Infokiri

Diphtheria Reporting Protocol 2024.pdf

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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.

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• 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

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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

E-kiri.eml

Tähelepanu! Tegemist on väljastpoolt asutust saabunud kirjaga. Tundmatu saatja korral palume linke ja faile mitte avada.

ECDC NORMAL

To: National Focal Points for Surveillance (members)

cc. National Focal Points for Surveillance (alternates), National Coordinators (members/alternates)

Dear National Focal Points for Surveillance,

I’m very pleased to share with you the transition plan from TESSy to EpiPulse cases which will start in September.

Please take the time to go through the attached letter and documents and send us your feedback.

We are sharing this information simultaneously with National Focal Points for diseases and National Microbiology Focal Points.

Kind regards,

Bruno Ciancio

Head of Section Surveillance

Attachments:

Letter to NFPs on EPC go-live
EpiPulse Cases metadata for VPI and most molecular surveillance (including the changes)
PDF extract highlighting the metadata changes (from the file above)
EpiPulse Cases quick guide
Machine to Machine Communication - API Specification
VPI reporting protocols (Diphtheria, IBD, Measles and Rubella, other VPD)

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