case definition, fever and at least two of: swelling of the parotid or other salivary glands, orchitis or meningitis are required for a case to fit the clinical criteria. The 2002 EU case definition gives a more general description of clinical criteria and does not define a possible case.

2 Commission Implementing Decision 2018/945/EU of 22 June 2018 on the communicable diseases and related special health issues to be covered by epidemiological surveillance as well as relevant case definitions.

Clinical criteria

Any person with:

— Fever;

AND at least one of the following three:

— Sudden onset of unilateral or bilateral tender swelling of the parotid or other salivary glands without other apparent cause;

— Orchitis;

— Meningitis.

Laboratory criteria

At least one of the following three:

— Isolation of mumps virus from a clinical specimen;

— Detection of mumps virus nucleic acid;

— Mumps virus specific antibody response characteristic for acute infection in serum or saliva.

Laboratory results need to be interpreted according to the vaccination status.

Epidemiological criteria

An epidemiological link by human to human transmission

Additional information: incubation period lasting 14-25 days, but more often 16-18 days

Case classification:

A. Possible case: any person meeting the clinical criteria

B. Probable case: any person meeting the clinical criteria and with an epidemiological link

C. Confirmed case: any person not recently vaccinated and meeting the laboratory criteria

In case of recent vaccination: any person with detection of wild-type mumps virus strain

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Pertussis data collection and case definitions Data on pertussis have been collected on a European level since 1998. Initially, this data collection was coordinated by the European surveillance network for selected vaccine-preventable diseases (EUVAC.NET), hosted at the Istituto Superiore di Sanità from 1998 - 2002 and then at the Statens Serum Institute in Denmark from 2003 - 2011. In 2011, the coordination of this network was transferred to ECDC.

Possible, probable and confirmed cases should be reported according to the 2018 EU case definition for pertussis3:

The 2018 EU case definition repeated the definition from 2012 but was expanded by including the notes relating to the clinical criteria and laboratory criteria (both on direct and indirect diagnosis). The 2012 and 2008 EU case definitions (unchanged between 2008 and 2012), differed from the 2002 EU case definition, which defined clinical criteria as a “clinical picture compatible with pertussis, e.g. a cough illness lasting at least two weeks with one of the following: paroxysms of coughing, inspiratory ‘whoop’ or post-tussive vomiting without other apparent cause” and did not include an epidemiological criterion.

3 Commission Implementing Decision 2018/945/EU of 22 June 2018 on the communicable diseases and related special health issues to be covered by epidemiological surveillance as well as relevant case definitions.

Clinical criteria

Any person with a cough lasting at least two weeks;

AND at least one of the following three:

— Paroxysms of coughing;

— Inspiratory ‘whooping’;

— Post-tussive vomiting;

OR Any person diagnosed as pertussis by a physician;

OR Apnoeic episodes in infants.

Notes: All individuals including adults, adolescents or vaccinated children can present with atypical symptoms. Characteristics of cough should be investigated, particularly whether the cough is paroxysmal in nature, increases during

the night and occurs in the absence of fever.

Laboratory criteria

At least one of the following three:

(i) Isolation of Bordetella pertussis from a clinical specimen;

(ii) Detection of Bordetella pertussis nucleic acid in a clinical specimen;

(iii) Bordetella pertussis specific antibody response.

Direct diagnosis (i)-(ii): Bordetella pertussis and its nucleic acid are best isolated/detected from nasopharyngeal samples. Indirect diagnosis (iii): if possible ELISA should be performed using highly purified Pertussis Toxin and WHO reference sera as a standard. Results need to interpreted according to pertussis vaccination status. If vaccinated within the last few years before specimen collection, the titre of specific antibodies against Bordetella pertussis toxin may be a consequence of, or modified by, previous vaccination.

Epidemiological criteria

An epidemiological link by human-to-human transmission

Case classification:

A. Possible case: any person meeting the clinical criteria.

B. Probable case: any person meeting the clinical criteria and with an epidemiological link.

C. Confirmed case: any person meeting the clinical and the laboratory criteria.

Invasive Bacterial Diseases (IBD) Reporting Protocol 2023

22

Poliomyelitis data collection and case definitions

Confirmed cases should be reported according to the 2018 EU case definition for acute poliomyelitis4:

4 Commission Implementing Decision 2018/945/EU of 22 June 2018 on the communicable diseases and related special health issues to be covered by epidemiological surveillance as well as relevant case definitions.

Clinical criteria

Any person <15 years of age with Acute flaccid paralysis (AFP)

OR

Any person in whom polio is suspected by a physician

Laboratory criteria

At least one of the following three:

— Isolation of a polio virus and intratypic differentiation – Wild polio virus (WPV)

— Vaccine derived poliovirus (VDPV) (for the VDPV at least 85% similarity with vaccine virus in the nucleotide

sequence in the VP1 section)

— Sabin-like poliovirus: intratypic differentiation performed by a WHO-accredited polio laboratory (for the

VDPV a >1% up to 15% VP1 sequence difference compared with vaccine virus of the same serotype)

Epidemiological criteria

At least one of the following two epidemiological links:

— Human to human transmission

— An history of travel to a polio-endemic area or an area with suspected or confirmed circulation of poliovirus

Case classification:

A. Possible case: Any person meeting the clinical criteria

B. Probable case: any person meeting the clinical criteria with an epidemiological link

C. Confirmed case: any person meeting the clinical and the laboratory criteria

Invasive Bacterial Diseases (IBD) Reporting Protocol 2023

23

Tetanus data collection and case definitions

Probable and confirmed cases should be reported according to the 2018 EU case definition for tetanus5:

The 2018 EU case definition is the same as the 2012 and 2008 case definitions. By contrast, the 2002 EU case definition gave a more general description of clinical criteria. Laboratory criteria for diagnosis were defined as ‘the detection of tetanus toxoid antibody in an unvaccinated and untreated patient’ and ‘demonstration of a specific tetanus toxoid antibody response’. The 2002 definition does not define a probable case and defines a confirmed case as a “clinically compatible case”.

5 Commission Implementing Decision 2018/945/EU of 22 June 2018 on the communicable diseases and related special health issues to be covered by epidemiological surveillance as well as relevant case definitions.

Clinical criteria

Any person with the following three:

— Painful muscular contractions primarily of the masseter and neck muscles leading to facial spasms known as

trismus and ‘risus sardonicus’;

— Painful muscular contractions of trunk muscles;

— Generalised spasms, frequently position of opisthotonus.

Laboratory criteria

At least one of the following two:

— Isolation of Clostridium tetani from an infection site;

— Detection of tetanus toxin in a serum sample.

Case classification:

A. Probable case: any person meeting the clinical criteria

B. Confirmed case: any person meeting the clinical and the laboratory criteria

1

Contents INTRODUCTION .................................................................................................................................................. 2

HOW TO USE THIS DOCUMENT ........................................................................................................................................ 2 FINDING FURTHER INFORMATION .................................................................................................................................... 2 COPYRIGHT ................................................................................................................................................................ 2

REPORTING TO EPIPULSE CASES ......................................................................................................................... 3

CHECKING THE DATA COLLECTION SCHEDULE ..................................................................................................................... 3 PREPARING DATA ......................................................................................................................................................... 3 CHECKING METADATA ................................................................................................................................................... 3 CHECKING YOUR SURVEILLANCE SYSTEM DESCRIPTORS........................................................................................................ 4 UPLOADING YOUR DATA ................................................................................................................................................ 4 FINALISING YOUR SUBMISSION........................................................................................................................................ 5 EPIPULSE CASES HELPDESK ............................................................................................................................................ 9

DIPHTHERIA-SPECIFIC REPORTING ................................................................................................................... 10

MONTHLY AND ANNUAL REPORTING .............................................................................................................................. 10 NARRATIVE INFORMATION ........................................................................................................................................... 10

ANNEX 1. DIPHTHERIA METADATA .................................................................................................................. 12

DIPHTHERIA METADATA SET ......................................................................................................................................... 12 Current record type versions ............................................................................................................................. 12 Case-based reporting ........................................................................................................................................ 12 Aggregated reporting ....................................................................................................................................... 18 Changes to the diphtheria metadata ................................................................................................................ 20

ANNEX 2. CHANGES IN CASE DEFINITION ......................................................................................................... 23

Diphtheria Reporting Protocol 2024

Surveillance data for 2023 - 2024

EpiPulse Cases

2

Introduction

This reporting protocol describes the reporting of 2024 measles and rubella cases to EpiPulse Cases, which is replacing TESSy.

Please note:

• Since February 2023, the reporting of diphtheria is described in a separate reporting protocol: Diphtheria, Reporting Protocol 2023, Version 1.0.

• The Vaccine Preventable Diseases (VPD) reporting protocol 2024 describes reporting of: pertussis, mumps, poliomyelitis and tetanus.

• The Invasive Bacteria Diseases (IBD) reporting protocol 2024 describes reporting of: invasive H. influenzae disease, invasive meningococcal disease, Neisseria Meningitidis isolates, and invasive pneumococcal disease.

Reporting protocols are data collection guidelines for the data managers of reporting countries and the protocol design is intended to improve user-friendliness by:

• introducing a uniform structure to make it easier for data managers to find data collection information across different subjects;

• removing information which is not relevant for data managers.

Similarly, the surveillance protocol will contain some of the generic information previously contained in the reporting protocols.

Since the data managers in reporting countries often have multiple roles, subject-specific material is sometimes distributed together with a reporting protocol. To maintain the uniform structure, this type of material is now included in Annex 1 and Annex 2.

How to use this document

This reporting protocol provides information for the data managers of reporting countries in three main sections:

• Reporting to EpiPulse Cases which contains guidelines on how to prepare data for submission to EpiPulse Cases, deadlines, subject-specific information (e.g. new changes to metadata), and links to further information.

• Annex 1 which contains:

− the metadata set for the subject(s) covered by this reporting protocol. − a list of metadata changes for the subject(s) covered by this reporting protocol.

• Annex 2 which contains subject-specific material relevant for distribution with the reporting protocol.

Finding further information Updated links to all the schedules, documentation and training materials mentioned in this reporting protocol are included in the Documentation and Help pages, including links to:

• EpiPulse Cases Metadata

• TESSy Metadata sets and change history • EpiPulse Cases Machine to Machine Technical Documentation • Tutorials for data transformation using respectively Excel and Access

Copyright © European Centre for Disease Prevention and Control, 2024. Reproduction is authorised, provided the source is acknowledged.

3

Reporting to EpiPulse Cases

In September 2024 EpiPulse Cases is expected to go live. We have built it as a replacement for TESSy, with the aim of improving the process of reporting, reviewing, and updating surveillance data.

Only Vaccine-Preventable Diseases will be reported to EpiPulse Cases in 2024, all other diseases will continue to be reported to TESSy for now.

This section provides both an overview of the EpiPulse Cases reporting process and tips on where you can find useful information.

The overall process is as follows:

• Familiarise yourself with the data collection deadlines. • Prepare (export and transform) your data. • Check that your data complies with the EpiPulse Cases metadata. • Check that your data sources are up to date. • Submit your file(s) to EpiPulse Cases.

• Finalise and approve your submission.

Checking the data collection schedule

A link to the current data collections schedule can be found in the Communication section of the ‘Documentation and Help’ pages.

Preparing data

After you have exported the data from your national database, you need to ensure that the data are in a format that EpiPulse Cases can accept. EpiPulse Cases accepts only CSV and XML files, optionally ZIP-compressed. The EpiPulse Cases metadata has been developed from the TESSy Metadata, with the aim to make only the minimal number of changes necessary, and to hopefully provide a better experience when reporting your datasets to ECDC.

Specific guidelines for measles and rubella data collection and preparation for EpiPulse Cases are provided in Annex 1 and Annex 2.

Checking metadata

The metadata defines the fields and data formats that are valid as input to EpiPulse Cases for a given subject. The EpiPulse Cases metadata includes a section that compares and highlights the changes between TESSy and EpiPulse Cases, to facilitate the transition.

As the requirements for data to be shared among ECDC Stakeholders can change, the data format changes needed to support the new requirements are identified and agreed upon between the National Surveillance Contact Points, the Network Coordination Groups and ECDC’s Disease Experts. These changes are then implemented to the EpiPulse Cases metadata.

Changes to the metadata for the subject of this reporting protocol are described in Annex 1.

It is especially important to focus on:

• Field formats Many fields require the data to be formatted in a specific way. For example, dates must be in the YYYY-MM- DD format; dates in the DD/MM/YYYY format will be rejected.

• Reference Values (the equivalent of TESSy Coded Values) Some fields only permit the use of specific values (reference values). For example, M, F or OTH are the coded values for ‘Gender’ and any other value in a ‘Gender’ field will be rejected. Please note that UNK is no longer a valid code, you may leave the field empty instead.

The EpiPulse Cases metadata Excel file contains all the definitions and rules necessary to format data correctly. The READ ME sheet of the Excel document explains how to work with the metadata. It can be downloaded from the Technical Guidelines & Tools section of the ‘TESSy Help & Docs’ pages.

Filtering the fields in the file by subject will enable you to see the fields required for your subject and the rules that apply to these fields.

4

Checking your Surveillance System Descriptors Before submitting file(s), please review your data source(s) in EpiPulse (in the menu, go to ‘Report’ -> ‘Surveillance systems descriptors’) and update the information as necessary.

Complete and up-to-date data source information for each subject is important for improving the interpretation of data - each surveillance system has different features that need to be taken into account when comparing data European level.

If your data source information is out-of-date and you do not have access rights to update it, please ask your National Focal Point for Surveillance or National Coordinator to do so.

Information on data sources is available in the TESSy User Guide, as this functionality is still only available through TESSy.

Uploading your data Data is submitted through the EpiPulse web interface (in the menu, go to Report -> EpiPulse Cases).

The visual interface for reporting new data and editing existing records has remained very similar to that of TESSy. For those of you that are also responsible for reporting diseases outside of the Vaccine Preventable Diseases group, you will continue to use TESSy (under EpiPulse) in parallel with the new EpiPulse Cases, until all disease groups will have been migrated to the new tool.

5

Similar to TESSy, you can Add/Update or Replace data with new uploads, using either CSV or XML files. You can

also manually create records for some diseases, and report zero cases where appropriate.

The functionality for manually editing existing records is also a familiar experience. Search for the record you wish to edit, and modify the existing information as needed.

Finalising your submission The compliance of your data with the validation rules in the metadata is checked automatically during the data upload process. In EpiPulse Cases this process is called “Technical Validation”, and it is the only step where your upload can be rejected, for severe data quality issues, such as the file format not being readable by the system, or

(one of the few) mandatory variables having missing values.

If your file has been rejected, there will be a message explaining each instance of non-compliance with the metadata that needs correcting.

The significant new feature in EpiPulse Cases is the Data Validation Report, which puts your data in the context of the already existing information for the same disease, and provides you with a detailed overview of the new data in the file you have just uploaded, as well as the resulting overall epidemiological situation painted by the existing (past) data together with the newly uploaded file(s). This means much more timely feedback on your uploads, including details on data quality, as well as outputs (graphs, charts, and tables) on some of epidemiological indicators. The Data Validation reports will evolve and grow based on your feedback in collaboration with our Disease Experts. These reports will provide a new and better way of understanding and updating the information collected at European level, and will hopefully increase the quality and timeliness of the data, while reducing workloads.

Below you can find a few screenshots of the Data Validation Report.

6

1. Begin by opening the report:

2. View the report in a window, download the list of eventual validation messages, or download the report

7

3. Check data completeness; both for the new upload, and in the context of historical data

8

4. The downloaded report can be opened full screen for easier viewing and navigation. This is a preview of the currently developed epidemiological indicators/stratifications.

9

5. After reviewing the information in the Data Validation Report you can choose to approve or reject it.

If you choose to reject it, no data will be saved in the EpiPulse Cases system, but your file will remain visible should you wish to re-download it, or resubmit it for a new Data Validation at a later date or after further checks. Please check the Epi Validation Report carefully, there might be warnings and remarks relating to possible data quality issues or potential overwriting of existing records that you should consider.

When your file has been validated and you are satisfied that all corrections have been made, please ensure prompt approval or rejection. Unapproved uploads can block the approval of other related uploads.

EpiPulse Cases Helpdesk

Email: [email protected]

Telephone number: +46-(0)8-5860 1601

Availability: 9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC holidays)

10

Diphtheria-specific reporting

Monthly and annual reporting

Monthly data collection – deadline last day of each month

Diphtheria data should be uploaded monthly by the last day of the month. Possible, probable and

confirmed cases should be reported.

Annual data collection – deadline 15 October of each year

An annual data call will still be carried out in order to finalise datasets for the previous year for use in

the annual epidemiological report. In the annual data call it will also be necessary to report “zero cases”

if no cases have occurred.

Once the data are validated by the disease experts at ECDC, they are made publicly available on a monthly basis on the Surveillance Atlas of Infectious Diseases with a choice of weekly, monthly and

annual temporal resolution, and through annual surveillance reports on the ECDC website.

Narrative information

Changes over time in the number of cases reported in a surveillance system do not always reflect true

changes in the incidence of disease. New reporting practices, improved laboratory capacities and

changes in legislation are some of the factors that can influence the number of cases reported. It is important to be aware of such “surveillance artefacts” when analysing surveillance data and countries

are encouraged to describe changes in the surveillance environment that may impact on the number of cases reported. It is equally important to report if the surveillance environment has remained the same

from one year to the next. We encourage reporting countries to provide this information at the same

time as data submission to TESSy and to [email protected].

11

Case definition

Cases of diphtheria should be reported to TESSy if they meet any of the following criteria:

Clinical Criteria

Any person with at least one of the following clinical forms:

Classic Respiratory Diphtheria:

An upper respiratory tract illness with laryngitis or nasopharyngitis or tonsillitis

AND

an adherent membrane/pseudomembrane

Mild Respiratory Diphtheria:

An upper respiratory tract illness with laryngitis or nasopharyngitis or tonsillitis

WITHOUT

an adherent membrane/pseudomembrane.

Cutaneous Diphtheria:

Skin lesion

Diphtheria of other sites:

Lesion of conjunctiva or mucous membranes

Laboratory Criteria

Isolation of toxin-producing Corynebacterium diphtheriae, Corynebacterium ulcerans or

Corynebacterium pseudotuberculosis from a clinical specimen.

Epidemiological Criteria

At least one of the following epidemiological links:

— Human to human transmission

— Animal to human transmission

Case Classification

A. Possible case

Any person meeting the clinical criteria for classical respiratory diphtheria

B. Probable case

Any person meeting the clinical criteria for diphtheria (Classic Respiratory Diphtheria, Mild

Respiratory Diphtheria, Cutaneous Diphtheria, Diphtheria of other sites) with an epidemiological link to a human confirmed case or with an epidemiological link to animal

to human transmission

C. Confirmed case

Any person meeting the laboratory criteria AND at least one of the clinical forms.

12

Annex 1. Diphtheria metadata

This section describes:

• The diphtheria metadata set • Changes to the diphtheria metadata

Diphtheria metadata set

Current record type versions

Table 1 shows the subject codes to be used when reporting diphtheria surveillance data to TESSy. Cases

should be reported according to the EU Case Definition1.

We strongly encourage case-based reporting. If case-based data are not available, aggregated data

may be reported.

Table 1. Diphtheria subject code

Disease Case-based subject code Aggregated subject code

Diphtheria DIPH DIPHAGGR

Case-based reporting

The metadata set has variables that are common across the VPD and disease specific variables. All

variables relevant to the reporting of diphtheria are summarised in alphabetical order in Table 2.

Table 2. Case-based metadata for the reporting of diphtheria (DIPH)

Variable Description Coded value list

Age Age of patient in years as reported in the

national system at the time of disease onset.

AgeMonth Age of patient in months as reported in

the national system for cases < 2 years of age at the time of disease onset.

AntimicrobialAgent Antibiotic tested for susceptibility. CIP = Ciprofloxacin

CLI = Clindamycin

ERY = Erythromycin

LNZ = Linezolid

MEM = Meropenem

PEN = Penicillin

RIF = Rifampin

SXT =

Sulfamethoxazole + trimethoprim

TCY = Tetracyclines

Biotype Biotype of DIP - C. diphtheriae only NST = Not subtypeable

OTH = Other

1 EU case definitions (europa.eu)

13

VARBELF = var belfanti

VARGRAV = var gravis

VARINTMED = var intermedius

VARMITIS = var mitis

CaseClassification Case classification according to EU case definition.

CONF = Confirmed

DISCARDED = Discarded

POSS = Possible

PROB = Probable

ClinicalCriteria Clinical presentation (criteria) of the case. CONJ = Conjunctival

presentation

CUTA = Cutaneous

GEN = Genital presentation

NASAL = Uni- or bilateral nasal

discharge intially clear becoming bloody

OTH = Other

RESPCUTA = Respiratory and

cutaneous presentation

RESPMEMBR = Classic Respiratory with membrane

RESPNOMEMBR =

Respiratory with no membrane

ClusterID Unique identifier of the cluster as provided by the country epidemiologist.

ClusterRelated Is the case part of an outbreak/cluster?

ClusterSetting Setting of the cluster (for epidemiologically-linked cases).

CHILDCARE =

Kindergarten or child care

DET = Migrant detention centre

FAM = Family

MIL = Military

NOS = Nosocomial (hospital)

OTH = Other

SCH = School

SPORT = Sports team

UNI = University

ComplicationDiagnosis Any secondary disease that occurs as a consequence of Diphtheria.

CARDIACDIS = Cardiac disorder

NEURO = Neurological complications

14

NEUROCARD =

Neurological & Cardiac disorder

OTH = Other

CountryOfBirth Country of birth of the case. Consult the reference values in mdLocation dataset

DataSource The data source (surveillance system) that the record originates from. The

DataSource value must be a special

reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateOfDiagnosis First date of clinical or lab diagnosis. In

case the DateOfOnset is missing this date is used for analysis.

DateOfEntry Date of entry into country where sampling and diagnosis occurred.

DateOfFirstSample The date of the first diagnostic sample that was positive for diphtheria.

DateOfLastVaccination

Date of administration of the last

vaccination dose - indicates the date when the last dose of vaccine was given before

disease onset (if exact date is not known, then provide month or year).

DateOfNotification

Date when the case report is first notified to public health authorities.

DateOfOnset

Date of onset of disease. Leave empty for

asymptomatic cases.

DateUsedForStatistics

The reference date used for standard

reports that is compared to the reporting

period. The date used for statistics can be any date that the reporting country finds

applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being

reported.

DIPH = Diphtheria

EpiLinkCaseId Provide record identifiers

(NationalRecordId) of epilinked cases.

Gender Gender of the reported case. F = Female

M = Male OTH = Other

ImportedStatus Imported: Having been outside the

country of notification during the incubation period of the reported disease,

and no links to local transmisison has been

identified. Import related case: case epidemiologically linked to an imported

case, i.e. cases that acquired the infection locally through a direct link to an imported

case in the first chain (only) of

transmission as supported by

END = Endemic case

IMP = Imported case

IMPREL = Import related case

15

epidemiological and/or virological

evidence. Indigenous case: is a case

infected within the country of residence (based on epidemiological and virological

evidence) and that is not import-related, or any case with unknown source of

infection (no epidemiological or virological evidence).

MainPathogenDetectionMethod Pathogen detection method used on

MainSpecimen for confirmation of the case (Isolation of toxin-producing C.

diphtheriae/C. ulcerans/C pseudotuberculosis from a clinical

specimen). More than one method can be reported.

CULT = Culture

ELEK = Elek plate test

OTH = Other

PCR = PCR confirmation

RTPCR = Real time PCR

Main Specimen Main type of specimen with positive result

to be reported (can include material and/or sampling method and/or site).

MEMBR = Membrane

NASALSWAB = Nasal swab

OTH = Other

SKINSWAB = Skin swab

THROATSWAB = Throat swab

NationalRecordId Unique identifier for each record within and across the specified surveillance

system (data source) – selected and

generated by the country reporting the record.

Outcome Information on whether the case is alive or

deceased. The death should be due to the reported disease.

A = Alive

D = Died

Pathogen Species and genus of the pathogen which is the cause of the reported disease.

CORDIP =

Corynebacterium diphtheriae

CORPSE = Corynebacterium pseudotuberculosis

CORSPP =

Corynebacterium species, not specified

CORULC =

Corynebacterum ulcerans

PlaceOfInfection If ImportedStatus = 'IMP': The probable

place of infection should be provided at the country level. One entry for each

country visited before or during the diagnosis of the disease. Note this is a repeatable field.

Consult the reference values in mdLocation dataset

PlaceOfNotification Place of the first notification of the case to

a regional authority. Select the most detailed NUTS level possible.

Consult the reference values in mdLocation dataset

16

PlaceOfResidence Place of residence of patient at the time of

disease onset. Select the most detailed NUTS level possible.

Consult the reference values in mdLocation dataset

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

SecondPathogenDetectionMethod Pathogen detection method used on

SecondSpecimen for confirmation of the case (Isolation of toxin-producing C.

diphtheriae/C. ulcerans/C

pseudotuberculosis from a clinical specimen). More than one method can be reported.

CULT = Culture

ELEK = Elek plate test

OTH = Other

PCR = PCR confirmation

RTPCR = Real time PCR

SecondSpecimen Second type of specimen with positive

result to be reported as optional (can include material and/or sampling method and/or site).

MEMBR = Membrane

NASALSWAB = Nasal swab

OTH = Other

SKINSWAB = Skin swab

THROATSWAB = Throat swab

SequenceType Diphtheria sequence type. Obtained by

multi locus sequence typing (MLST) or core genome multi locus sequence typing (cgMLST).

SIR_CIP Susceptibility to Ciprofloxacin as the final

interpretation based on one or more test results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_CLI Susceptibility to Clindamycin as the final

interpretation based on one or more test

results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_ERY Susceptibility to Erythromycin as the final

interpretation based on one or more test

results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_LNZ Susceptibility to Linezolid as the final interpretation based on one or more test

results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_MEM Susceptibility to Meropenem as the final

interpretation based on one or more test results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_PEN Susceptibility to Benzylpenicillin (penicillin

G) as the final interpretation based on one or more test results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_RIF Susceptibility to Rifampicin as the final

interpretation based on one or more test

I = Intermediate

R = Resistant

17

results according to clinical breakpoints from EUCAST.

S = Susceptible

SIR_SXT Susceptibility to Trimethoprim-

sulfamethoxazole as the final

interpretation based on one or more test results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

SIR_TCY Susceptibility to Tetracycline as the final

interpretation based on one or more test results according to clinical breakpoints from EUCAST.

I = Intermediate

R = Resistant

S = Susceptible

Status The Status value is used to provide the

functionality for a record within EpiPulse

Cases database. Default value: NEW/UPDATE. If set to DELETE, the

record with the specified NationalRecordId is deleted (invalidated) from EpiPulse

Cases database, if it exists. If set to

NEW/UPDATE, the record is inserted into the database: If the same

NationalRecordId already exists for the same data source and subject code, then

the current submitted record updates (replace) the existing one.

DELETE = Delete a

previously reported record

NEW/UPDATE = Update a previously

reported record (default)

SubjectCode SubjectCode is a reporting model for a disease/health topic - identifies the

reporting structure and format of a record (case based or aggregate reporting).

DIPH = Diphtheria

SuspectedVehicle Suspected vehicle or source of infection -

contact within the last 1-7 days (C. ulcerans only).

FARMANIMAL = Farm

animal such as cattle or sheep

OTH = Other

OTHERANIM = Other animal

PET = Pet animal such as dog or cat

RAWMILK = Raw milk/raw milk products

TravelPlaces Only applicabel if case is imported

(ImportedStatus = 'IMP'). The list can be

left empty even if the case is known to be imported. Note that this is a repeatable

field: List each country visited recently before/during diagnosis.

Consult the reference values in mdLocation dataset

VaccinationStatus Indicates if the case is vaccinated and

number of vaccine doses received.

10DOSE = 10 doses

1DOSE = 1 dose

2DOSE = 2 doses

3DOSE = 3 doses

4DOSE = 4 doses

5DOSE = 5 doses

6DOSE = 6 doses

7DOSE = 7 doses

8DOSE = 8 doses

18

9DOSE = 9 doses

NOTVACC = Not vaccinated

UNKDOSE = Vaccinated, dose unknown

Wgs Information on whether whole genome

sequencing has been performed on isolates from the case.

WgsAccession Accession number if sequencing data have

already been uploaded to any public repository.

WgsSequenceId Sequence Read Archive (SRA) run

identifier, based on which the sequence read data can be retrieved.

Aggregated reporting

Please refer to Table 3 to see the format for aggregated reporting for diphtheria.

If only a few variables can be reported, it is recommended to give the following priority for reporting:

AgeGroup, CaseClassification, VaccinationStatus, Gender.

Table 3: Aggregate metadata for diphtheria (DIPHAGGR)

Variable Description Coded value list

AgeGroup Age group of the reported record. See Table 4 below.

CaseClassification Case classification according to EU

case definition.

CONF = Confirmed

POSS = Possible

PROB = Probable

DataSource The data source (surveillance system)

that the record originates from. The

DataSource value must be a special reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateUsedForStatistics

The reference date used for standard

reports that is compared to the

reporting period. The date used for statistics can be any date that the

reporting country finds applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being reported.

DIPH = Diphtheria

Gender Gender of the reported case. F = Female

M = Male OTH = Other

NumberOfCases Total number of cases during the reported period for the specified disease.

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

19

SubjectCode SubjectCode is a reporting model for

a disease/health topic - identifies the reporting structure and format of a

record (case based or aggregate reporting).

DIPH = Diphtheria

VaccinationStatus Indicates if the case is vaccinated and number of vaccine doses received.

10DOSE = 10 doses

1DOSE = 1 dose

2DOSE = 2 doses

3DOSE = 3 doses

4DOSE = 4 doses

5DOSE = 5 doses

6DOSE = 6 doses

7DOSE = 7 doses

8DOSE = 8 doses

9DOSE = 9 doses

NOTVACC = Not vaccinated

UNKDOSE = Vaccinated, dose unknown

When reporting age, the age groups listed in Table 4 should be used.

Table 4. Age categories compatible with aggregate diphtheria reporting

Variable Narrative description Coded value of the variable AgeGroup

AgeGroup <1 year

1-4 years

5-9 years

10-14 years

15-19 years

20-24 years

25-29 years

30-34 years

35-39 years

40-44 years

45-49 years

50-54 years

55-59 years

60-64 years

65 and over

0

01-04

05-09

10-14

15-19

20-24

25-29

30-34

35-39

40-44

45-49

50-54

55-59

60-64

65+

Diphtheria Reporting Protocol 2024

20

Changes to the diphtheria metadata

Metadata changes prior to 2014 can be found on the TESSy documents website. Changes from 2014

onwards have been summarised in Table 5 below.

Table 5. Summary of implemented changes in case-based and aggregated record types for diphtheria from 2014 to current Year of change

Subject Variables Description

2024 DIPH ALL Reporting moved from TESSy to the Epipulse Cases platform. This transition has led to changes in some variable names and categorical values (see below).

DIPH AccNumber Antibiotic Classification ClinicalPresentation ClusterIdentification Complications DateLastVaccDose EpiLinkCaseID Imported ProbablyCountryOfInfection RecordId RecordType ResultBiotype ResultSeqType Specimen1 Specimen2 Subject TestMethod1 TestMethod2 VaccStatus WGS

Variable names changed from (TESSy) → to (Epipulse Cases): AccNumber → WgsAccession Antibiotic → AntimicrobialAgent Classification → CaseClassification ClinicalPresentation → ClinicalCriteria ClusterIdentification → ClusterId Complications → ComplicationDiagnosis DateLastVaccDose → DateOfLastVaccination EpiLinkCaseID → EpiLinkCaseId Imported → ImportedStatus ProbablyCountryOfInfection → PlaceOfInfection RecordId → NationalRecordId RecordType → SubjectCode ResultBiotype → Biotype ResultSeqType → SequenceType Specimen1 → MainSpecimen Specimen2 → SecondSpecimen Subject → Disease TestMethod1 → MainPathogenDetectionMethod TestMethod 2→ SecondPathogenDetectionMethod VaccStatus → VaccinationStatus WGS → Wgs

ResultRibotype RecordTypeVersion

Variable removed

AntimicrobialAgent

SIR_CIP

SIR_CLI

SIR_ERY

SIR_LNZ

SIR_MEM

SIR_PEN

SIR_RIF

SIR_SXT

SIR_TCY

Discontinued values: “NA”, “UNK”

ClinicalCriteria Gender MainSpecimen SecondSpecimen MainPathogenDetectionMethod

SeondPathogenDetectioMethod

Discontinued values: UNK;

Remapping of: “O” to “OTH”

Biotype Discontinued values: “NA”, “NUS”, “UNK”; Remapping of: “O” to “OTH”

CaseClassification Discontinued values: UNK

ClusterRelated Wgs

Discontinued values: UNK; Variable changed from coded value to Boolean (0 = No ; 1 = Yes)

ClusterSetting Discontinued values: “NA”, “UNK”; Remapping of: “HOSP” to “NOS”, “MIGR” to “DET”

ComplicationDiagnosis Discontinued values: UNK; Remapping of: “NEURODIS” to “NEURO”, “O” to “OTH”

ImportedStatus Discontinued values: UNK; Remapping of: ”N” to “END”, “Y” to “IMP”

Outcome Discontinued values: NUS, UNK

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Pathogen Discontinued values: NUS Remapping of: “DIP” to “CORDIP”, “PSEU” to “CORPSE”, “ULC” to “CORULC”, “O” to “CORSPP”, “UNK” to “CORSPP”

SuspectedVehicle Discontinued values: “NA”, “NUS”, “UNK”; Remapping of: “FARMAN” to “FARMANIMAL”, “O” to “OTH”

VaccinationStatus Discontinued values: UNK; Remapping of: ”DOSEUNK” to “UNKDOSE”

Disease Status

Changed “Required” from “Yes” to “No”

DIPHAGGR

AgeClass Classification RecordType Subject

Variable names changed from (TESSy) → to (Epipulse Cases): AgeClass → AgeGroup Classification → CaseClassification RecordType → SubjectCode Subject → Disease

AgeGroup CaseClassification

Discontinued values: “UNK”

Disease Changed “Required” from “Yes” to “No”

Gender Discontinued values: “UNK” Remapping of: “O” to “OTH”

RecordTypeVersion Variable removed

SubjectCode Remapping of: “AGGR” to “DIPHAGGR”

VaccinationStatus New variable

2023 DIPH • The following variables were added:

DateOfEntry

o CountryOfBirth

TravelPlaces

o ClusterIdentification o ClusterRelated o ClusterSetting o EpiLinkCaseId o WGS o WgsSequenceId o AccNumber o DateOfFirstSample o ResultSeqType o Antibiotic o SIR_PEN o SIR_ERY o SIR_CIP o SIR_CLI o SIR_LNZ o SIR_MEM o SIR_RIF o SIR_TCY o SIR_SXT

2017 All VPD DateLastVaccDose • The description of the variable ‘DateLastVaccDose’ was updated to specify that the date given should be the date of last dose before

disease onset.

DIPH Classification

Pathogen

ClinicalPresentation

TestMethod

• The validation rules regarding the variables ‘Classification’ and ‘Pathogen’ were changed to ‘error’ so that cases with Classification==CONF could not be reported with unknown or missing data on Pathogen.

• A validation rule (warning) was added for cases reported as Classification==CONF but ClinicalPresentation==”UNK”.

• A validation rule (warning) for cases of Pathogen==ULC with ClinicalPresentation!=CUTA was removed.

• For the variable ‘ClinicalPresentation’, the coded value ‘NUS’ (not under surveillance) was dropped.

• For the variable ‘ClinicalPresentation’, the coded values ‘CONJ’ (conjunctival) and “GEN” (genital) were added.

• The variable ‘ClinicalPresentation’ was made a mandatory variable.

• The variable ‘TestMethod’ was made a mandatory variable.

22

• A validation rule (warning) was added where, for cases reported

as Classification==CONF, at least one of TestMethod1 or

TestMethod2 must be reported as 'PCR', 'RTPCR' , 'ELEK' or 'O'.

2016 DIPH TestMeth1 TestMeth2 AgeMonth ClinicalPresentation’

• The variables ‘TestMeth1’ and TestMeth2’ were renamed

‘TestMethod1’ and ‘TestMethod2’, in line with other VPDs.

• The variable ‘AgeMonth’ was added.

• The description of the variable ‘ClinicalPresentation’ was edited to match other VPDs.

2015 All VPD EpiLink ClinicalCriteria Labresult

• The variables ‘EpiLink’, ‘ClinicalCriteria’ and ‘Labresult’ were removed.

DIPH Classification

DateLastVaccDose

Pathogen

• The description of the variable ‘Classification’ was edited to ensure consistency with the EU case definition.

• The RecordType ‘HAGGR’ was removed.

• The variable ‘DateLastVaccDose’ was added.

• Two new coded values were added to the variable ‘Pathogen’. The coded value were PSEU=Corynebacterium pseudotuberculosis and NUS = Not under surveillance. This change reflects the update of the case definition in 2012.

2014 All VPD VaccStatus • The description of the coding for DOSEUNK (VaccStatus variable) was changed in the 2014 metadata for Measles, Mumps, Rubella, Pertussis, and Diphtheria. The name of the DOSEUNK coding was changed from “Unknown number of doses” to “Vaccinated with unknown number of doses”. This modification did not imply any operational change during data upload.

All • Update NUTS codes according to the NUTS Codes 2010

classification from EUROSTAT.

Diphtheria Reporting Protocol 2024

23

Annex 2. Changes in case definition

Countries are encouraged to use the 2018 EU case definition for the data collection. In the 2018 definition, no changes are implemented for diphtheria. For the 2018 EU Case Definition, see:

https://eur-lex.europa.eu/legal-content/EN/TXT/PDF/?uri=CELEX:32018D0945&from=EN

or https://ecdc.europa.eu/en/surveillance-and-disease-data/eu-case-definitions

The changes in the 2012 EU case definition as compared to 2008 are indicated in red:

(Corynebacterium diphtheriae, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis)

Clinical Criteria

Any person with at least one of the following clinical forms:

Classic Respiratory Diphtheria:

An upper respiratory tract illness with laryngitis or nasopharyngitis or tonsillitis

AND

an adherent membrane/pseudomembrane

Mild Respiratory Diphtheria:

An upper respiratory tract illness with laryngitis or nasopharyngitis or tonsillitis

WITHOUT

an adherent membrane/pseudomembrane.

Cutaneous Diphtheria:

Skin lesion

Diphtheria of other sites:

Lesion of conjunctiva or mucous membranes

Laboratory Criteria

Isolation of toxin-producing Corynebacterium diphtheriae, Corynebacterium ulcerans or

Corynebacterium pseudotuberculosis from a clinical specimen.

Epidemiological Criteria

At least one of the following epidemiological links:

— Human to human transmission

— Animal to human transmission

Case Classification

A. Possible case

Any person meeting the clinical criteria for classical respiratory diphtheria

B. Probable case

Any person meeting the clinical criteria for diphtheria (Classic Respiratory Diphtheria, Mild Respiratory Diphtheria, Cutaneous Diphtheria, Diphtheria of other sites) with an epidemiological

link to a human confirmed case or with an epidemiological link to animal to human transmission

C. Confirmed case

Any person meeting the laboratory criteria AND at least one of the clinical forms

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Machine to Machine Communication API Specification

EpiPulse Cases

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Document Version Version Date Comments

1.0 2024-07-06 Technical Documentation for Machine to Machine Interconnection

1. Introduction

1.1. Purpose

The Technical Design (TD) document provides an overview of the interfaces that are available for external systems to

interact with EpiPulse Cases.

1.2. Definitions

This table describes terms and abbreviations used in this document. Commonly used IT terms and abbreviations can

be found in ECDC’s IT Glossary Error! Bookmark not defined..

Term/Acronym Definition

JWT JSON Web Token Error! Reference source not found.

OIDC Open ID Connect

FME Feature Manipulation Engine

API Application Programming Interface

DUAPI Data Upload API

TV Technical Validation

EV Epidemiological Validation

WS Web Service

M2M Machine-to-Machine

WGS Whole Genome Sequencing

AWS Amazon Web Services

FMV File Mapping Validation

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1.3. Provide API for machine-to-machine interfacing.

The DUAPI is the externally exposed endpoint of the EpiPulse Cases architecture. It’s utilized by the DUUI to allow

users to access the system and it can also be used by external systems to interface as M2M. The interfaces provided

can be split in 3 major groups and are described in detail in Error! Reference source not found., section Error!

Reference source not found..

• Uploads, which provides functionality related to uploaded files (submitting, searching, retrieving)

• Technical Validation, which provides functionality related to the flow of technical validation (starting, retrieving

status and output, etc)

• Epidemiological Validation, which provides similar functionality to TV for EV

Appendix A – APIs This section describes the various interfaces of the system grouped per component and per area of functionality

provided. Payload or response attributes in grey are optional and may be omitted.

A.1 Authentication

This is the first call we have to do in order to gain access to the EpiPulse Cases. This call ADFS to get a JWT token.

URL: https://zfs.ecdc.europa.eu/adfs/oauth2/token

Authentication:

Authorization:

HTTP Method: POST

Payload as urlencoded:

{

grant_type:password

client_id:f142116f-a5d0-4089-bfaf-46bb0e5dd340

client_secret:a0P5pZqkIJKORIqoLzwoYr_PJDZdpv86nA7k_48u

username:ecdcdmz\EPC_NL_GENERAL-U

password:P@ssw0rd

resource: https://epipulse.ecdc.europa.eu/api/epipulsecases/dataupload

scope:openid

}

Response: {

"access_token": "TOKEN",

"token_type": "bearer",

"expires_in": 3600,

"resource": "https://epipulse.ecdc.europa.eu/api/epipulsecases/dataupload",

"refresh_token": "",

"refresh_token_expires_in": 28800,

"scope": "user_impersonation openid",

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"id_token": ""

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

A.2 Data Upload

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/Uploads

Authentication: JWT Barer Token

Authorization: Environment Access + Upload

HTTP Method: POST

Payload: {

"stream": "BASE64",

"fileName": "STRING",

"start": "DATETIME",

"end": "DATETIME", "ignoreDateStartEnd": "BOOLEAN"

"uploadType": "STRING",

"chunkIdentifier": "GUID"

}

Response: {

"fileName": "STRING",

"uploadGuid": "GUID",

"children": [{

"fileName": "STRING",

"uploadGuid": "GUID"

},...]

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 409 Conflict. If there is an ongoing metadata synchronization

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller • DUUI

Comments: Uploads a file and returns one or more (in case of a zip file containing multiple files) GUID(s). If the file is a zip, then the first entry returned will correspond to the zip file itself and the remaining to each of the children

URL: https://epipulse.ecdc.europa.eu /api/v1/DataUploadAPI/Uploads/UploadSaveStatus

Authentication JWT Barer Token

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Authorization: Environment Access + Upload

HTTP Method: POST

Payload: {

"uploadGuids": [

"GUID", … ],

}

Response: {

"uploadGuids": [

"GUID", … ],

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the content is 0 length or if the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Checks if the save was completed in the database for the given Guids and returns the list of Guids to start the technical validation if the file(s) was successfully saved.

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/Uploads/{uploadGuid}

Authentication JWT Barer Token

Authorization: Environment Access + UploadApprove

HTTP Method: PUT

Payload: {

"reportingPeriodStart": "DATETIME",

"reportingPeriodEnd": "DATETIME"

}

Response: {

"isSuccessful": BOOLEAN,

"taskCorrelationGuid": "GUID"

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the uploadGuid is not provided

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If the provided uploadGuid is not found in the Upload database

• 500 Internal Server Error. If an exception is thrown while servicing the request

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Caller

Comments: Allows the UI to update the reporting period start and end date.

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/Uploads/Search

Authentication JWT Barer Token

Authorization: Environment Access

HTTP Method: GET

Payload: {

"uploadDate": "STRING",

"subjectCode": "STRING",

"diseaseCode": "STRING",

"healthTopicCode": "STRING",

"fileName": "STRING",

"userName": "STRING",

"hasErrors": "BOOLEAN",

"hasWarnings": "BOOLEAN",

"uploadGuids": [

"GUID", …],

"onlySubmittedByMe", "BOOLEAN"

"orderBy": "STRING",

"pageNumber": INTEGER,

"pageSize": INTEGER

"allowedStatuses": ["STRING", …],

"notAllowedStatuses": ["STRING", …]

}

Response: {

"uploads": [ {

"uploadGuid": "GUID",

"technicalValidationJobGroupGuid": "GUID",

"epidemiologicalValidationGuid": "GUID",

"dateUploaded": "DATETIME",

"dateEpiStarted": "DATETIME",

"dateTechnicalValidationStarted": "DATETIME",

"subjectCode": "STRING",

"fileName": "STRING",

"userName": "STRING",

"uploadState": "STRING",

"recordCount": INTEGER,

"deletedRowCount": INTEGER,

"numberOfErrors": INTEGER,

"numberOfWarnings": INTEGER,

"technicalValidationProgressPercentage": INTEGER,

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"epidemiologicalValidationProgressPercentage": INTEGER,

"parentUploadGuid": "GUID",

"parentUploadFileName": "STRING",

"hasComplesSubjectCode": "BOOLEAN", "reportingPeriodStartDate": "DATETIME",

"reportingPeriodEndDate": "DATETIME",

"minDateUsedForStatistics": "DATETIME",

"maxDateUsedForStatistics": "DATETIME",

"uploadType": "STRING",

"uploadTypeName": "STRING",

"hasOngoingEpiValidation": "BOOLEAN",

"diseaceCode": "STRING",

"fileSize": LONG,

"fileTypeID": SHORT,

"reportingCountry": "STRING",

"ignoreDateStartEnd: "BOOLEAN",

"parentComplexUploadGuid": "GUID",

"uiSubjectCodeColumn": "STRING",

"healthTopicCode": "STRING"

}, … ],

"totalUploadsCount": INTEGER

}

HTTP codes: • 200 Success. Response returned as documented above

• 401 Unauthorized. If authorization checks fail

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Performs a query on the uploaded files based on provided filters providing ordering and paging functionality

A.3 Technical validation

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations

Authentication JWT Barer Token

Authorization: Environment Access + UploadApprove

HTTP Method: POST

Payload: {

"uploadGuids": [

"GUID", … ],

"autoStartEpidemiologicalValidation": BOOLEAN

}

Response: {

"technicalValidationJobGroupCount": INTEGER

}

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HTTP codes: • 200 Success. Response returned as documented above

• 401 Unauthorized. If authorization checks fail

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Starts the Technical Validation for an upload.

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations/ {technicalValidationJobGroupGuid}

Authentication JWT Barer Token

Authorization: Environment Access

HTTP Method: GET

Response: {

"startDateTime": "DATETIME",

"currentStep": "STRING",

"progressPercentage": INTEGER

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If technicalValidationJobGroupGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Queries the status/progress of a technical validation job

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations/ {technicalValidationJobGroupGuid}/Results

Authentication JWT Barer Token

Authorization: Environment Access

HTTP Method: GET

Response: {

"messages": [ {

"location": {

"recordIdentifier": "STRING",

"variable": "STRING",

"rowNumber": "STRING",

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"columnIndex": "STRING"

},

"severity": "STRING",

"subjectCode": "STRING",

"validationRuleCode": "STRING",

"validationMessage": "STRING",

"solutionMessage": "STRING"

}, … ],

"identityFieldName": "STRING"

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If technicalValidationJobGroupGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Retrieves the messages generated as a result of the technical validation process directly from the EpiPulseCasesTechnicalValidation database

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations/ {uploadGuid}

Authentication JWT Barer Token

Authorization: Environment Access + UploadApprove

HTTP Method: DELETE

Response: {

"isSuccessful": BOOLEAN,

"taskCorrelationGuid": "GUID"

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the provided uploadGuid is empty

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If uploadGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Cancel a running technical validation

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URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations/ {technicalValidationJobGroupGuid}?Action=Reject

Authentication JWT Barer Token

Authorization: Environment Access + UploadApprove

HTTP Method: PUT

Response: {

"isSuccessful": BOOLEAN,

"taskCorrelationGuid": "GUID"

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the provided technicalValidationJobGroupGuid is empty or the action is not “Reject”

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If technicalValidationJobGroupGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller

Comments: Reject a completed technical validation

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/TechnicalValidations/ {technicalValidationJobGroupGuid}/Results/csv

Authentication JWT Barer Token

Authorization: Environment Access

HTTP Method: GET

Response: CSV file containing the technical validation messages for a given technicalValidationJobGroupGuid. The MIME types used is "Text/csv" and the file name "TechnicalValidationMessages – {technicalValidationJobGroupGuid}.csv"

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If technicalValidationJobGroupGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller • DUUI

Comments: Retrieves the messages generated as a result of the technical validation process as a CSV file directly from the EpiPulseCasesTechnicalValidation database

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A.4 Data (Epidemiological) Validation

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/EpidemiologicalValidations

Authentication JWT Barer Token

Authorization: Environment Access + Upload

HTTP Method: POST

Payload: {

"uploadGuids": [

"GUID"

]

}

Response: {

"isSuccessful": BOOLEAN,

"taskCorrelationGuid": "GUID"

}

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception)

• 401 Unauthorized. If authorization checks fail

• 409 Conflict. If there is another running epidemiological validation for the same country and disease

• 500 Internal Server Error. If an exception is thrown while servicing the request

Caller • DUUI

Comments: Starts the Epidemiological Validation for an upload.

URL: https://epipulse.ecdc.europa.eu/api/v1/DataUploadAPI/EpidemiologicalValidations/ OngoingStatus/{subjectGuid}

Authentication JWT Barer Token

Authorization: Environment Access

HTTP Method: GET

Response: BOOLEAN

HTTP codes: • 200 Success. Response returned as documented above

• 400 Bad Request. If the request failed to process (but not due to an exception) or the provide subjectGuid was not a valid GUID

• 401 Unauthorized. If authorization checks fail

• 404 Not Found. If subjectGuid is not found in the database

• 500 Internal Server Error. If an exception is thrown while servicing the request

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Caller

Comments: Returns if a particular subject has an ongoing epidemiological validation (for the country of the caller)

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EpiPulse Cases.

Quick guide.

The new design of EpiPulse Cases is the first step of improving user experience during submitting epidemiological surveillance data for the communicable diseases and related special health issues.

A new (single page) EpiPulse Cases application is available for the users. When a nominated user selects to use the new EpiPulse Cases lands in the main page of the application (called “Submissions page”):

This page provides an overview of the current state of the already submitted data, with some useful searching or sorting functionalities:

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Additional functionalities for the way information appears is also available. The user is able to add or remove columns or select to view only files uploaded from the current user:

Multiple options are available for the user to upload data.

Depending on the permissions of the user, all or some of the following options are available:

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The user can upload data (for both “Add/Update” or “Replace” upload action types) by using three different types of files: csv, xml or zip (that contain csv or/and xml files).

The application automatically performs all required checks, so that the user could proceed with the upload:

The user can also create manually the required data submission, using the “Manually create” and/or “Zero reporting” functionalities.

A wizard, using all required fields as specified in metadata, will help user fill the data. Auto-validation functionality during the process helps user avoid errors:

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The user can proceed through the flow by using an emerging floating “actions” bar:

The actions appearing are controlled by configuration related to the combination of rules for each file selected (submission status, subjectcode etc.) and the user’s permissions:

The reporting of molecular surveillance and required WGS data (Raw reads and/or Assembly files) is also a user-friendly process for the user.

Data could be uploaded using some of the options mentioned above and/or as a hierarchy of datasets which is used to submit complex files:

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Or, in case of additional data required, after selecting the related action from the actions bar, a pop- up window guides the user to the next steps.

Uploading the WGS data files, using the related window:

And then, after using the required genomic files naming conventions, proceed to the WGS file validation:

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During the submission flow for both types, epidemiological and molecular surveillance, user can follow up the progress of his submission(s) and view details of the current submission state as well as some useful information about the content of the submitted file and the timeline of the previous steps:

Viewing “Data validation report” is the next-to-last step in order for the user to conclude with the submission of the data:

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The user reviews information included in the report:

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and then decides whether submitted data should be stored (approved) or discarded (rejected):

Given that the user approves data submission, information is updating the ECDC data warehouse.

User is also able to access stored data and edit or delete records:

Page 1 of 30

Contents INTRODUCTION ......................................................................................................................................... 2

HOW TO USE THIS DOCUMENT ............................................................................................................................... 2 FINDING FURTHER INFORMATION ........................................................................................................................... 2 COPYRIGHT ........................................................................................................................................................... 2

REPORTING TO EPIPULSE CASES ......................................................................................................... 3

CHECKING THE DATA COLLECTION SCHEDULE .......................................................................................................... 3 PREPARING DATA ................................................................................................................................................... 3 CHECKING METADATA ............................................................................................................................................ 3 CHECKING YOUR SURVEILLANCE SYSTEM DESCRIPTORS .......................................................................................... 4 UPLOADING YOUR DATA ......................................................................................................................................... 4 FINALISING YOUR SUBMISSION ............................................................................................................................... 5 EPIPULSE CASES HELPDESK ................................................................................................................................... 9

ANNEX 1. IBD METADATA ...................................................................................................................... 10

IBD METADATA SET ............................................................................................................................................. 10 Current subject codes ................................................................................................................................. 10 Case-based reporting.................................................................................................................................. 10 Aggregated reporting ................................................................................................................................. 19

CHANGES TO THE IBD METADATA ........................................................................................................................ 21

ANNEX 2. IBD-SPECIFIC MATERIAL ................................................................................................... 26

IBD DATA REPORTING FREQUENCY ....................................................................................................................... 26 REPORTING OF MENINGOCOCCAL DISEASE ISOLATES (MENIISO) ......................................................................... 26 NARRATIVE INFORMATION ................................................................................................................................... 27 INVASIVE H. INFLUENZAE DISEASE DATA COLLECTION AND CASE DEFINITIONS ....................................................... 28 INVASIVE MENINGOCOCCAL DISEASE DATA COLLECTION AND CASE DEFINITIONS ..................................................... 29 INVASIVE PNEUMOCOCCAL DISEASE DATA COLLECTION AND CASE DEFINITIONS ...................................................... 30

Invasive Bacterial Diseases (IBD) Reporting Protocol 2024

Invasive H. influenzae Disease, Invasive Meningococcal disease, Neisseria Meningitidis Isolate, Invasive Pneumococcal Disease

Surveillance data for 2023

EpiPulse Cases

Page 2 of 30

Introduction

This reporting protocol describes the reporting of 2024 measles and rubella cases to EpiPulse Cases, which is replacing TESSy.

Please note:

• Since February 2023, the reporting of diphtheria is described in a separate reporting protocol: Diphtheria, Reporting Protocol 2023, Version 1.0.

• The Vaccine Preventable Diseases (VPD) reporting protocol 2024 describes reporting of: pertussis, mumps, poliomyelitis and tetanus.

• The Invasive Bacteria Diseases (IBD) reporting protocol 2024 describes reporting of: invasive H. influenzae disease, invasive meningococcal disease, Neisseria Meningitidis isolates, and invasive pneumococcal disease.

Reporting protocols are data collection guidelines for the data managers of reporting countries and the protocol

design is intended to improve user-friendliness by:

• introducing a uniform structure to make it easier for data managers to find data collection information across different subjects;

• removing information which is not relevant for data managers.

Similarly, the surveillance protocol will contain some of the generic information previously contained in the reporting protocols.

Since the data managers in reporting countries often have multiple roles, subject-specific material is sometimes distributed together with a reporting protocol. To maintain the uniform structure, this type of material is now included in Annex 2.

How to use this document

This reporting protocol provides information for the data managers of reporting countries in three main sections:

• Reporting to EpiPulse Cases which contains guidelines on how to prepare data for submission to EpiPulse

Cases, deadlines, subject-specific information (e.g. new changes to metadata), and links to further information.

• Annex 1 which contains:

− the metadata set for the subject(s) covered by this reporting protocol. − a list of metadata changes for the subject(s) covered by this reporting protocol.

• Annex 2 which contains subject-specific material relevant for distribution with the reporting protocol.

Finding further information Updated links to all the schedules, documentation and training materials mentioned in this reporting protocol are included in the Documentation and Help pages, including links to:

• EpiPulse Cases Metadata • TESSy Metadata sets and change history • EpiPulse Cases Machine to Machine Technical Documentation • Tutorials for data transformation using respectively Excel and Access

Copyright

© European Centre for Disease Prevention and Control, 2024. Reproduction is authorised, provided the source is acknowledged.

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Reporting to EpiPulse Cases

In September 2024 EpiPulse Cases is expected to go live. We have built it as a replacement for TESSy, with the aim of improving the process of reporting, reviewing, and updating surveillance data.

Only Vaccine-Preventable Diseases will be reported to EpiPulse Cases in 2024, all other diseases will continue to be reported to TESSy for now.

This section provides both an overview of the EpiPulse Cases reporting process and tips on where you can find useful information.

The overall process is as follows:

• Familiarise yourself with the data collection deadlines. • Prepare (export and transform) your data. • Check that your data complies with the EpiPulse Cases metadata. • Check that your data sources are up to date. • Submit your file(s) to EpiPulse Cases. • Finalise and approve your submission.

Checking the data collection schedule

A link to the current data collections schedule can be found in the Communication section of the ‘Documentation and Help’ pages.

Preparing data After you have exported the data from your national database, you need to ensure that the data are in a format that EpiPulse Cases can accept. EpiPulse Cases accepts only CSV and XML files, optionally ZIP-compressed. The EpiPulse Cases metadata has been developed from the TESSy Metadata, with the aim to make only the minimal number of changes necessary, and to hopefully provide a better experience when reporting your datasets to ECDC.

Specific guidelines for measles and rubella data collection and preparation for EpiPulse Cases are provided in Annex 1 and Annex 2.

Checking metadata The metadata defines the fields and data formats that are valid as input to EpiPulse Cases for a given subject. The EpiPulse Cases metadata includes a section that compares and highlights the changes between TESSy and EpiPulse Cases, to facilitate the transition.

As the requirements for data to be shared among ECDC Stakeholders can change, the data format changes needed to support the new requirements are identified and agreed upon between the National Surveillance Contact Points, the Network Coordination Groups and ECDC’s Disease Experts. These changes are then implemented to the EpiPulse Cases metadata.

Changes to the metadata for the subject of this reporting protocol are described in Annex 1.

It is especially important to focus on:

• Field formats Many fields require the data to be formatted in a specific way. For example, dates must be in the YYYY- MM-DD format; dates in the DD/MM/YYYY format will be rejected.

• Reference Values (the equivalent of TESSy Coded Values) Some fields only permit the use of specific values (reference values). For example, M, F or OTH are the coded values for ‘Gender’ and any other value in a ‘Gender’ field will be rejected. Please note that UNK is no longer a valid code, you may leave the field empty instead.

The EpiPulse Cases metadata Excel file contains all the definitions and rules necessary to format data correctly. The READ ME sheet of the Excel document explains how to work with the metadata. It can be downloaded from the Technical Guidelines & Tools section of the ‘TESSy Help & Docs’ pages.

Filtering the fields in the file by subject will enable you to see the fields required for your subject and the rules that apply to these fields.

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Checking your Surveillance System Descriptors Before submitting file(s), please review your data source(s) in EpiPulse (in the menu, go to ‘Report’ -> ‘Surveillance systems descriptors’) and update the information as necessary.

Complete and up-to-date data source information for each subject is important for improving the interpretation of data - each surveillance system has different features that need to be taken into account when comparing data European level.

If your data source information is out-of-date and you do not have access rights to update it, please ask your National Focal Point for Surveillance or National Coordinator to do so.

Information on data sources is available in the TESSy User Guide, as this functionality is still only available through TESSy.

Uploading your data

Data is submitted through the EpiPulse web interface (in the menu, go to Report -> EpiPulse Cases).

The visual interface for reporting new data and editing existing records has remained very similar to that of TESSy. For those of you that are also responsible for reporting diseases outside of the Vaccine Preventable Diseases group, you will continue to use TESSy (under EpiPulse) in parallel with the new EpiPulse Cases, until all disease groups will have been migrated to the new tool.

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Similar to TESSy, you can Add/Update or Replace data with new uploads, using either CSV or XML files. You can

also manually create records for some diseases, and report zero cases where appropriate.

The functionality for manually editing existing records is also a familiar experience. Search for the record you wish to edit, and modify the existing information as needed.

Finalising your submission The compliance of your data with the validation rules in the metadata is checked automatically during the data upload process. In EpiPulse Cases this process is called “Technical Validation”, and it is the only step where your upload can be rejected, for severe data quality issues, such as the file format not being readable by the system, or (one of the few) mandatory variables having missing values.

If your file has been rejected, there will be a message explaining each instance of non-compliance with the metadata that needs correcting.

The significant new feature in EpiPulse Cases is the Data Validation Report, which puts your data in the context of the already existing information for the same disease, and provides you with a detailed overview of the new data in the file you have just uploaded, as well as the resulting overall epidemiological situation painted by the existing (past) data together with the newly uploaded file(s). This means much more timely feedback on your uploads, including details on data quality, as well as outputs (graphs, charts, and tables) on some of epidemiological indicators. The Data Validation reports will evolve and grow based on your feedback in collaboration with our Disease Experts. These reports will provide a new and better way of understanding and updating the information collected at European level, and will hopefully increase the quality and timeliness of the data, while reducing workloads.

Below you can find a few screenshots of the Data Validation Report.

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1. Begin by opening the report:

2. View the report in a window, download the list of eventual validation messages, or download the report

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3. Check data completeness; both for the new upload, and in the context of historical data

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4. The downloaded report can be opened full screen for easier viewing and navigation. This is a preview of the currently developed epidemiological indicators/stratifications.

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5. After reviewing the information in the Data Validation Report you can choose to approve or reject it.

If you choose to reject it, no data will be saved in the EpiPulse Cases system, but your file will remain visible should you wish to re-download it, or resubmit it for a new Data Validation at a later date or after further checks. Please check the Epi Validation Report carefully, there might be warnings and remarks relating to possible data quality issues or potential overwriting of existing records that you should consider.

When your file has been validated and you are satisfied that all corrections have been made, please ensure

prompt approval or rejection. Unapproved uploads can block the approval of other related uploads.

EpiPulse Cases Helpdesk

Email: [email protected]

Telephone number: +46-(0)8-5860 1601

Availability: 9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC holidays)

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Annex 1. IBD metadata

This section describes:

• The IBD metadata set • Changes to the IBD metadata

IBD metadata set

Current subject codes

Table 1 shows the subject codes (formerly ‘record types’) to be used when reporting 2023 VPD surveillance data to Epipulse Cases (EPC). Cases should be reported according to the relevant EU Case

Definition1.

We strongly encourage case-based reporting. If case-based data are not available, aggregated data

may be reported.

Table 1: IBD subject codes

Disease Case-based

subject code

Aggregated

subject code

Invasive Haemophilus influenzae disease HAEINF HAEINFAGGR

Invasive meningococcal disease MENI MENIAGGR

Invasive pneumococcal disease PNEU PNEUAGGR

Neisseria Meningitidis Isolates (Molecular surveillance) MENIISO n/a

Comment: An aggregated format called “AGGR” was previously available. From 2024, with the move

from TESSy reporting to Epipulse Cases, aggregated subject codes HAEINFAGGR, MENIAGGR and

PNEUAGGR have been launched. An aggregated subject code is not available for MENIISO.

Case-based reporting

The metadata set has variables that are common across all the Invasive Bacterial Diseases (IBD): invasive H. influenzae disease (HAEINF), invasive meningococcal disease (MENI), invasive

pneumococcal disease (PNEU), which are summarised in Table 2. Disease-specific variables (in addition to the common variables) are subsequently summarised in Table 3 (HAEINF), Table 4 (MENI)

and Table 5 (PNEU). Case-based variables for the Neisseria meningitidis Isolates (MENIISO) dataset

are summarised in Table 6.

1 EU case definitions (europa.eu)

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Table 2: Case-based metadata common across IBD data (subject codes: HAEINF, MENI, PNEU)

2 For both PNEU and HAEINF: only confirmed cases should be reported according to the EU Case Definition. For MENI: confirmed, probable and possible cases can be reported according to the EU Case Definition. 3 Only reported for HAEINF and MENI - not included in PNEU dataset.

Variable Description Coded value list

Age Age of patient in years as reported in the national system at the time of disease onset.

AgeMonth Age of patient in months as reported in the national system for cases < 2 years of age at the time of disease onset.

CaseClassification 2 Case classification according to EU case definition. CONF = Confirmed POSS = Possible

PROB = Probable

DataSource The data source (surveillance system) that the record originates from. The DataSource value must be a special reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateOfDiagnosis First date of clinical or lab diagnosis. In case the DateOfOnset is missing this date is used for analysis.

DateOfLastVaccination Date of administration of the last vaccination dose - indicates the date when the last dose of vaccine was given before disease onset (if exact date is not known, then provide month or year).

DateOfNotification Date when the case report is first notified to public health authorities.

DateOfOnset 3 Date of onset of disease. Leave empty for asymptomatic cases.

DateUsedForStatistics The reference date used for standard reports that is compared to the reporting period. The date used for statistics can be any date that the reporting country finds applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being reported. HAEINF = Haemophilus infection MENI = Invasive meningococcal disease PNEU = Invasive pneumococcal disease

Gender Gender of the reported case. F = Female M = Male OTH = Other

NationalRecordId Unique identifier for each record within and across the specified surveillance system (data source) – selected and generated by the country reporting the record.

Outcome Information on whether the case is alive or deceased. The death should be due to the reported disease. A = Alive D = Died

PlaceOfNotification Place of the first notification of the case to a regional authority. Select the most detailed NUTS level possible. Consult the reference values in mdLocation dataset

PlaceOfResidence Place of residence of patient at the time of disease onset. Select the most detailed NUTS level possible. Consult the reference values in mdLocation dataset

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

Status The Status value is used to provide the functionality for a record within EpiPulse Cases database. Default value: NEW/UPDATE. If set to DELETE, the record with the specified NationalRecordId is deleted (invalidated) from EpiPulse Cases database, if it exists. If set to NEW/UPDATE, the record is inserted into the database: If

DELETE = Delete a previously reported record. NEW/UPDATE = Update a previously reported record (default).

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Table 3: Case-based metadata – additional HAEINF-specific variables

the same NationalRecordId already exists for the same data source and subject code, then the current submitted record updates (replace) the existing one.

SubjectCode SubjectCode is a reporting model for a disease/health topic - identifies the reporting structure and format of a record (case based or aggregate reporting).

HAEINF = Haemophilus infection MENI = Meningococcal disease PNEU = Pneumococcal infection

Variable Description Coded value list

ClinicalCriteria Clinical presentation of the disease. CELL = Cellulitis EPIG = Epiglottitis MENI = Meningitis/Meningeal/ Meningoencephalitic MENISEPTI = Meningitis and septicaemia OSE = Osteomyelitits/septic arthritis OTH = Other PNEU = Pneumonia

SEPTI = Septicaemia

MainPathogenDetectionMethod Pathogen detection method used on the primary laboratory specimen with a positive result for case confirmation and further characterisation of the disease. More than one method can be reported.

ANTIGEN = Antigen detection CULT = Culture GENOSEQ = Genotyping/Sequencing IMMUNO = Immunodiagnostic tests NUCLACID = Detection of nucleic acid OTH = Other

SecondPathogenDetectionMethod Pathogen detection method used on the second type of laboratory specimen with a positive result (if taken) for diagnosis or further characterisation of the disease. More than one method can be reported.

ANTIGEN = Antigen detection CULT = Culture GENOSEQ = Genotyping/Sequencing

IMMUNO = Immunodiagnostic tests NUCLACID = Detection of nucleic acid OTH = Other

Serotype Serotype of the pathogen which is the cause of the reported disease. HAEINF_A = H. influenzae type a HAEINF_B = H. influenzae type b HAEINF_C = H. influenzae type c HAEINF_D = H. influenzae type d HAEINF_E = H. influenzae type e HAEINF_F = H. influenzae type f HAEINF_NONCAPS = H. influenzae non-capsulated strain

HAEINF_NOT_B = H. influenzae non-b strain HAEINF_UNK = H. influenzae type unknown

VaccinationStatus Indicates if the case is vaccinated against serotype b and number of vaccine doses received.

10DOSE = 10 doses 1DOSE = 1 dose

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Table 4: Case-based metadata – additional MENI-specific variables

2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses 5DOSE = 5 doses 6DOSE = 6 doses 7DOSE = 7 doses 8DOSE = 8 doses 9DOSE = 9 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

Variable Description Coded value list

ClinicalCriteria Clinical presentation of the disease according to the EU case definition. MENI = Meningitis/Meningeal/ Meningoencephalitic MENISEPTI = Meningitis and septicaemia OTH = Other PNEU = Pneumonia SEPTI = Septicaemia

Imported Infection has occurred following exposure outside the reporting country during a time compatible with the incubation period of the infection.

0 = No 1 = Yes

IsolateId Unique identifier for each isolate within the data source/laboratory system related to the case. In option1 in the Reporting Protocol, this variable corresponds to the EMERT II identifier.

MainPathogen DetectionMethod

Pathogen detection method used on the primary laboratory specimen with a positive result for case confirmation and further characterisation of the disease. More than one method can be reported.

ANTIGEN = Antigen detection CULT = Culture GENOSEQ = Genotyping/Sequencing

MICRO = Microscopy NUCLACID = Detection of nucleic acid OTH = Other

MICSign_CIP This field can indicate if a value of the MICValueAST_CIP test is "less than" (<); "equal to or less than" (<=); "equal to" (=); "equal to or greater than"(>=); or "greater than" (>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

MICSign_CTX_CFX This field can indicate if a value of the MICValueAST_CTX_CFX test is "less than"(<); "equal to or less

than"(<=); "equal to"(=); "equal to or greater than"(>=); or "greater than"(>) the value indicated in the following field.

< = Less than

<= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

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MICSign_PEN This field can indicate if a value of the MICValueAST_PEN test is "less than" (<); "equal to or less than" (<=); "equal to" (=); "equal to or greater than"(>=); or "greater than" (>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

MICSign_RIF This field can indicate if a value of the MICValueAST_RIF test is "less than" (<); "equal to or less than" (<=); "equal to" (=); "equal to or greater than"(>=); or "greater than" (>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

MICValueAST_CIP MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

MICValueAST_CTX_CFX MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

MICValueAST_PEN MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

MICValueAST_RIF MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

PlaceOfInfection If Imported = 1 (TRUE): The probable place of infection should be provided at the country level. One entry for each country visited during the incubation period of the disease. Note this is a repeatable field.

Consult the reference values in mdLocation dataset

ReportedEMERTII Describe if the isolate related to the case was reported to EMERT II. 0 = No 1 = Yes

ResultFetVR Serotype Gene FetA VR variable region. Values from http://neisseria.org/nm/typing/tessy/. Consult the reference values for SubjectCode = MENI and Variable = ResultFetVR

ResultMLST Multilocus Sequence Typing clonal complex of strain. Values from http://neisseria.org/nm/typing/tessy/. Consult the reference values for SubjectCode = MENI and Variable = ResultMLST

ResultPorA1 Serotype Gene PorA variable region 1. Values from http://neisseria.org/nm/typing/tessy/. Consult the reference values for SubjectCode = MENI and Variable = ResultPorA1

ResultPorA2 Serotype Gene PorA variable region 2. Values from http://neisseria.org/nm/typing/tessy/. Consult the reference values for SubjectCode = MENI and Variable = ResultPorA2

SecondPathogen DetectionMethod

Pathogen detection method used on the second type of laboratory specimen with a positive result (if taken) for diagnosis or further characterisation of the disease. More than one method can be reported.

ANTIGEN = Antigen detection CULT = Culture GENOSEQ = Genotyping/Sequencing MICRO = Microscopy NUCLACID = Detection of nucleic acid OTH = Other

Serogroup Serogroup will not be known if clinical diagnosis only used to identify disease. NEIMENI_29E = N. meningitidis serogroup 29E NEIMENI_A = N. meningitidis serogroup A NEIMENI_B = N. meningitidis serogroup B NEIMENI_C = N. meningitidis serogroup C NEIMENI_NGA = N. meningitidis not groupable

NEIMENI_OTH = N. meningitidis other serogroup NEIMENI_W = N. meningitidis serogroup W NEIMENI_X = N. meningitidis serogroup X NEIMENI_Y = N. meningitidis serogroup Y

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Table 5: Case-based metadata – additional PNEU-specific variables

NEIMENI_Z = N. meningitidis serogroup Z NEIMENI_Z/29E = N. meningitidis serogroup Z/29E

SIR_CIP Susceptibility to Ciprofloxacin as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

SIR_CTX_CFX Susceptibility to Cefotaxime or Ceftriaxone as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

SIR_PEN Susceptibility to Penicillin as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

SIR_RIF Susceptibility to Rifampicin as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

VaccinationStatus Indicates if the case is vaccinated against the serogroup of meningococcus that was the cause of infection and number of vaccine doses received.

1DOSE = 1 dose 2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

Variable Description Coded value list

ASTMethod Test method(s) used for MIC determination. AGARDIL = Agar dilution AUTOM = Automated instrument method BROTHDIL = Broth microdilution GRAD = Antimicrobial gradient (E-test, etc) OTH = Other

BrandPCV1 Type of PCV at first dose. PCV10 = Pneumococcal conjugate vaccine 10 PCV13 = Pneumococcal conjugate vaccine 13 PCV15 = Pneumococcal conjugate vaccine 15 PCV20 = Pneumococcal conjugate vaccine 20 PCV7 = Pneumococcal conjugate vaccine 7

BrandPCV2 Type of PCV at second dose. PCV10 = Pneumococcal conjugate vaccine 10

PCV13 = Pneumococcal conjugate vaccine 13 PCV15 = Pneumococcal conjugate vaccine 15 PCV20 = Pneumococcal conjugate vaccine 20 PCV7 = Pneumococcal conjugate vaccine 7

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BrandPCV3 Type of PCV at third dose. PCV10 = Pneumococcal conjugate vaccine 10 PCV13 = Pneumococcal conjugate vaccine 13 PCV15 = Pneumococcal conjugate vaccine 15 PCV20 = Pneumococcal conjugate vaccine 20 PCV7 = Pneumococcal conjugate vaccine 7

BrandPCV4 Type of PCV at fourth dose. PCV10 = Pneumococcal conjugate vaccine 10 PCV13 = Pneumococcal conjugate vaccine 13 PCV15 = Pneumococcal conjugate vaccine 15 PCV20 = Pneumococcal conjugate vaccine 20 PCV7 = Pneumococcal conjugate vaccine 7

ClinicalCriteria Clinical presentation of the disease. BACTERPNEUMO = Bacteraemic pneumonia MENI = Meningitis/Meningeal/Meningoencephalitic MENISEPTI = Meningitis and septicaemia OTH = Other SEPTI = Septicaemia

DatePCV1 Date of first dose of PCV.

DatePCV2 Date of second dose of PCV.

DatePCV3 Date of third dose of PCV.

DatePCV4 Date of fourth dose of PCV.

DatePPV Date of PPV.

DosePCV1 First dose of vaccination with a PCV. 0 = No 1 = Yes

DosePCV2 Second dose of vaccination with a PCV. 0 = No 1 = Yes

DosePCV3 Third dose of vaccination with a PCV. 0 = No 1 = Yes

DosePCV4 Fourth dose of vaccination with a PCV. 0 = No

1 = Yes

DosePPV Vaccinated with PPV. 0 = No 1 = Yes

MICSign_CTX_CFX This field can indicate if a value of the MICValueAST_CTX_CFX test is "less than"(<); "equal to or less than"(<=); "equal to"(=); "equal to or greater than"(>=); or "greater than"(>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

MICSign_ERY This field can indicate if a value of the MICValueAST_ERY test is "less than" (<); "equal to or less than" (<=); "equal to" (=); "equal to or greater than"(>=); or "greater than" (>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

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MICSign_PEN This field can indicate if a value of the MICValueAST_PEN test is "less than" (<); "equal to or less than" (<=); "equal to" (=); "equal to or greater than"(>=); or "greater than" (>) the value indicated in the following field.

< = Less than <= = Less than or equal = = Equal > = Greater than >= = Greater than or equal

MICValueAST_CTX_CFX MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

MICValueAST_ERY MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

MICValueAST_PEN MIC (Value in mg/l). Use '.' as decimal delimiter, e.g. 0.25.

NRLData If 1 (TRUE) - data is based on data from National Reference laboratory, if 0 (FALSE) - data is based on

clinical and non-reference-laboratory data.

0 = No

1 = Yes

PathogenDetectionMethod Pathogen detection method used for serotyping. More than one method can be reported. COAGG = Coagglutination GDIFF = Gel diffusion MPCR = Multiplex PCR OTH = Other PTEST = Pneumotest QUE = Quellung SLAGG = Slide agglutination

PCVDoses Total number of PCV doses received by case prior to onset.

PPVDoses Total number of PPV doses received by case prior to onset.

Serotype Serotype of the pathogen which is the cause of the reported disease. Consult the reference values for SubjectCode = PNEU and Variable = Serotype

SIR_CTX_CFX Susceptibility to Cefotaxime or Ceftriaxone as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

SIR_ERY Susceptibility to Erythromicin as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

SIR_PEN Susceptibility to Penicillin as the final interpretation based on one or more test results. I = Intermediate R = Resistant S = Susceptible

VaccinationStatus Indicates if the case is vaccinated and number of vaccine doses received. 10DOSE = 10 doses 1DOSE = 1 dose 2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses 5DOSE = 5 doses 6DOSE = 6 doses 7DOSE = 7 doses 8DOSE = 8 doses 9DOSE = 9 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

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Table 6: Case-based metadata – MENIISO-specific variables

Vaccine Type of pneumococcal vaccine; if the last vaccine given in the series was different from the vaccine with which the series was initiated, indicate the last vaccine in the series.

PCV10 = Pneumococcal conjugate vaccine 10 PCV13 = Pneumococcal conjugate vaccine 13 PCV15 = Pneumococcal conjugate vaccine 15 PCV20 = Pneumococcal conjugate vaccine 20 PCV3 = Pneumococcal conjugate vaccine - third dose PCV7 = Pneumococcal conjugate vaccine 7 PPV23 = Pneumococcal polysaccharide vaccine

Variable Description Coded value list

CaseId Unique identifier for each case within the data source / surveillance system related to the isolate, so that isolate records can be linked to case records. This should match the corresponding NationalRecordId of MENI case-based data in option 2, as per Reporting Protocol.

DataSource The data source (laboratory) that the record originates from. Consult the reference values in mdDataSource dataset

DateOfReceiptReferenceLab Date of receipt in reference laboratory or typing laboratory with reference function.

DateOfReceiptSourceLab Date of receipt in source laboratory, i.e. the laboratory the sample was first sent to.

DateOfSampling Date the sample from which the isolate was derived, was taken.

DateUsedForStatistics The most epidemiologically relevant date for the isolate. Equal to the date of sampling if available. If not, equal to the date of receipt in the source lab, and if that is not available, the date of receipt in the reference lab.

Disease The code of the disease that is being reported. MENI = Invasive meningococcal disease

HealthTopic The code of the health topic that is being reported. ISO = Isolate data

ItemCode Item code.

NationalRecordId Unique identifier for each record within and across the specified surveillance system (data source) – selected and generated by the country reporting the record.

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

Status The Status value is used to provide the functionality for a record within EpiPulse Cases database. Default value: NEW/UPDATE. If set to DELETE, the record with the specified NationalRecordId is deleted (invalidated) from EpiPulse Cases database, if it exists. If set to NEW/UPDATE, the record is inserted into the database: If the same NationalRecordId already exists for the same data source and subject code, then the current submitted record updates (replace) the existing one.

DELETE = Delete a previously reported record. NEW/UPDATE = Update a previously reported record (default).

SubjectCode SubjectCode is a reporting model for a disease/health topic - identifies the reporting structure and format of a record (case based or aggregate reporting).

MENIISO = Neisseria meningitidis isolate

WgsAccession European Nucleotide Archive (ENA) run identifier, based on which the sequence read data can be retrieved / Sequence Read Archive (SRA) run identifier, based on which the sequence read data can be retrieved. Starts with ERR or SRR, i.e. not the sample or experiment which ERS/ERX or SRS/SRX.

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Aggregated reporting

Please refer to Table 7 to see the format for aggregated reporting of IBD data. If only a few variables can be reported, it is recommended to give the following priority for

reporting: AgeGroup, Classification, VaccStatus, Gender.

Table 7: Aggregate metadata for reporting of IBD data (record type: AGGR)

WgsAssembler The assembler used for sequencing, optionally including parameter settings. MAP_TO_LOCI1 = Mapping to individual loci, variant 1 for IonTorrent SKESA = SKESA assembler SPADES = SPAdes without read mapping and consensus calling SPADES_READMAP = SPAdes either including or followed by read mapping and consensus calling VELVET = Velvet without read mapping and consensus calling VELVET_READMAP = Velvet using k-mer optimisation, and followed by read mapping and consensus calling

WgsAssembly The assembled genome, as a gzipped FASTA file. The file contents are subsequently converted into a Base64-encoded string for inclusion into either the XML or CSV data for the isolate.

WgsProtocol Protocol used for sequencing, limited to the sequencing technology used (today Illumina or IonTorrent) and the read length.

HISEQ_2X100 = Illumina HiSeq 2x100 IONTORRENT = IonTorrent MINISEQ_2X150 = Illumina MiniSeq 2x150 MISEQ_2X150 = Illumina MiSeq 2x150 MISEQ_2X250 = Illumina MiSeq 2x250 MISEQ_2X300 = Illumina MiSeq 2x300 NEXTSEQ_2X150 = Illumina NextSeq 2x150 PAIRED_END_ILLUMINA = Illumina HiSeq, MiSeq, NextSeq or MiniSeq

WgsRawReads The raw reads obtained from the sequencer stored as FASTQ files. Each FASTQ file is a text file which represents sequence readouts for a sample.

Variable Description Coded value list

AgeGroup Age group of the reported record. 0 = <1 year 01-04 = 1-4 years 05-09 = 5-9 years 10-14 = 10-14 years 15-19 = 15-19 years 20-24 = 20-24 years 25-29 = 25-29 years 30-34 = 30-34 years 35-39 = 35-39 years 40-44 = 40-44 years

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4 For PNEU and HAEINF, only confirmed cases should be reported according to the EU Case Definition. For MENI, confirmed, probable and possible cases can be reported.

45-49 = 45-49 years 50-54 = 50-54 years 55-59 = 55-59 years 60-64 = 60-64 years 65+ = 65 and over

CaseClassification 4 Case classification according to EU case definition. CONF = Confirmed POSS = Possible PROB = Probable

DataSource The data source (surveillance system) that the record originates from. The DataSource value must be a special reference value from EpiPulse Cases metadata.

Consult the reference values in mdDataSource dataset

DateUsedForStatistics The reference date used for standard reports that is compared to the reporting period. The date used for statistics can be any date that the reporting country finds applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being reported. HAEINF = Haemophilus infection MENI = Invasive meningococcal disease PNEU = Invasive pneumococcal disease

Gender Gender of the reported record. F = Female M = Male OTH = Other

NumberOfCases Total number of cases during the reported period for the specified disease.

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

SubjectCode SubjectCode is a reporting model for a disease/health topic - identifies the reporting structure and format of a record (case based or aggregate reporting).

HAEINFAGGR = Haemophilus infection aggregated MENIAGGR = Meningococcal disease aggregated PNEUAGGR = Pneumococcal infection aggregated

VaccinationStatus Indicates if the case is vaccinated and number of vaccine doses received. 1DOSE = 1 dose 2DOSE = 2 doses 3DOSE = 3 doses 4DOSE = 4 doses NOTVACC = Not vaccinated UNKDOSE = Vaccinated, dose unknown

21

Changes to the IBD metadata

Metadata changes prior to 2014 can be found on the TESSy documents website. Changes from 2014 onwards have been summarised in Table 8 below.

Table 8: Summary of implemented changes in case-based and aggregated subject codes (formerly ‘record types’) for IBD from 2014 to current

Year of change

Subject Variables Description

2024 HAEINF MENI PNEU MENIISO HAEINFAGGR MENIAGGR PNEUAGGR

ALL Reporting moved from TESSy to the Epipulse Cases platform. This transition has led to changes in some variable names and categorical values (see below).

RecordTypeVersion Remove variable

MENI ECDCIsolateID Remove variable

PNEU DosePCV1; DatePCV1; BrandPCV1; DosePCV2; DatePCV2; BrandPCV2; DosePCV3; DatePCV3; BrandPCV3; DosePCV4; DatePCV4; BrandPCV4; PCVDoses; DosePPV; DatePPV; PPVDoses

ADD variables: DosePCV1: First dose of vaccination with a PCV DatePCV1: Date of first dose of PCV BrandPCV1: Type of PCV at first dose DosePCV2: Second dose of vaccination with a PCV DatePCV2: Date of second dose of PCV BrandPCV2: Type of PCV at second dose DosePCV3: Third dose of vaccination with a PCV DatePCV3: Date of third dose of PCV BrandPCV3: Type of PCV at third dose DosePCV4: Fourth dose of vaccination with a PCV DatePCV4: Date of fourth dose of PCV BrandPCV4: Type of PCV at fourth dose PCVDoses: Total number of PCV doses received prior to onset DosePPV: Vaccinated with PPV DatePPV: Date of PPV PPVDoses: Total number of PPV doses received prior to onset

HAEINFAGGR MENIAGGR PNEUAGGR

VaccinationStatus ADD Variable

HAEINF MENI PNEU

Classification → CaseClassification; ClinicalPresentation → ClinicalCriteria ; DateLastVaccDose → DateOfLastVaccination; RecordId → NationalRecordId; RecordType → SubjectCode; Subject → Disease; VaccStatus → VaccinationStatus

Variable names changed from (TESSy) → to (Epipulse Cases): Classification → CaseClassification; ClinicalPresentation → ClinicalCriteria; DateLastVaccDose → DateOfLastVaccination; RecordId → NationalRecordId; RecordType → SubjectCode; Subject → Disease; VaccStatus → VaccinationStatus

HAEINF MENI

TestMethod1 → MainPathogenDetectionMethod; TestMethod2 → SecondPathogenDetectionMethod

Variable names changed from (TESSy) → to (Epipulse Cases): TestMethod1 → MainPathogenDetectionMethod; TestMethod2 → SecondPathogenDetectionMethod

MENI ResultMICSign_CTX_CFX → MICSign_CTX_CFX; Variable names changed from (TESSy) → to (Epipulse Cases):

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PNEU ResultMICSign_PEN → MICSign_PEN; ResultMICValueCTX_CFX → MICValueAST_CTX_CFX; ResultMICValuePEN → MICValueAST_PEN

ResultMICSign_CTX_CFX → MICSign_CTX_CFX; ResultMICSign_PEN → MICSign_PEN; ResultMICValueCTX_CFX → MICValueAST_CTX_CFX; ResultMICValuePEN → MICValueAST_PEN

MENI ProbableCountryOfInfection → PlaceOfInfection; ResultMICSign_CIP → MICSign_CIP; ResultMICSign_RIF → MICSign_RIF; ResultMICValueCIP → MICValueAST_CIP; ResultMICValueRIF → MICValueAST_RIF

Variable names changed from (TESSy) → to (Epipulse Cases): ProbableCountryOfInfection → PlaceOfInfection; ResultMICSign_CIP → MICSign_CIP; ResultMICSign_RIF → MICSign_RIF; ResultMICValueCIP → MICValueAST_CIP; ResultMICValueRIF → MICValueAST_RIF

PNEU ResultMICSign_ERY → MICSign_ERY ResultMICValueERY → MICValueAST_ERY TestMethodMIC → ASTMethod; VaccType → Vaccine

Variable names changed from (TESSy) → to (Epipulse Cases): ResultMICSign_ERY → MICSign_ERY ResultMICValueERY → MICValueAST_ERY TestMethodMIC → ASTMethod; VaccType → Vaccine

HAEINFAGGR MENIAGGR PNEUAGGR

AgeClass → AgeGroup; Classification → CaseClassification; RecordType → SubjectCode; Subject → Disease;

Variable names changed from (TESSy) → to (Epipulse Cases): AgeClass → AgeGroup; Classification → CaseClassification; RecordType → SubjectCode; Subject → Disease;

HAEINF MENI PNEU

CaseClassification Discontinued “UNK” categorical value

ClinicalCriteria Discontinued “UNK” and “NUS” categorical values, and “O” remapped to “OTH”

Status Remapping of “NEW/UPDATE” to “ADD/UPDATE”

HAEINF MENI

MainPathogenDetectionMethod; SecondPathogenDetectionMethod Discontinued “UNK” and “NA” categorical values, and “O” remapped to “OTH”

Outcome Discontinued “UNK” and “NUS” categorical values

HAEINF PNEU

VaccinationStatus Discontinued “UNK” categorical value and “DOSEUNK” remapped to “UNKDOSE”

MENI PNEU

SIR_CTX_CFX; SIR_PEN Discontinued “UNK” categorical value

HAEINF Serotype Discontinued “NUS” categorical values and remapping of:

“A” to “HAEINF_A” “B” to “HAEINF_B” “C” to “HAEINF_C” “D” to “HAEINF_D” “E” to “HAEINF_E”

“F” to “HAEINF_F” “UNK” to “HAEINF_UNK” “non-b” to “HAEINF_NOT_B” “non-caps” to “HAEINF_NONCAPS”

MENI Imported; ReportedEMERTII Discontinued “UNK” categorical value and variable changed from coded value to Boolean (0 = No ; 1 = Yes)

ResultFetVR; ResultPorA1; ResultPorA2

Discontinued “UNK” and “NUS” categorical values

ResultMLST; SIR_CIP; SIR_RIF Discontinued “UNK” categorical value

VaccinationStatus Discontinued “UNK”, “5DOSE”, “6DOSE”, “7DOSE”, “8DOSE”, “9DOSE”, “10DOSE” categorical values and “DOSEUNK” remapped to “UNKDOSE”

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Serogroup Discontinued “UNK” and “NUS” categorical values and remapping of:

“29E” to “NEIMENI_29E” “A” to “NEIMENI_A” “B” to “NEIMENI_B” “C” to “NEIMENI_C” “NGA” to “NEIMENI_NGA” “O” to “NEIMENI_OTH”

“W” to “NEIMENI_W” “X” to “NEIMENI_X” “Y” to “NEIMENI_Y” “Z” to “NEIMENI_Z” “Z/29E” to “NEIMENI_Z/29E”

ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST

Update coded values (once a year or upon request) from the following list: http://neisseria.org/nm/typing/tessy/

PNEU ASTMethod Discontinued “UNK” categorical value and “O” remapped to “OTH”

NRLData Variable changed from coded value to Boolean (0 = No ; 1 = Yes)

Outcome; SIR_ERY Discontinued “UNK” categorical value

PathogenDetectionMethod Discontinued “UNK” and “NA” categorical values, and “O” remapped to “OTH”

Vaccine Discontinued “UNK” and “NA” categorical values

Serotype

Discontinued “NT” and “O” categorical values and remapping of:

“1” to “STRPNE_1” “10” to “STRPNE_10” “10A” to “STRPNE_10A” “10B” to “STRPNE_10B” “10C” to “STRPNE_10C” “10F” to “STRPNE_10F” “11” to “STRPNE_11” “11A” to “STRPNE_11A” “11B” to “STRPNE_11B” “11C” to “STRPNE_11C” “11D” to “STRPNE_11D” “11E” to “STRPNE_11E” “11F” to “STRPNE_11F” “12” to “STRPNE_12” “12A” to “STRPNE_12A” “12B” to “STRPNE_12B” “12F” to “STRPNE_12F” “13” to “STRPNE_13” “14” to “STRPNE_14” “15” to “STRPNE_15” “15A” to “STRPNE_15A” “15B” to “STRPNE_15B” “15B/C” to “STRPNE_15B/C” “15C” to “STRPNE_15C” “15F” to “STRPNE_15F” “16” to “STRPNE_16” “16A” to “STRPNE_16A” “16F” to “STRPNE_16F” “17” to “STRPNE_17” “17A” to “STRPNE_17A”

“28” to “STRPNE_28” “28A” to “STRPNE_28A” “28F” to “STRPNE_28F” “29” to “STRPNE_29” “3” to “STRPNE_3” “31” to “STRPNE_31” “32” to “STRPNE_32” “32A” to “STRPNE_32A” “32F” to “STRPNE_32F” “33” to “STRPNE_33” “33A” to “STRPNE_33A” “33B” to “STRPNE_33B” “33C” to “STRPNE_33C” “33D” to “STRPNE_33D” “33F” to “STRPNE_33F” “34” to “STRPNE_34” “35” to “STRPNE_35” “35A” to “STRPNE_35A” “35B” to “STRPNE_35B” “35C” to “STRPNE_35C” “35F” to “STRPNE_35F” “36” to “STRPNE_36” “37” to “STRPNE_37” “38” to “STRPNE_38” “39” to “STRPNE_39” “4” to “STRPNE_4” “40” to “STRPNE_40” “41” to “STRPNE_41” “41A” to “STRPNE_41A” “41F” to “STRPNE_41F”

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“17F” to “STRPNE_17F” “18” to “STRPNE_18” “18A” to “STRPNE_18A” “18B” to “STRPNE_18B” “18C” to “STRPNE_18C” “18F” to “STRPNE_18F” “19” to “STRPNE_19” “19A” to “STRPNE_19A” “19B” to “STRPNE_19B” “19C” to “STRPNE_19C” “19F” to “STRPNE_19F” “2” to “STRPNE_2” “20” to “STRPNE_20” “21” to “STRPNE_21” “22” to “STRPNE_22” “22A” to “STRPNE_22A” “22F” to “STRPNE_22F” “23” to “STRPNE_23” “23A” to “STRPNE_23A” “23B” to “STRPNE_23B” “23F” to “STRPNE_23F” “24” to “STRPNE_24” “24A” to “STRPNE_24A” “24B” to “STRPNE_24B” “24F” to “STRPNE_24F” “25” to “STRPNE_25” “25A” to “STRPNE_25A” “25F” to “STRPNE_25F” “27” to “STRPNE_27”

“42” to “STRPNE_42” “43” to “STRPNE_43” “44” to “STRPNE_44” “45” to “STRPNE_45” “46” to “STRPNE_46” “47” to “STRPNE_47” “47A” to “STRPNE_47A” “47F” to “STRPNE_47F” “48” to “STRPNE_48” “5” to “STRPNE_5” “6” to “STRPNE_6” “6A” to “STRPNE_6A” “6B” to “STRPNE_6B” “6C” to “STRPNE_6C” “6D” to “STRPNE_6D” “7” to “STRPNE_7” “7A” to “STRPNE_7A” “7B” to “STRPNE_7B” “7C” to STRPNE_7C” “7F” to “STRPNE_7F” “8” to “STRPNE_8” “9” to “STRPNE_9” “9A” to “STRPNE_9A” “9L” to “STRPNE_9L” “9N” to “STRPNE_9N” “9V” to “STRPNE_9V” “NTYP” to “STRPNE_NTYP” “UNK” to “STRPNE_UNK”

HAEINF MENI PNEU HAEINFAGGR MENIAGGR PNEUAGGR

Gender Discontinued “UNK” categorical value and “O” remapped to “OTH”

HAEINFAGGR MENIAGGR PNEUAGGR

AgeGroup Discontinued “UNK” categorical value

SubjectCode “AGGRVPD” value remapped to “HAEINFAGGR” / “MENIAGGR” / “PNEUAGGR”

HAEINFAGGR PNEUAGGR

CaseClassification Discontinued “UNK”, “POSS” and “PROB” categorical values

MENIAGGR CaseClassification Discontinued “UNK” categorical value

2023 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

2022 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

2021 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

ReportedEMERTII New variable: Describe if the isolate related to the case was reported to EMERT II

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2020 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

MENIISO DateUsedForStatistics Change to date format to allow other date formats like: yyyy, yyyy-Qq, yyyy-mm, yyyy-Www, yyyy-mm-dd

2019 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

MENIISO New record type added

2018 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

2017 MENI ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST Update coded values once a year or upon request from the following list: http://neisseria.org/nm/typing/tessy/

2016 HAEINF Specimen1; Specimen2; Pathogen Variables dropped

TestMethod1; TestMethod2; Age; ClinicalPresentation Description changed

DateLastVaccDose Variable added

Classification Coded value ‘PROB’ removed, as EU case definition disease does not include probable cases

MENI TestMethod1; TestMethod2; ResultPorA1; ResultPorA2; ResultMLST Description changed

ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST The available coded values for all fine typing variables were updated from http://neisseria.org/nm/typing/tessy/

DateLastVaccDose Variable added

Pathogen Variable dropped

PNEU Specimen; DateOfSpecimen Variables dropped

TestMethod1; TestMethod2; VaccType Description changed

DateLastVaccDose Variable added

ClinicalPresentation The coded values were edited. ‘Bacteraemia’ was replaced with ‘Septicaemia’, and ‘Meningitis’ was split into ‘Meningitis’ and ‘Meningitis and Septicaemia’.

2015 HAEINF MENI PNEU

EpiLink; ClinicalCriteria; Labresult Variables dropped

HAEINF ClinicalPresentation; VaccinationStatus Description changed

HAGGR All variables Record type removed

MENI ClinicalPresentation; VaccinationStatus Description changed

Specimen1; Specimen2 Variables dropped

Serogroup The coded value W135 was replaced with W

ResultFetVR; ResultPorA1; ResultPorA2; ResultMLST The available coded values for all fine typing variables were updated from http://neisseria.org/nm/typing/tessy/

PNEU ClinicalPresentation; Classification; VaccinationStatus Description changed

2014 MENI MIC_CIP; MIC_CTX; MIC_PEN; MIC_RIF Variables dropped

SIR_CIP; SIR_CTX_CFX; SIR_PEN; SIR_RIF; ResultMICValueCIP; ResultMICValueCTX_CFX; ResultMICValuePEN; ResultMICValueRIF

Variables added

26

Annex 2. IBD-specific material

IBD data reporting frequency

The surveillance data for the IBDs (invasive H. influenzae disease, invasive meningococcal disease and invasive pneumococcal disease) should be uploaded annually. In 2024, uploaded data will relate

to cases with date used for statistics in 2023.

The deadline for uploading all data for invasive H. influenzae disease, invasive

meningococcal disease, and invasive pneumococcal disease is 15 October 2024.

As per the case definition for invasive meningococcal disease: possible, probable and confirmed cases should be reported. For invasive H. influenzae disease and invasive pneumococcal disease, the case

definition requires only confirmed cases to be reported. See below for further details of the case

definition for each disease.

It is also possible to update case information retrospectively, i.e. for cases reported in previous years with a date used for statistics prior to 2023. For all diseases, any update of previously reported cases

should be done before the reporting deadline in order for data to be included in the annual

epidemiological report and surveillance atlas.

Once the data are validated by the disease experts at ECDC, they are then made publicly available on

the Surveillance Atlas of Infectious Diseases and through annual surveillance reports on the ECDC

website.

Reporting of meningococcal disease isolates (MENIISO)

ECDC recently launched a project for genomic-based EU/EEA surveillance for invasive meningococcal

disease, in which Member States submit genomic data from linked N. meningitidis isolates to the

European Meningococcal Epidemiology in Real Time II (EMERT-II), for sequence analysis and definition of sequence-derived isolate characterisation data and nomenclature. Sequence-derived data

are then imported to Epipulse Cases and linked to the case-based epidemiological data for integrated

analysis. Data visualisation and joint interpretation are conducted and presented in EpiPulse.

In preparation of this genomic surveillance, in 2019 a subject called “Neisseria Meningitidis Isolate”

and a new record type (MENIISO) were created to capture information on the WGS (whole genome sequence) typing of Neisseria meningitidis submitted to the EMERT II database. The MENIISO

records hold the sequence-derived data imported from EMERT-II, as well as information on relevant

dates for cases, and country of the submitting user, and the EMERT-II ID.

To facilitate linkage of the MENI and MENIISO datasets, two variables were added to the MENI

subject code: IsolateId and ReportedEMERTII. The IsolateId variable is used in the linking of a MENI record (with epidemiological and microbiological characterisation data) with a MENIISO record (with

genomic data). The variable “ReportedEMERTII” is used to include information on whether the isolate

related to the case has been reported in EMERT-II.

The specificities of MENIISO data collection are included in a separate reporting protocol “Protocol for genomic-based EU/EEA surveillance of invasive meningococcal disease” which is available in the

Epipulse platform.

During the pilot phase, ECDC encourages data submission as close to real time as possible, for both the genomic and epidemiological data. If epidemiological data aimed to be submitted directly to

Epipulse Cases is not available, genomic data could be reported to EMERT-II and epidemiological data

submitted at the earliest convenience.

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In the event of an investigation of a signal detected from molecular typing data, Member States may be asked to submit relevant and selected epidemiological information to EpiPulse or Epipulse Cases

for the cases included in the signal to ECDC for EU-level analysis.

Starting in September 2023, a monthly cluster analysis will be done at the end of each month, with

the clusters being refreshed in the EpiPulse molecular typing tool.

Narrative information

Changes over time in the number of cases reported in a surveillance system do not always reflect true

changes in the incidence of disease. New reporting practices, improved laboratory capacities and changes in legislation are some of the factors that can influence the number of cases reported. It is

important to be aware of such “surveillance artefacts” when analysing surveillance data and countries are encouraged to describe changes in the surveillance environment that may impact on the number

of cases reported. It is equally important to report if the surveillance environment has remained the same from one year to the next. We encourage reporting countries to provide this information at the

same time as data submission to TESSy and to [email protected].

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Invasive H. influenzae disease data collection and case definitions

Prior to 2007, data on invasive disease caused by H. influenzae were collected by The European Union Invasive

Bacterial Infections Surveillance Network (EU-IBIS) and subsequently transferred to The European Surveillance

System (TESSy).

From 2018, confirmed cases should be reported according to the following 2018 EU case definition5:

Previous versions of the case definition were published in 2012, 2008 and 2002. The 2018, 2012 and 2008 EU case definitions are identical and differ from the 2002 case definition in (i) their specification of invasive H. influenzae type b (Hib), and (ii) definition of possible and probable cases.

5Commission Implementing Decision 2018/945/EU of 22 June 2018 on the communicable diseases and related special health issues to be covered by epidemiological surveillance as well as relevant case definitions.

Clinical criteria

Not relevant for surveillance purposes

Laboratory criteria

At least one of the following two:

— Isolation of Haemophilus influenzae from a normally sterile site

— Detection of Haemophilus influenzae nucleic acid from a normally sterile site

Epidemiological criteria

Not applicable

Case classification

A. Confirmed case: Any person meeting the laboratory criteria

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Invasive meningococcal disease data collection and case definitions Prior to 2007, data on IMD were collected by The European Union Invasive Bacterial Infections Surveillance Network (EU-IBIS) and subsequently imported into The European Surveillance System database (TESSy).

From 2018, cases (possible, probable and confirmed) should be reported according to the following 2018 case definition6:

Previous versions of the case definition were published in 2002, 2008 and 2012. The EU case definitions of 2018 and 2012 differ in the clinical criteria; in 2018 fever was removed, and petechial rash was replaced with haemorrhagic rash. In 2008, the case definition removed (from the 2002 definition) reporting of a probable case when N. meningitidis was identified from a non-sterile site. From 2008 onwards, only isolations from sterile sites are to be considered for reporting.

6Commission Implementing Decision 2018/945/EU of 22 June 2018 on the communicable diseases and related

special health issues to be covered by epidemiological surveillance as well as relevant case definitions.

Clinical criteria

Any person with at least one of the following symptoms:

— Meningeal signs

— Haemorrhagic rash

— Septic shock

— Septic arthritis

Laboratory criteria

At least one of the following four:

— Isolation of Neisseria meningitidis from a normally sterile site, or from purpuric skin lesions

— Detection of Neisseria meningitidis nucleic acid from a normally sterile site, or from purpuric skin lesions

— Detection of Neisseria meningitidis antigen in CSF

— Detection of gram-negative stained diplococcus in CSF

Epidemiological criteria

An epidemiological link by human-to-human transmission

Case classification

A. Possible case: Any person meeting the clinical criteria

B. Probable case: Any person meeting the clinical criteria and with an epidemiological link

C. Confirmed case: Any person meeting the laboratory criteria

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Invasive pneumococcal disease data collection and case definitions

Data on IPD have been reported by the EU/EEA Member States from 2010, when enhanced surveillance of IPD was first implemented on a European level and the majority of Member States began reporting case-based data from national reference laboratories.

From 2018, confirmed cases should be reported according to the following 2018 EU case definition7:

* The criteria for reporting are published each year as part of the Antimicrobial resistance (AMR) reporting protocol. See: TESSy Antimicrobial resistance (AMR) reporting protocol 2023. European Antimicrobial Resistance Surveillance Network (EARS-Net).

Previous versions of the case definition were published in 2002, 2008 and 2012. The 2018 and 2012 case definitions do not differ with the exception of the note on antimicrobial resistance, which was added to the 2018

case definition. The 2012 and 2008 case definitions were identical but differed from the 2002 EU case definition.

The 2002 EU case definition included possible and probable cases, and considered detection of S. pneumoniae

antigen from a normally sterile site a probable case.

7 Commission Implementing Decision 2018/945/EU of 22 June 2018 on the communicable diseases and related special health issues to be covered by epidemiological surveillance as well as relevant case definitions.

Clinical criteria

Not relevant for surveillance purposes.

Laboratory criteria

At least one of the following three:

— Isolation of Streptococcus pneumoniae from a normally sterile site

— Detection of Streptococcus pneumoniae nucleic acid from a normally sterile site

— Detection of Streptococcus pneumoniae antigen from a normally sterile site

Epidemiological criteria

Not applicable

Case classification

A. Possible case – Not applicable

B. Probable case – Not applicable

C. Confirmed case – Any person meeting the laboratory criteria

Antimicrobial resistance

The results of antimicrobial susceptibility tests must be reported according to the methods and criteria* agreed between ECDC and Member States as specified by ECDC's European Antimicrobial Resistance Surveillance Network (EARS-Net)

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To: National Focal Points for Surveillance Cc: National Coordinators

Dear National Focal Points for Surveillance, We are pleased to announce the upcoming launch of EpiPulse Cases in September 2024. This will be the new platform for reporting indicator-based surveillance data according to the list of EU/EEA notifiable diseases and their case definitions. EpiPulse Cases will be deployed progressively during the course of 2024 and 2025 to include all diseases, health issues, and reporting of isolates for molecular surveillance, according to the two timelines below:

ECDC NORMAL

Around two months prior to any group of diseases being included in EpiPulse Cases, you will receive a notification listing the metadata changes that come with it. Given the staggered deployment of the platform, there will exceptionally be several new metadata releases to review before the end of 2025. With the current communication you are receiving for approval the metadata changes for VPI diseases and most molecular surveillance subjects. Please provide your feedback by 9th August 2024. The metadata is being shared by ECDC VPI colleagues to the NFPs for VPI simultaneously. The deadline for reporting VPI diseases will be postponed to late November. The launch of EpiPulse Cases marks the beginning of the end of TESSy which is planned to be fully decommissioned by the end of 2025. Compared to TESSy, EpiPulse Cases offers the following advantages:

▪ It has been designed to handle large (e.g. pandemic) data volumes and will be cloud- based, which will make for faster processing and allow to scale up capacity as required.

▪ We have substantially reduced the number of mandatory variables. This will lower the threshold for the system accepting your data and will leave it to you to decide if your data quality is sufficient for approval of submission.

▪ EpiPulse Cases will offer an automated technical and epidemiological validation of your data directly upon upload. The epidemiological validation will be based on a combination of the previous TESSy-inbuilt validation rules, completeness checks for key variables and a comparison with historical data of yours to detect any unexplained aberrations. Instead of TESSy error and warning messages, you will receive a graphic online validation report, the content and format of which will be targeted at epidemiologists and data managers and will point you to possible data quality issues. The first release of this automated validation in EpiPulse Cases will not yet completely replace the expert-driven validation currently following the automated validation in TESSy, but over time, we do expect to fully integrate this second step in the system.

▪ EpiPulse Cases and the underlying data warehouse are set up in a way that will markedly facilitate its technical maintenance and hence render the platform more robust also from a user perspective.

In addition, national data providers should expect the following main changes:

▪ Metadata: ECDC has taken the opportunity of the new surveillance platform to increase consistency by harmonising variable names and reference values (formerly known as ‘coded values’) across diseases where previous differences were not needed from an

ECDC NORMAL

epidemiological perspective. The formerly mandatory nature of many variables has been removed as it only hampered data submission and resulted in many ‘Unknown’ values without truly improving overall data quality. Finally, the metadata will no longer be versioned. This means that only the latest metadata will be valid for reporting to EpiPulse Cases. For many diseases, these changes may exceed the scope of the annual routine metadata changes and may therefore require a greater one-off effort when implementing them at the national level. For your convenience, we have attached the updated VPI reporting protocols and the relevant metadata including the changes compared to the current TESSy metadata, which should facilitate the necessary mapping and conversion at national level.

▪ User experience: While the automated validation report in EpiPulse Cases does represent a new feature, the overall logic and steps of reporting national surveillance data to ECDC remain largely the same. However, the user interface will be different from TESSy, and users will need to learn how to navigate a familiar workflow that now comes with a new look and feel.

We believe that EpiPulse Cases will bring palpable improvements and convince users eventually, but we are also aware that the new system may initially pose certain challenges in some Member States. ECDC is committed to easing the transition as much as possible and actively supporting data providers whenever necessary. From September 2024, we will offer online training demos, video tutorials and platform-embedded contextual help for the relevant networks as well as individual hands-on data managerial assistance. Any questions in this context or user feedback may be directed to [email protected]. We would also be happy to receive any suggestions for improvement at future disease network meetings, and this year’s annual meeting of the National Focal Points for Surveillance may already offer an opportunity for a debrief on first user experiences with the new platform. We wish to thank you for your cooperation in advance and hope to be able to make EpiPulse Cases a success jointly with you. Kind regards, Bruno Ciancio on behalf of the TESSy and EpiPulse Cases teams1 In attachment

1. EpiPulse Cases metadata for VPI and most molecular surveillance (including the changes)

2. PDF extract highlighting the metadata changes (from the file above) 3. EpiPulse Cases quick guide 4. VPI reporting protocols 5. Machine to Machine Communication - API Specification

1Catalin Albu, Konstantinos Anthis, Zsolt Bartha, Bruno Ciancio, Emiliano Farinella, Erik Halm, Vicky Lefevre, Georgios Margaronis, Adrian Prodan, and Phillip Zucs.

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Contents INTRODUCTION .................................................................................................................................................. 2

HOW TO USE THIS DOCUMENT ........................................................................................................................................ 2 FINDING FURTHER INFORMATION .................................................................................................................................... 2 COPYRIGHT ................................................................................................................................................................ 2

REPORTING TO EPIPULSE CASES ......................................................................................................................... 3

CHECKING THE DATA COLLECTION SCHEDULE ..................................................................................................................... 3 PREPARING DATA ......................................................................................................................................................... 3 CHECKING METADATA ................................................................................................................................................... 3 CHECKING YOUR SURVEILLANCE SYSTEM DESCRIPTORS........................................................................................................ 4 UPLOADING YOUR DATA ................................................................................................................................................ 4 FINALISING YOUR SUBMISSION........................................................................................................................................ 5 EPIPULSE CASES HELPDESK ............................................................................................................................................ 9

ANNEX 1: MEASLES AND RUBELLA METADATA ................................................................................................ 10

MEASLES AND RUBELLA METADATA ............................................................................................................................... 10 Current subject codes ........................................................................................................................................ 10 Case-based reporting ........................................................................................................................................ 10 Aggregated reporting ....................................................................................................................................... 16 Changes to the measles and rubella metadata ................................................................................................. 18

ANNEX 2. MEASLES & RUBELLA-SPECIFIC MATERIAL ........................................................................................ 21

MONTHLY REPORTING ................................................................................................................................................ 21 NARRATIVE INFORMATION ........................................................................................................................................... 21 MEASLES DATA COLLECTION AND CASE DEFINITIONS ......................................................................................................... 21 RUBELLA DATA COLLECTION AND CASE DEFINITIONS .......................................................................................................... 23 REFERENCES ............................................................................................................................................................. 24

Measles & Rubella Reporting Protocol 2024

Surveillance data for 2024

EpiPulse Cases

Measles & Rubella Reporting Protocol 2024

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Introduction

This reporting protocol describes the reporting of 2024 measles and rubella cases to EpiPulse Cases, which is replacing TESSy.

Please note:

• Since February 2023, the reporting of diphtheria is described in a separate reporting protocol: Diphtheria, Reporting Protocol 2023, Version 1.0.

• The Vaccine Preventable Diseases (VPD) reporting protocol 2024 describes reporting of: pertussis, mumps, poliomyelitis and tetanus.

• The Invasive Bacteria Diseases (IBD) reporting protocol 2024 describes reporting of: invasive H. influenzae disease, invasive meningococcal disease, Neisseria Meningitidis isolates, and invasive pneumococcal disease.

Reporting protocols are data collection guidelines for the data managers of reporting countries and the protocol design is intended to improve user-friendliness by:

• introducing a uniform structure to make it easier for data managers to find data collection information across different subjects;

• removing information which is not relevant for data managers.

Similarly, the surveillance protocol will contain some of the generic information previously contained in the reporting protocols.

Since the data managers in reporting countries often have multiple roles, subject-specific material is sometimes distributed together with a reporting protocol. To maintain the uniform structure, this type of material is now included in Annex 2.

How to use this document

This reporting protocol provides information for the data managers of reporting countries in three main sections:

• Reporting to EpiPulse Cases which contains guidelines on how to prepare data for submission to EpiPulse Cases, deadlines, subject-specific information (e.g. new changes to metadata), and links to further information.

• Annex 1 which contains:

− the metadata set for the subject(s) covered by this reporting protocol. − a list of metadata changes for the subject(s) covered by this reporting protocol.

• Annex 2 which contains subject-specific material relevant for distribution with the reporting protocol.

Finding further information Updated links to all the schedules, documentation and training materials mentioned in this reporting protocol are included in the Documentation and Help pages, including links to:

• EpiPulse Cases Metadata

• TESSy Metadata sets and change history • EpiPulse Cases Machine to Machine Technical Documentation • Tutorials for data transformation using respectively Excel and Access

Copyright © European Centre for Disease Prevention and Control, 2024. Reproduction is authorised, provided the source is acknowledged.

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Reporting to EpiPulse Cases

In September 2024 EpiPulse Cases is expected to go live. We have built it as a replacement for TESSy, with the aim of improving the process of reporting, reviewing, and updating surveillance data.

Only Vaccine-Preventable Diseases will be reported to EpiPulse Cases in 2024, all other diseases will continue to be reported to TESSy for now.

This section provides both an overview of the EpiPulse Cases reporting process and tips on where you can find useful information.

The overall process is as follows:

• Familiarise yourself with the data collection deadlines. • Prepare (export and transform) your data. • Check that your data complies with the EpiPulse Cases metadata. • Check that your data sources are up to date. • Submit your file(s) to EpiPulse Cases.

• Finalise and approve your submission.

Checking the data collection schedule

A link to the current data collections schedule can be found in the Communication section of the ‘Documentation and Help’ pages.

Preparing data

After you have exported the data from your national database, you need to ensure that the data are in a format that EpiPulse Cases can accept. EpiPulse Cases accepts only CSV and XML files, optionally ZIP-compressed. The EpiPulse Cases metadata has been developed from the TESSy Metadata, with the aim to make only the minimal number of changes necessary, and to hopefully provide a better experience when reporting your datasets to ECDC.

Specific guidelines for measles and rubella data collection and preparation for EpiPulse Cases are provided in Annex 1 and Annex 2.

Checking metadata

The metadata defines the fields and data formats that are valid as input to EpiPulse Cases for a given subject. The EpiPulse Cases metadata includes a section that compares and highlights the changes between TESSy and EpiPulse Cases, to facilitate the transition.

As the requirements for data to be shared among ECDC Stakeholders can change, the data format changes needed to support the new requirements are identified and agreed upon between the National Surveillance Contact Points, the Network Coordination Groups and ECDC’s Disease Experts. These changes are then implemented to the EpiPulse Cases metadata.

Changes to the metadata for the subject of this reporting protocol are described in Annex 1.

It is especially important to focus on:

• Field formats Many fields require the data to be formatted in a specific way. For example, dates must be in the YYYY-MM- DD format; dates in the DD/MM/YYYY format will be rejected.

• Reference Values (the equivalent of TESSy Coded Values) Some fields only permit the use of specific values (reference values). For example, M, F or OTH are the coded values for ‘Gender’ and any other value in a ‘Gender’ field will be rejected. Please note that UNK is no longer a valid code, you may leave the field empty instead.

The EpiPulse Cases metadata Excel file contains all the definitions and rules necessary to format data correctly. The READ ME sheet of the Excel document explains how to work with the metadata. It can be downloaded from the Technical Guidelines & Tools section of the ‘TESSy Help & Docs’ pages.

Filtering the fields in the file by subject will enable you to see the fields required for your subject and the rules that apply to these fields.

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Checking your Surveillance System Descriptors Before submitting file(s), please review your data source(s) in EpiPulse (in the menu, go to ‘Report’ -> ‘Surveillance systems descriptors’) and update the information as necessary.

Complete and up-to-date data source information for each subject is important for improving the interpretation of data - each surveillance system has different features that need to be taken into account when comparing data European level.

If your data source information is out-of-date and you do not have access rights to update it, please ask your National Focal Point for Surveillance or National Coordinator to do so.

Information on data sources is available in the TESSy User Guide, as this functionality is still only available through TESSy.

Uploading your data Data is submitted through the EpiPulse web interface (in the menu, go to Report -> EpiPulse Cases).

The visual interface for reporting new data and editing existing records has remained very similar to that of TESSy. For those of you that are also responsible for reporting diseases outside of the Vaccine Preventable Diseases group, you will continue to use TESSy (under EpiPulse) in parallel with the new EpiPulse Cases, until all disease groups will have been migrated to the new tool.

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Similar to TESSy, you can Add/Update or Replace data with new uploads, using either CSV or XML files. You can

also manually create records for some diseases, and report zero cases where appropriate.

The functionality for manually editing existing records is also a familiar experience. Search for the record you wish to edit, and modify the existing information as needed.

Finalising your submission The compliance of your data with the validation rules in the metadata is checked automatically during the data upload process. In EpiPulse Cases this process is called “Technical Validation”, and it is the only step where your upload can be rejected, for severe data quality issues, such as the file format not being readable by the system, or

(one of the few) mandatory variables having missing values.

If your file has been rejected, there will be a message explaining each instance of non-compliance with the metadata that needs correcting.

The significant new feature in EpiPulse Cases is the Data Validation Report, which puts your data in the context of the already existing information for the same disease, and provides you with a detailed overview of the new data in the file you have just uploaded, as well as the resulting overall epidemiological situation painted by the existing (past) data together with the newly uploaded file(s). This means much more timely feedback on your uploads, including details on data quality, as well as outputs (graphs, charts, and tables) on some of epidemiological indicators. The Data Validation reports will evolve and grow based on your feedback in collaboration with our Disease Experts. These reports will provide a new and better way of understanding and updating the information collected at European level, and will hopefully increase the quality and timeliness of the data, while reducing workloads.

Below you can find a few screenshots of the Data Validation Report.

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1. Begin by opening the report:

2. View the report in a window, download the list of eventual validation messages, or download the report

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3. Check data completeness; both for the new upload, and in the context of historical data

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4. The downloaded report can be opened full screen for easier viewing and navigation. This is a preview of the currently developed epidemiological indicators/stratifications.

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5. After reviewing the information in the Data Validation Report you can choose to approve or reject it.

If you choose to reject it, no data will be saved in the EpiPulse Cases system, but your file will remain visible should you wish to re-download it, or resubmit it for a new Data Validation at a later date or after further checks. Please check the Epi Validation Report carefully, there might be warnings and remarks relating to possible data quality issues or potential overwriting of existing records that you should consider.

When your file has been validated and you are satisfied that all corrections have been made, please ensure prompt approval or rejection. Unapproved uploads can block the approval of other related uploads.

EpiPulse Cases Helpdesk

Email: [email protected]

Telephone number: +46-(0)8-5860 1601

Availability: 9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC holidays)

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Annex 1: Measles and Rubella metadata

This section describes:

• The measles and rubella metadata set • Changes to the measles and rubella metadata

Measles and rubella metadata

Current subject codes

Table 1 shows the subject codes (formerly ‘record types’) to be used when reporting measles and rubella

surveillance data to Epipulse Cases (EPC). Cases should be reported according to the EU Case Definition1.

We strongly encourage case-based reporting. If case-based data are not available, aggregated data

may be reported.

Table 1: Measles and rubella subject codes

Disease Case-based subject code Aggregated subject code

Measles MEAS MEASAGGR

Rubella RUBE RUBEAGGR

Comment: An aggregated format called “AGGRVPD” was available for measles and rubella since 2013. This format was the same as the “AGGR” format, but with “Vaccination Status” as an additional variable. From 2024, with the move from TESSy reporting to Epipulse Cases, aggregated subject codes MEASAGGR and RUBEAGGR have been launched.

Case-based reporting

The metadata set has variables that are common for both measles (MEAS) and rubella (RUBE), which

are summarised in Table 2. Disease-specific variables (in addition to the common variables) are

subsequently summarised in Table 3 (measles) and Table 4 (rubella).

Table 2: Case-based metadata common for both measles (MEAS) and rubella (RUBE)

Variable Description Coded value list

Age Age of patient in years as reported in the national system at the time of disease

onset.

AgeMonth Age of patient in months as reported in the national system for cases < 2 years

of age at the time of disease onset.

CaseClassification Case classification according to EU case

definition.

CONF = Confirmed

PROB = Probable POSS = Possible

DISCARDED = Discarded

ClinicalCriteriaStatus The clinical criteria are met. 0 = No 1 = Yes

ClusterID Unique identifier of the cluster as provided by the country epidemiologist.

ClusterRelated Is the case part of an outbreak/cluster? 0 = No 1 = Yes

1 EU case definitions (europa.eu)

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ClusterSetting Setting of the cluster (for

epidemiologically-linked cases).

CHILDCARE = Kindergarten or

childcare

FAM = Family MIL = Military

NOS = Nosocomial (hospital) OTH = Other

SCH = School

SPORT = Sports team UNI = University

DataSource The data source (surveillance system)

that the record originates from. The DataSource value must be a special

reference value from EpiPulse Cases

metadata.

Consult the reference values in mdDataSource dataset

DateOfInvestigation Date of start of epidemiological investigation of case by public health

authorities.

DateOfLabResult

Date when laboratory results become

available (first validated result to confirm or invalidate the case).

DateOfLastVaccination

Date of administration of the last vaccination dose - indicates the date

when the last dose of vaccine was given

before disease onset (if exact date is not known, then provide month or year).

DateOfNotification

Date when the case report is first

notified to public health authorities.

DateOfOnset

Date of onset of disease. Leave empty for asymptomatic cases.

DateOfSpecimen

Date when first specimen was collected from patient regardless of test results.

DateUsedForStatistics

The reference date used for standard

reports that is compared to the reporting period. The date used for statistics can

be any date that the reporting country

finds applicable, e.g. date of notification, date of diagnosis or any other date.

Disease The code of the disease that is being

reported.

MEAS = Measles

RUBE = Rubella

Gender Gender of the reported case. F = Female M = Male

OTH = Other

Hospitalisation History of hospitalisation due to the

disease or related complications. Hospitalisation defined as at least one

overnight stay.

0 = No 1 = Yes

ImportedStatus Definition of the origin of infection as per

Surveillance Guidelines for Measles Rubella and Congenital Rubella

Syndrome in the WHO European region.

END = Endemic case

IMP = Imported case IMPREL = Import related case

NationalRecordId Unique identifier for each record within and across the specified surveillance

system (data source) – selected and

generated by the country reporting the record.

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Outcome Information on whether the case is alive

or deceased. The death should be due to

the reported disease.

A = Alive

D = Died

PlaceOfInfection If ImportedStatus = 'IMP': The probable place of infection should be provided at

the country level. One entry for each country visited during the incubation

period of the disease. Note this is a

repeatable field.

Consult the reference values in mdLocation dataset

PlaceOfNotification Place of the first notification of the case to a regional authority. Select the most

detailed NUTS level possible.

Consult the reference values in mdLocation dataset

PlaceOfResidence Place of residence of patient at the time

of disease onset. Select the most detailed NUTS level possible.

Consult the reference values in mdLocation dataset

ReportingCountry The country reporting the record. Consult the reference values in mdLocation dataset

ResultIgG Result of serologic test for IgG (at least

a fourfold rise in specific antibodies titre or seroconversion in paired serum

samples).

EQUI = Equivocal

NEG = Negative NOTEST = Not tested

POS = Positive

ResultIgM Result of serologic test for IgM. EQUI = Equivocal NEG = Negative

NOTEST = Not tested

POS = Positive

ResultVirDetect Validated result of virus detection or isolation, by for example RT-PCR or

culture.

EQUI = Equivocal NEG = Negative

NOTEST = Not tested POS = Positive

SpecimenSero Type of specimen(s) collected for

serological analysis.

DRYBLOSP = Dry blood spot

EDTA = EDTA whole blood

NASALSWAB = Nasal swab OTH = Other

SALOR = Saliva/oral fluid SER = Serum

URINE = Urine

SpecimenVirDetect Type of specimen(s) collected. DRYBLOSP = Dry blood spot

EDTA = EDTA whole blood NASALSWAB = Nasal swab

OTH = Other SALOR = Saliva/oral fluid

SER = Serum

URINE = Urine

Status The Status value is used to provide the functionality for a record within EpiPulse

Cases database. Default value: NEW/UPDATE. If set to DELETE, the

record with the specified

NationalRecordId is deleted (invalidated) from EpiPulse Cases database, if it

exists. If set to NEW/UPDATE, the record is inserted into the database: If

the same NationalRecordId already

exists for the same data source and subject code, then the current submitted

record updates (replace) the existing one.

DELETE = Delete a previously reported record.

NEW/UPDATE = Update a previously reported record (default).

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SubjectCode SubjectCode is a reporting model for a

disease/health topic - identifies the

reporting structure and format of a record (case based or aggregate

reporting).

MEAS = Measles

RUBE = Rubella