Edastuskiri

Annex1and2_Training programme in genomic epidemiology and public health bioinformatics.pdf

1/5

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

ECDC Training programme

Training programme in genomic epidemiology and public

health bioinformatics – “GenEpi-BioTrain”

10 October 2025, Solna

Background:

In 2021, ECDC and the European Commission have launched several initiatives to strengthen EU/EEA Member States’ capacity for whole genome sequencing (WGS) and the detection of SARS-CoV-2 variants, including a

83 Mio EUR national infrastructure programme. In addition, the new Regulation on serious cross-border threats to health (Regulation (EU) 2022/237) and the updated ECDC mandate (as of 23 November 2022) include

provisions for the collection of “molecular pathogen data, if required, for detecting or investigating serious cross-border threats to health”.

Building on these initiatives and the updated regulatory framework, ECDC is conducting a set of support

activities, including an ambitious training programme in genomic epidemiology and public health bioinformatics (~5.2 Mio EUR) and the disease-specific implementation of WGS into EU level surveillance

and outbreak response.

The training programme in genomic epidemiology and public health bioinformatics, the “GenEpi-BioTrain”,

was initiated in January 2023 and is scheduled to continue until the end of 2026.

We will host a meeting on Friday, 24 October 2025, 13:00 - 14:30 CEST, with all relevant stakeholders to outline the upcoming training activities and provide more detailed information.

Of note: there will be no costs for training participants or countries, all costs for training, per diem, accommodation and travel arrangements will be covered.

Contractors:

The contract project managers for the GenEpi-BioTrain are Rene Hendriksen, Technical University of Denmark,

DTU (main) and Anders Rhod Larsen, Statens Serum Institut, SSI (deputy). The consortium includes DTU &

SSI (DK), Institut Pasteur, IP (FR), Research Centre Borstel, RCB (DE), Finnish Institute for Health and Welfare,

THL (FI) and Karolinska Institutet & University Hospital, KUH (SE).

Objectives and aims of the training:

The primary objectives of the training programme are to support countries strengthen their capacity in genomic epidemiology and bioinformatics for public health purposes, and to promote interdisciplinary collaboration

among bioinformaticians, epidemiologists, and microbiologists at the national level. This will facilitate the

Annex 1: Information letter “Training programme in genomic epidemiology and public health bioinformatics GenEpi-BioTrain”

2/5

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

routine use of genomic data for surveillance, preparedness, and outbreak response. Additionally, the activities

aim to enhance data sharing and collaboration between public health institutions and the ECDC, as well as

support network activities that foster cross-border cooperation.

Specific objectives are:

• To allow professionals with a background in computational biology and bioinformatics to:

o enhance and extend their skills to strengthen their capacity in the field of public health

bioinformatics.

o better understand the needs and concepts of epidemiology and public health microbiology,

with a focus on the inputs and outputs needed by their counterparts (i.e., microbiologists,

epidemiologists, and professionals in public health surveillance and response) to take rapid

and informed public health action.

• To allow professionals without a background in computational biology/bioinformatics to:

o enhance and extend their understanding of the field of public health bioinformatics.

o gain a better understanding of how bioinformatics and genomic epidemiology can be applied

in a public health context with a special focus on how traditional and genomic data can be

jointly analysed, interpreted and used for public health purposes.

o become more familiar with the concepts, formats and conventions commonly used in

microbial genomics and get a better understanding of how the structure and format of the

data can be used to streamline the data analysis process.

o better understand the concepts behind and use of the most common bioinformatic tools and

pipelines used for epidemiological analyses, including limitations and possible alternatives;

and

o gain a better overview of the basic principles, options for and best practices of data storage,

management and sharing, with a specific focus on sequencing data and associated

metadata.

Training activities in GenEpi-BioTrain, 2023 - 2026:

• Face-to-face workshops “Bridging the gaps in bioinformatics” (4 x 2 weeks; i.e. once per year) o Trainees might have no or limited background in computational biology/bioinformatics and

may have limited knowledge of public health and proficiency in bioinformatics for public

health. The forthcoming edition of this activity is scheduled for February–March 2026.

• Face-to-face workshops “Interdisciplinary genomic epidemiology and public health bioinformatics” (8 x 2 weeks; i.e. twice per year)

o Each workshop may include up to ten “country teams” of one bioinformatician, one microbiologist, and one epidemiologist to promote the collaboration of inter-disciplinary teams within the public health sector. The forthcoming edition of this activity is scheduled for April– May 2026

▪ Important note: for the upcoming “One Health” wave (Wave 7), and specifically for this activity, professionals working in the food sector are also eligible to be part of the country teams, and it is recommended to consider including such a role, which can replace the epidemiologist one. If this is not possible, the team will receive an additional assignment to ensure that all One Health aspects are fully covered and that participants can maximize the benefit of the training.

• Face-to-face training on specific topics in genomic epidemiology and/or public health bioinformatics

• Exchange visits for bioinformaticians from the public health sector in EU/EEA countries to one of the

consortium partners

o The trainee shall have clearly defined public health bioinformatics-related learning needs

and goals that the exchange visit is expected to address • Virtual information and training sessions (up to 40 x 1 day or 2 half-days; up to 10 times per year)

o Specific topics in genomic epidemiology aimed at different proficiency levels

3/5

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Structure of the training:

• The overall training activities will take place over a period of four years (2023 - 2026)

• Each year, training activities will be dedicated to two pathogen groups (“pathogen

waves”), around six months each.

• The programme of pathogen waves is as follows: o Respiratory viruses (2023/1) and antimicrobial resistant pathogens (2023/2) (already

concluded) o Food- and waterborne diseases (2024/1; Listeria, Salmonella, STEC) and vaccine-

preventable diseases (2024/2; N. meningitidis, B. pertussis) (ongoing) o Tuberculosis (2025/1) and antimicrobial resistant pathogens (2025/2). To some extent, the

pathogen wave 2025/2 will be similar in content and format to the pathogen wave 2023/2.

The decision to repeat this pathogen wave was triggered by the high number of requests we

received from Member States. o One Health, with a particular emphasis on antimicrobial resistance (AMR) and

food- and waterborne (FWD) pathogens (2026/1). The final pathogen wave (2026/2) will be defined at a later stage.

• Face-to-face training activities are going to be at the training sites either in Denmark, Germany or

France, depending on the pathogen wave

• Exchange visits for bioinformaticians can be in any of the five institutions/countries involved in the training (Denmark, Germany, France, Finland and Sweden)

• Several training activities (see above) are planned per pathogen wave; these activities build on each

other

• Since activities build on each other, selected participants will be trained for several weeks per year,

depending on availabilities

Training target groups:

• Professionals working in the public health sector as bioinformaticians, or “bioinformaticians-to-be” who are already analysing/will analyse genomic data for public health surveillance purposes. This

group may come from diverse backgrounds and fields of study, including bioinformatics, biology, computer science, biochemistry, microbial genomics, metagenomics, algorithm development,

microbiology, molecular genetics, biomedical sciences, forensic biology, comparative and molecular

bioscience, epidemiology, etc; and

• Professionals working in the public health sector who do not have a specific background in bioinformatics but need to understand and interpret genomic data for surveillance (i.e.

microbiologists, epidemiologists, professionals in public health response and surveillance).

Nomination process:

• The National Focal Points for Microbiology in coordination with National Focal Points of relevant

disease groups are kindly invited to select nominees for the training activities described above. o For the face-to-face workshop “Interdisciplinary genomic epidemiology and public health

bioinformatics”, nominees should also be selected in coordination with the National Focal

Points for Surveillance. Different persons can be selected for the role of bioinformatician in the country team, and for the other training activities.

• For each pathogen wave, ECDC will send out invitation letters to the National Focal Points specified

above, and countries should nominate and rank up to two individuals per training

• For the “Interdisciplinary genomic epidemiology and public health bioinformatics” workshop, countries should nominate and rank up to two bioinformaticians, epidemiologists and microbiologists

each for each pathogen wave

• When selecting nominees, the following should apply:

o Nominees must currently be employed in the public health sector in one of the EU/EEA countries and their work should include tasks to actively apply skills acquired as part of the

training.

4/5

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

o Nominees should be selected to ensure the maximum impact of the training on the public

health sector they serve, taking into consideration their projected period of implementation of skills at the institute, possibilities of potentially cascading training nationally and direct

use of the acquired skills. o A link to a survey will be distributed to each country which should be filled out by the

nominee (including a short version of the current CV and a short paragraph of their

motivation) o The NFPs for Microbiology should write a letter with a short paragraph to justify why the

nominee should be selected for training and how the host institute can benefit from it (the letter can be uploaded in the survey).

Selection process:

• For training activities of each pathogen wave, ECDC will send out invitations after the information

meeting on Friday, 24 October 2025 to relevant stakeholders to select nominees. After that,

nominees can submit their applications via a survey link until Friday, 28 November 2025

• ECDC will review the applications and select candidates based on professional background,

maximum impact and course availability. Notification letters will be sent to successful candidates

until 19 December 2025.

• For the Interdisciplinary genomic epidemiology and public health bioinformatics workshop, ECDC will

select one country team/country (=3 persons per country) per pathogen wave.

Of note: there will be no costs for training participants or countries, all costs for training, per diem, accommodation and travel arrangements will be covered.

Further details about the different training activities, and the nomination and selection process

will be provided during the meeting on Friday, 24 October 2025, 13:00 - 14:30 CEST.

Best regards,

the ECDC Microbiology & GenEpi-BioTrain teams

5/5

European Centre for Disease Prevention and Control (ECDC)

Gustav den III:s Boulevard 40, 169 73 Solna, Sweden Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01

www.ecdc.europa.eu

Annex 2: Overview of the training blocks per pathogen wave

Combined slides - Information meeting (24.10.2025).pdf

Background of the training programme

Training programme in genomic epidemiology and public health bioinformatics –

“GenEpi-BioTrain”

Theresa Enkirch, ECDC (Microbiology and Bioinformatics Section, ECDC)

24 October 2025

EU investments triggered by the pandemic

• ‘HERA Incubator’ (February 2021), a new EU bio-defence preparedness plan against SARS-CoV-2 variants

• Rapid detection of SARS-CoV-2 variants

• On 25 February 2021, President Ursula von der Leyen announced that the EU would provide EUR 200 M to strengthen detection and monitoring of SARS-CoV-2 variants:

• Whole genome sequencing (WGS)

• short-term support for access to high-capacity WGS services

• longer-term support for national investments into WGS infrastructure for the public health laboratories

• cross-border networking activities such as bioinformatics, standardisations, and training

2

Overview of European Commission/ECDC* activities to boost genomic epidemiology

*: Either implemented directly by ECDC, or implemented by HERA/HaDEA with ECDC technical input and support 3

2021 2022 2023 2024

Access to high-capacity, rapid turn-around time WGS services

National WGS and RT-PCR infrastructure projects

Cross-border capacity-building support programme

National WGS and RT-PCR infrastructure projects (EU4Health) Consolidation of national infrastructure (EU4Health)

4

Updated ECDC mandate Regulation on serious cross-border threats to health and repealing Decision No 1082/2013/EU

The national competent authorities ….shall communicate the following information…to the participating authorities of the network for epidemiological surveillance:

…molecular pathogen data, if required for detecting or investigating serious cross-border threats to health

The Centre should broaden its collection and analysis of data in terms of epidemiological surveillance and related special health issues, progression of epidemic situations, unusual epidemic phenomena or new diseases of unknown origin, including in third countries, molecular pathogen data and health systems data.

Updated EU regulations, November 2022

ECDC strategy for integrated genomic typing

ECDC strategic framework for the integration of molecular and genomic typing into European surveillance and multi-country outbreak investigations – 2019–2021 (europa.eu) 5

Support to multi-country outbreak investigations through sequence-based typing:

Campylobacter spp., Clostridium difficile, hepatitis A virus, Legionella spp., Listeria monocytogenes, multidrug- resistant Mycobacterium tuberculosis (MDR TB), Neisseria meningitidis, Salmonella enterica, Shiga-toxin producing E. coli, West Nile virus and emerging multi- or extensively drug-resistant (MDR or XDR) bacteria, Methicillin-resistant Staphylococcus aureus (MRSA), new pathogens or new modes of transmission of healthcare-associated or community pathogens.

EU-wide sequence-based continuous surveillance:

Influenza virus, Listeria monocytogenes, MDR TB, Neisseria meningitidis, Salmonella enterica and Shiga-toxin producing E. coli.

Sentinel surveillance or surveys:

Antibiotic-resistant Neisseria gonorrhoeae, Bordetella pertussis, carbapenem- or colistin-resistant Enterobacteriaceae, carbapenem- resistant Acinetobacter baumannii, HIV-transmitted drug resistance, and Streptococcus pneumoniae.

Whole Genome Sequencing in EpiPulse WGS surveillance expanded to new pathogens

6

ECDC Bioinformatic training needs assessment, November 2021

• Survey was sent to the NMFPs of all EU/EEA and Western Balkan countries

• Objectives

• Identify training needs for bioinformatics, microbiology and epidemiology in order to build and deliver a genomic

epidemiology training programme

• Key findings

• Two main groups: 40% low or no knowledge in bioinformatics, 40% need advanced training

• 89% interested in evolutionary biology; 93% in metagenomics for surveillance

• >60% of microbiologists want training in phylogenetic analysis

• All countries stress need for standardised data collection/sharing

• 93% of microbiologists and 89% of epidemiologists value multidisciplinary exercises

7

Cross-border capacity-building support programme in genomic epidemiology

Framework contract:

“Training programme in genomic epidemiology and public health bioinformatics”

- GenEpi-BioTrain

Aim:

Increase capacity to respond to Covid-19 pandemic

Increase capacity for genomic epidemiology for other diseases

• Value of the contract: ~5.2 Mio EUR for up to 48 months

• The kick off meeting was held in January 2023

8

Training programme in genomic epidemiology and public health bioinformatics “GenEpi-BioTrain”

Information meeting – 24 October 2025

Anders Rhod Larsen

Statens Serum Institut (SSI), Denmark

What’s in the next 10 minutes

1. Overview of the training programme

2. Pathogen waves

3. Training activities and timeline

4. Why applying for GenEpi-BioTrain activities

10

GenEpi-BioTrain at a glance

11

Support countries in building capacity for the routine use of genomic information for surveillance, preparedness and

outbreak response

Public health professionals:

• w. background in computational biology/bioinformatics

• w/o. specific background in bioinformatics (e.g. microbiologists and epidemiologists)

• SSI & DTU, Denmark; IP, France; RCB, Germany;

THL, Finland; KUH, Sweden;

• In person & Online

• 2023 - 2026

WHY?

WHERE? HOW?

WHEN?

Pathogen waves

WHO?

WHAT?

Pathogen waves

12

One Health (bacteria) To be announced in 2026

Year

1

2

3

4

Respiratory viruses (SARS-CoV-2, influenza) AMR (CCRE, MRSA and C. difficile)

FWD (Listeria, Salmonella, STEC) VPI (N. meningitidis, B. pertussis)

Tuberculosis AMR

DK

FR

DE DK/FR

Site

AMR

DK FIN FR

13

Bridging the Gap

Interdisciplinary GenEpi and PH Bioinformatics

Specific topics

Exchange visits

Virtual trainings

Country team

1 day

2 days

3 days

1x

(2x)

(3x)

Training activities per wave

Bridging the gaps in bioinformatics (BTG)

14

In-person

10 trainees/course

2 weeks

• The aims are to strengthen programming knowledge

and skills for use and development of bioinformatics tools

in the public health context

• Trainees have basic bioinformatics skills (beginners)

• Dates: 23 February - 6 March 2026

Interdisciplinary genomic epidemiology and public health bioinformatics (InterD)

15

In-person

30 trainees/course (10 country teams)

2 weeks

• The aim is to improve the knowledge of and capacity for applied

genomic epidemiology and bioinformatics for public health action

• Trainees will be “country teams”. It is up to each country to decide if

the country team should be composed by:

• three nominees from public health OR

• two nominees from public health and one from the food/veterinary

sector

In any case, the country team should be composed by a

bioinformatician, a microbiologist and an epidemiologist.

If support to nominate colleagues from the food/veterinary sector is

needed, please contact the ECDC Microbiology team

• Dates: 27 April – 8 May 2026

Exchange visits for bioinformaticians

16

In-person

3-5 trainees/visit

40 trainees x 1 week 15 trainees x 2 weeks

• The aims are to learn best practices for public health

bioinformatics and to build a network for support

• Host institutions for 1-week visits for Block 1 trainees in 2026:

• IP – time to be decided, but no earlier than May 2026

• THL - time to be decided, sometime in autumn 2026

• Trainee should express their training needs and possibly bring

their own data to analyse during the visit

• 2-week visits are announced separately

Specific topics in genomic epidemiology and/or public health bioinformatics

17

In-person

3 days

10 trainees/course

• Topics to be defined based on trainees’ skills. Different

trainings can cover different proficiency levels

• Dates for 2026:

• Course on SQL (or similar topic based on needs of Block

1 trainees): @SSI, late May/early June 2026

• Course on plasmids: @SSI, 1-3 September 2026

• Course on Legionella: IP (with contributions from EURL-

PH-LEGI are currently explored)

Virtual trainings on genomic epidemiology and public health bioinformatics

18

Virtual

Open to many trainees

1 day

• Wide range of topics

• Countries are welcome to express needs for specific topics

• It does not need to follow the pathogen waves strictly

• Approximately once per month

• Announced via the ECDC Learning Portal

Information sharing activities

• Yearly virtual meeting with ECDC national contact points (24 October 2025)

• Yearly virtual information sessions with the appointed trainees (January 2026)

• Quarterly newsletter

• ECDC Learning Portal – open to everyone!

https://learning.ecdc.europa.eu/

19

What are the benefits of attending GenEpi-BioTrain activities?

Improve individual and institutional bioinformatic skills for routine use of WGS in public health

From basic bioinformatics to tailored trainings through mixed training activities

Network creation, national and international

20

Trainees' survey: long-term impact of GenEpi- BioTrain

67 respondents (45% response rate), one or two years after the training

Details on Block 1 activities

Kirsten Ellegaard, PhD

Department of Bioinformatics Statens Serum Institut

Denmark

Block 1 content

• “Bridging the gaps in bioinformatics” (face- to-face)

• “Crash-course” in bioinformatics

• 23 February – 6 March 2026 (2 weeks, face-to-face)

• At SSI (Copenhagen, Denmark)

Block 1 content

• “Bridging the gaps in bioinformatics” (face- to-face)

• “Crash-course” in bioinformatics

• 23 February – 6 March 2026 (2 weeks, face-to-face)

• At SSI (Copenhagen, Denmark)

• 3-day specialized course (face-to-face)

• Introduction to SQL (or similar topic, based on training needs of participants

• Late May/early June 2026

• At SSI (Copenhagen, Denmark)

Block 1 content

• “Bridging the gaps in bioinformatics” (face- to-face)

• “Crash-course” in bioinformatics

• 23 February – 6 March 2026 (2 weeks, face-to-face)

• At SSI (Copenhagen, Denmark)

• 3-day specialized course (face-to-face)

• Introduction to SQL (or similar topic, based on training needs of participants

• Late May/early June 2026

• At SSI (Copenhagen, Denmark)

• 1-week exchange visit

• Topic adjusted to individual participants needs

• Possibilities for trainees to bring their own data for analysis

• Location ( participants on each):

• Finnish institute for Health and Welfare (THL): Helsinki or Kuopio, Finland

• Time to be decided, no earlier than May 2026

OR

• Institut Pasteur (IP): Paris, France

• Autumn 2026

Bridging the gaps in Bioinformatics - 4th edition

❖ We (the trainers) are also learning

❖ Course continues to evolve, but overall schedule is settled

Intended learning outcomes

❖ Process sequencing data (from raw data to genomes)

❖ Perform basic analysis supporting epidemiological investigations, including interaction with public databases

❖ Critically evaluate data quality at all steps of the process

❖ Write basic python/bash scripts, to extract relevant information from processed data

❖ Write a basic processing pipeline

Intended learning outcomes

❖ Process sequencing data (from raw data to genomes)

❖ Perform basic analysis supporting epidemiological investigations, including interaction with public databases

❖ Critically evaluate data quality at all steps of the process

❖ Write basic python/bash scripts, to extract relevant information from processed data

❖ Write a basic processing pipeline

Intended learning outcomes

❖ Process sequencing data (from raw data to genomes)

❖ Perform basic analysis supporting epidemiological investigations, including interaction with public databases

❖ Critically evaluate data quality at all steps of the process

❖ Write basic python/bash scripts, to extract relevant information from processed data

❖ Write a basic processing pipeline

The programme at a glance

Command-line

Python

Rawdata

QC

(illumina/

nanopore)

Genome assembly

(short/long reads

& hybrid)

Phylogenies Pathogen-

wave tools*

Pipeline

develop-

ment

Data-

sharing

Wrap-

up/next

steps

Week 1

Week 2

* Programme changes each year. Focused on methods.

How the training is done

Hands-on

• Practicals with real data

• Minimal theory/lectures

Team-work

• Peer-to-peer learning

The trainers

We are

bioinformaticians

Each trainer team is

responsible for 1-2

days of the programme

We work in teams of

two (minimum) Experts in their fields

Who should apply

❖ It’s a two-week course, aimed at beginners

❖ Motivation is key

➢ It takes years to become proficient

➢ We aim to get the participants started on the journey

GenEpi-BioTrain - Pathogen Wave 7, One Health (bacteria)

Details on Block 2 and Block 3 activities at SSI

Information meeting – 24 October 2025

Interdisciplinary genomic epidemiology and public health bioinformatics (Block 2) 27 April – 8 May 2026

Main topics:

• Training will focus mainly on FW pathogens

• such as Campylobacter, Salmonella, Listeria and AMR-related issues

• Plasmid-related topics in One Health (cross-species analyses, outbreak

tracking)

• Host-factor analysis to trace spill-over events Issues at the interface of food,

animals, and human health

• Other (details to be defined)

34

Interdisciplinary genomic epidemiology and public health bioinformatics (Block 2)

- Hands on experience for outbreak

investigations under a One Health approach

Enhanced knowledge and skills in the use of

open source tools for integrated analysis

and visualisation of WGS and

epidemiological data

35

Practical experience on how

interdisciplinary integration

of microbiology,

epidemiology and

bioinformatics can inform

public health action

What participants will gain from this course:

Who should apply to InterD 2026

• Bioinformaticians, epidemiologists/food specialists and

microbiologists working with FWD and AMR surveillance

• Bioinformaticians should have at least basic skills in using the

command-line and working in Linux. Beginners in bioinformatics are

still encouraged to apply but will be asked to follow some E-learnings

before the course

36

3-day course on plasmids (Block 3) 1-3 September 2026

What participants will learn in this course:

• Biology of plasmids in Enterobacterales, focusing on AMR plasmids

• Plasmid sequencing – short-reads, long- reads - and bioinformatics analyses

• Epidemiology of plasmids carrying carbapenemase-encoding genes

37

Generated by AI

3-day course on plasmids (Block 3) – Who should apply

Prerequisites:

• Ability to use the command-line and work in Linux

• Capacity for WGS by long-read data (ONT, Pacbio,..) at the home institute

• Willingness to contribute to a field not fully established

38

On-site course in Institut Pasteur — Wave 7 (2026)

•GenEpi-BioTrain

October 24th, 2025

40

Block 1 Wave 7

o June 2026 (dates to be confirmed)

o We encourage participants to bring their own genomic datasets

o The focus will be on Listeria and Salmonella, but we could also involve experts on E. coli and Yersinia.

o The content will be tailored to participants’ needs; however, based on our expertise, we could cover the following topics: • Tools and approaches for genomic taxonomy of bacterial strains • Genomic surveillance using NGS data

o Pr Sylvain Brisse will be the course director.

1-week exchange visits

Wave 7: One Health approach

41

Block 3 Wave 7

o May 2026 (dates to be confirmed)

o The focus will be on Legionella.

o Target groups: advanced bioinformaticians who works with Legionella typing/Legionella genomic surveillance

o The following topics could be covered: • Quality control methods and challenges • Data submission and analysis in national and in EU levels • Species ID • ST determination and cgMLST • SNPs detection and phylogenetics in outbreak investigation • AMR detection

3-days face to face training

Wave 7: One Health approach

42

Thank you for your attention!

Contact at Institut Pasteur: [email protected]

Acknowledgements

The creation of this training material was commissioned by ECDC to Institut Pasteur with the direct involvement of Dr Solène Cottis, Pr Sylvain Brisse and Dr Thierry Lang.

DTU FoodSeptember 2022

Prof. René S. Hendriksen

National Food Institute,

Technical University of Denmark (DTU FOOD)

43

Research Group for Global Capacity Building National Food Institute

Technical University of Denmark

DTU FoodSeptember 2022

Who we are

44

~ 30 employees; projects in Europe, Asia, Africa, …

SeqAfrica + EQUAfrica

EURL-AR

EQAsia + SeqAsia

UNSGM

FAO RL for AMR

WHO CC for AMR

GenEpi BioTrain

EURL- PH-AMR

Subject matter experts in

• Classical microbiology

• Molecular microbiology

• Whole-genome sequencing

• Bioinformatics

• External quality assessments

• Capacity building

• Among others…

DTU FoodSeptember 2022

What we work on –

on a global scale building capacity for AMR

• WHO Collaborating Centre for Antimicrobial Resistance and Foodborne Pathogens and Genomics

• FAO reference laboratory for Antimicrobial Resistance (joint IAEA program)

• European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR) in Feed, Food, Animal

Health

• Partner in the European Union Reference Laboratory for Antimicrobial Resistance (EURL-PH AMR) in

Public Health

• Program contractors for European CDC

– GenEpi-BioTrain

• UK Aid Fleming Fund regional project grantee

– SeqAfrica

– EQAsia and SeqAsia

• UNSGM grantee (bio-terrorism preparedness)

45

DTU FoodSeptember 2022

What we do

• Improve global surveillance of antimicrobial resistance (AMR) through capacity building,

implementing and operational research

• Develop and implement methods and guidelines to support building the capacity of AMR and

whole genome sequencing (WGS) surveillance

- in collaboration with the EU, EFSA, ECDC, WHO, FAO/ IAEA, UK AID/ Fleming Fund

(DHSC), UNEP, US CDC, US FDA among others

• Give scientific and technical assistance to supranational organizations, national reference

laboratories, health organizations and foundations, globally

• Perform External Quality Assessment (EQA’s) trials and training activities in detection of

infectious diseases and AMR by phenotypic and genomic methodologies

DTU FoodSeptember 2022

Prof. Rene S. Hendriksen, PhD

Head of Research Group Global Capacity Building

WHO Collaborating Centre for Antimicrobial Resistance in Food borne Pathogens and

Genomics

European Union Reference Laboratory for Antimicrobial Resistance

FAO Reference Laboratory for Antimicrobial Resistance

National Food Institute, Technical University of Denmark

[email protected]

Thank you for your attention

Prof Sylvain Brisse & coll.

24 OCTOBER 2025

Pasteur team

Institut Pasteur

➢ A non-profit foundation with recognized

charitable status, founded by Louis

Pasteur, in 1885

➢ Staff ~2700

➢ 4 missions:

1. Research

2. Public Health

3. Training

4. Research applications

➢146 research units

➢16 National Reference Centers; WHO-CCs

➢35 Core facilities (Omics, …)

PAGE 49

IP teams involved in GenEpi-BioTrain

Biodiversity and Epidemiology of Bacterial Pathogens Unit

National Reference Center for diphtheria

National Reference Center for Whooping cough and other Bordetella

infections

Genomic taxonomies of bacterial strains (BIGSdb-Pasteur)

Klebsiella genomics

Sylvain BRISSE, Head of Unit (coordinator for IP)

Solène COTTIS and Anvita BHARGAVA, Project Manager

Education Department

Monica SALA, Director of Education Department

Thierry LANG, International teaching, Education Department

Other research Units, NRCs and core facilities:

E. coli-Shigella-Salmonella, Vibrio (FX WEILL)

Meningococci / Haemophilus influenza (MK TAHA)

Hub for Bioinformatics and Biostatistics

Listeria, Legionella, Leptospira, Polio, Rabies, … experts/labs

PAGE 50

Merci

GenEpi-BioTrain: Introduction of the Host Institute

| Forschungszentrum Borstel, Leibniz Lungenzentrum28.10.2025

?Founded in 1947

Member of the Leibniz Association - theoria cum praxi

368

Annual budget (Federal, State, Third Party) - ca. 36 Mio. Euro

Nationally and internationally linked within networks

Research Center Borstel – Leibniz Lung Center

Hamburg Borstel

Berlin

| Forschungszentrum Borstel, Leibniz Lungenzentrum

Elucidation of the causes and mechanisms of chronic inflammatory lung diseases

Development of new innovative concepts for their monitoring, diagnostics, prevention and therapy

CURE tuberculosis

PREVENT asthma, COPD

28.10.2025

Research Center Borstel – Leibniz Lung Center

| Forschungszentrum Borstel, Leibniz Lungenzentrum

Genomics/Bioinformatics Experimental Mycobacteriology

Host –Pathogen Interaction

field studies

REM-Pictures: S. Homolka, T. Gutsmann

Experimental evolution

Implementation team

field studies

28.10.2025

RCB: Key competences

| Forschungszentrum Borstel, Leibniz Lungenzentrum28.10.2025

Christiane Gerlach

Viola Dreyer

Stefan Niemann Christian Utpatel

Ivan Barilar

Matthias Merker Margo Diricks

RCB: Team

| Forschungszentrum Borstel, Leibniz Lungenzentrum28.10.2025

THANK YOU

Statens Serum Institut (SSI), established in 1902, is a governmental Public Health Institut

▪ The national center for infectious disease control and national reference laboratory for both human and animal health

• NRL- Antimicrobial resistance • Hospital Acquired infections

• Preclinical devlopment of antibiotics

• (32 employees)

Statens Serum Institut

Implementation of WGS at Statens Serum Institut

2013 2014 2015 2016

Listeria

VTEC

Salmonella

Campylobacter

C. difficile

Legionella

Meningococci

VRE

ESBL + CPO

Haemophilus

Gonococci

MRSA

Gr A Streptococci

Virus

TB

20182017 2019 2020 2021 2022

Covid-19

• Approx. 12,000 bacterial genomes in 2024

• Up to 15,000 SARS-CoV-2 genomes per week- > 1,100,000 in total

Bioinformatic

department

supporting

surveillance

/diagnostic/research

units

Bug A

B u

g C

Bug E

Combining WGS with clinical and epidemiological data for surveillance and outbreak investigations

Civil Registration System Key in all public health registers

National Microbiology Database • Results of all

microbiological test performed in hospitals

Surveillance and outbreak

Whole Genome Sequencing • Typing • Resistance genes • Clonal assembly

National Patient Register • Primary care • Hospital care

Ongoing support and capacity building programs- NRL-AMR

• HERA Incubator: Direct grant for National WGS infrastructure project: “Microbe- SEQ- Denmark”

• EURGen-RefLabCap: Increasing capacity in NRL functions, focus on implementing WGS for colistin and carbapenem resistant Enterobacterales, P. aeruginosa, A. baumanii

• GenEpi-BioTrain: Improving bioinformatic capacity and make WGS data useful in public health

• EURL-PH-AMR

• Fleming Fund -Fellows program in Bangladesh

• Strategic sector collaborations with • India CDC • UPC Ukraine • Tanzania

Finnish Institute for Health and Welfare

GenEpi- BioTrain

Site visit possibilities in Finland

28/10/2025 62

Duties and roles • Finnish Institute for Health and Welfare (THL)

• State-owned expert and research institute • Promotes welfare, health, and safety of the population • Operates and serves at national level

• Department of Public Health • Monitoring health and wellbeing • Preparedness for national and cross border health threats • Expertise in planetary health

• Microbiology Unit • Expertise on bacterial, viral, and parasite infections, AMR, and microbiological water analysis • Coordination of laboratory-based surveillance of infectious diseases • Offers microbiological analysis • Participates in outbreak investigations • Reference laboratory for polio, influenza, measles, and rubella • Accreditation for several methods

28/10/2025 63

WGS-based surveillance • WGS started in 2014 for bacteria

• ̴ 2200 sequenced strains/year • sequencing in-house and outsourced

• WGS started in 2021 for viruses • Influenza A and B

• since 2021, ∼ 60-240 genomes /year • SARS-Cov-2

• in house since 2022 • 2000-12 000 genomes/year • currently about 1 000 – 1 200 genomes/year

• Other respiratory viruses • adenovirus in 2024, ∼ 50 genomes

• Illumina (MiSeq, NextSeq) and Nanopore (MinION) technology

28/10/2025 Anni Vainio, Erika Lindh 64

WGS, Bacteria

Site-visit at THL • Planned for autumn 2026, one week • For early career bioinformaticians • Objectives

• To present bioinformatic tools and pipelines used in THL • To discuss how genomic data is integreted in infectious disease surveillance in Finland

• Suggested program • One Health approach • Topics: FWD, (AMR), avian influenza, waste-water surveillance, legionella, vibriosis • Also covered: reporting, standardization, laboratory infrastructure • Program to be adjusted according to needs

• Experts: • Bioinformatics: Jani Halkilahti, Anastasia Karaeva; Heidi Putkuri, Outi Nyholm • Bacteriology: Anni Vainio, Saara Salmenlinna • Virology: Erika Lindh, Niko Tervo, Niina Ikonen • Water microbiology: Elisa Salmivirta, Eveliina Nurmi, Outi Zacheus

28/10/2025 65

Karolinska University Hospital

Christian G. Giske, Professor Clinical Bacteriology

Jan Albert, Professor Clinical Virology

Robert Dyrdak, Specialist in Clinical Microbiology/PhD

Annika Tiveljung Lindell, Head of Department/PhD

24 October 2025

Karolinska University Hospital

• One of the largest university hospitals in Europe with 1.35 million patient visits annually

• Covers almost a quarter of the population in Sweden

• Clinical microbiology has 320 employees and offers a very broad range of diagnostic areas

• Clinical microbiology also has national reference function for a number of areas such as retroviruses, enteroviruses, TBE virus, respiratory viruses (except influenza), M. tuberculosis (primary diagnostics), atypical bacterial pneumonia, susceptibility testing of anaerobes, mycology, and metagenomics

• Available trainers in bioinformatics • Sofia Stamouli, bioinformatician with expertise on viruses and metagenomics

• Lili Li, bioinformatician with expertise on viruses

• Samuel Lampa, bioinformatician with expertise on workflow systems and bacterial typing

• Mohammad Razavi, bioinformatician with expertise on bacteria and metagenomics

• Patrik Jonsson, biomedical analyst with extensive experience on analysis of data from epidemiological typing of bacteria

• Martin Vondracek, molecular biologist with long experience regarding metagenomic diagnostics

Which areas of interest do we offer?

• Whole genome sequencing of S. aureus, Enterococcus spp., E. coli, K. pneumoniae, P. aeruginosa, A. baumannii, N. gonorrhoeae and M. tuberculosis

• For M. tuberculosis we also offer genomic AST, for others mostly epidemiological characterisation

• For Candida spp. work is ongoing to establish assays

• Molecular susceptibility testing of HIV and hepatitis B virus, and herpes simplex-virus; CMV in development

• Subtyping of SARS CoV-2, enteroviruses, and hepatitis C and D viruses

• Metagenomics (16S, ITS, shotgun metagenomics)

• 3-day on-site workshop (Block 3/Wave1) SARS-CoV-2 and influenza held 7-9 Nov 2023

Workshop proposal 2026

NGS clinical diagnostics, 3-day on-site workshop

(nominations will only start in 2026, not open for pathogen wave 7)

Aim: to provide the skills necessary to implement bioinformatics pipelines into routine clinical diagnostics

Objectives:

• To provide knowledge on existing pipelines: ometagenomics: 16S and shotgun

oHIV resistance typing

• To provide knowledge on quality assurance and accreditation of bioinformatics pipelines

Nomination and selection of training participants

Training programme in genomic epidemiology and public health bioinformatics –

“GenEpi-BioTrain”

Theresa Enkirch, ECDC (Microbiology and Bioinformatics Section, ECDC) 24 October 2025

Who did we invite for this meeting and why

• National Focal Points (Observer) for

• Microbiology

• Surveillance

• FWDs and Zoonoses

• AMR

• HAIs

• Legionnaires’ disease

• Training

• National Coordinators

71

• Operational Contact Points for Bioinformatics

• Operational Contact Points (Microbiology & Epidemiology) for

• Antimicrobial-resistant isolates

• Diseases Caused by Antimicrobial-Resistant Microorganisms

• Healthcare-Associated Infections: Clostridium difficile Infections & All

• Campylobacter isolates

• Campylobacteriosis

• E. Coli isolates, Shigellosis, Verotoxigenic Escherichia Coli Infection (VTEC)

• Legionellosis

• Listeria isolates, Listeriosis

• Salmonella isolates, Salmonellosis

→ To ensure the information reaches ALL relevant stakeholders

How can I apply for the training programme?

• Training participants should be nominated

• Nomination of participants should be done by the (Observer) National Focal Points for Microbiology (NMFPs)

➢ GenEpi-BioTrain is a microbiology capacity building activity

➢ NMFPs have contacts to the National and sub-national laboratories

➢ NMFPs know where training and capacity building is needed most

• Disease-specific NFPs and NFPs for Surveillance can contact the NFPs for Microbiology to coordinate the nominations

• NFPs for Microbiology lead the coordination of the nomination process in their country

72

NFPs for Microbiology

Disease- specific NFPs

NFPs for Surveillance

Microbiologists, bioinformaticians,… Epidemiologists,…

Other potential candidates,…

Nomination of training

participants

How does the nomination process work?

• Each country will receive a separate email containing an invitation letter to nominate potential candidates for the GenEpi-BioTrain

• A survey link will be provided in the email which can be distributed to potential candidates

• Interested candidates should contact their National Focal Point for Microbiology to receive the survey link

• The email will be sent:

To: (Observer) National Focal Points for Microbiology & Alternates

CC: National Focal Points for Surveillance, Disease-specific NFPs, Disease-specific

OCPs, NFPs for Training, National Coordinators

73

How does the nomination process work?

• Potential candidates are asked to fill the survey

• Choose the pathogen wave and training block of interest

• Contact details

• Short CV

• Short statement why they chose the training and how they can benefit from it

• Short questionnaire about bioinformatics skills

• NMFP should write a short paragraph (word document/pdf; signed) to be attached to the survey before submission

• To justify why this individual should be chosen for the training

• How the host institute can benefit from their participation

74

Example: Survey for nomination

75

Example: Survey for nomination

76

(10 questions in total)

Choose the training block of interest

77

Example: Survey for nomination

Click here to upload your short CV (word, pdf)

Free text fields to be filled

Click here to upload the justification letter from your NFP

Training “blocks” per pathogen wave

Block 2: • Interdisciplinary training

(“Country teams”)

Per country: 1 Bioinformatician 1 Microbiologist 1 Epidemiologist

Bioinformaticians should have some experience; No bioinformatic experience needed for microbiologists or epidemiologists

BEGINNER/ ADVANCED LEVEL

Target group:

Block 1: • “Bridging the gaps” • Exchange visits • Specific topics

BEGINNER LEVEL

Candidates should work/plan to work directly with public health sequencing- related activities

Bioinformaticians or “bioinformaticians- to-be”

Block 3: • Specific topics

BEGINNER/ ADVANCED LEVEL

Candidates should already have some experience in bioinformatics

Bioinformaticians, others (Microbiologists, epidemiologists,…)

Block 4: • Virtual training

sessions

BEGINNER/ ADVANCED LEVEL

Anyone who is interested

These activities will be announced separately

Level:

Further info:

Block 5: • Exchange visits

BEGINNER/ ADVANCED LEVEL

TBD

These activities will be announced separately

Nominations per country

• For each pathogen wave, each country can nominate up to two potential participants per training block

• One person as backup in case someone drops out

• Nominees should be selected by the NFPs in an effort to ensure maximum impact of the training on the public health sector they serve, taking into consideration:

• their projected period of implementation of skills at the institute

• possibilities of cascading training nationally

• direct use of the acquired skills

80

Nominations per country – “InterD course”

• F2F workshop “Interdisciplinary genomic epidemiology

and public health bioinformatics” (Block 2)

• Only one country team should be nominated

• But good to have a backup person

• Country team: 1x bioinformatician, 1x microbiologist, 1x epidemiologist/food safety expert

• Professionals working in the food sector are also eligible to be part of the country teams, and it is recommended to consider including such a role, which can replace the epidemiologist one.

• If this is not possible, the team will receive an additional assignment to ensure that all One Health aspects are fully covered and that participants can maximize the benefit of the training.

• Epidemiologists/food specialists should be nominated in coordination with the NFPs for Surveillance/Disease-specific NFPs/Food Authority (if applicable)

• Only complete country teams will be considered!

81

Country team

Eligibility and selection criteria

• Nominees must currently be employed in the public health sector in one of the EU/EEA countries

• ECDC will review applications and select candidates based on

• professional background

• training needs

• maximum impact

• course availability

82

Further information on the nomination and selection process

• ECDC will send out invitations to the NFPs to select nominees on 27/28 October 2025

• Deadline for nominations/submitting the survey is Wednesday, 26 November 2025

• ECDC will send an email to NMFPs, acknowledging the receipt of the nominations

• NMFPs then have the possibility to rank potential candidates

• Review of applications: 27 November – 12 December 2025

• Notification letter to successful candidates latest 19 December 2025

• Please send your acknowledgement and confirmation of attendance by 15 January 2026

• ECDC will select one participant/country/training block/pathogen wave

• For the Interdisciplinary genomic epidemiology and public health bioinformatics workshop, ECDC will select one country team/country per pathogen wave

• If a selected participant is not able to join an activity, another person (backup) from the respective country can attend 83

Additional information

• There is a dedicated space on ECDCs Learning Portal for GenEpi-BioTrain:

Course: GenEpi-BioTrain - Genetic Epidemiology and Bioinformatics Training Programme

• Information about the training programme

• Minutes and recording of this meeting

• Virtual trainings

• Training material from the different courses

If you have any further questions, please contact us!

[email protected]

84

E-kiri.eml

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

TO: National Focal Points for Microbiology, Observer National Focal Points for Microbiology

CC: National Focal Points (and Observer) for Surveillance, AMR, HAIs, FWD and Zoonoses, Legionnaires’ disease, Training;

Operational Contact Points for Bioinformatics, Operational Contact Points (Microbiology, Epidemiology, TESSy and EpiPulse Cases) for Antimicrobial-resistant isolates (AMRISO), Diseases Caused by Antimicrobial-Resistant Microorganisms (AMR), Healthcare-Associated Infections Campylobacter isolates, Campylobacteriosis, E. Coli isolates, Shigellosis, Verotoxigenic Escherichia Coli Infection (VTEC), Legionellosis, Listeria isolates, Listeriosis, Salmonella isolates, Salmonellosis;

ECDC National Correspondents, National Coordinators of ECDC Coordinating Competent Bodies

Dear colleagues,

Thank you for your interest and active participation in the information meeting on the Training programme in genomic epidemiology and public health bioinformatics (“GenEpi-BioTrain”) on Friday, 24 October 2025. Attached you can find the presentations. The recording of the information meeting is now available on ECDCs Learning Portal: Course: GenEpi-BioTrain - Genetic Epidemiology and Bioinformatics Training Programme

As promised, we would like to send you the official invitation letter (attached) to nominate participants for training blocks one, two and three. The topic of the upcoming trainings is One Health, with a particular emphasis on antimicrobial resistance (AMR) and food- and waterborne (FWD) pathogens (Wave 7), including trainings on plasmid analysis and legionella. We would also like to emphasize that professionals working in the food sector are also eligible to be part of the country teams for the Interdisciplinary course (Block 2), and it is recommended to consider including such a role. Further information on the content and the target group for each training block and activity can be found in the presentations attached.

You can nominate up to two candidates per training block per pathogen wave. To apply, potential candidates should complete the following survey by providing their contact details, a brief CV, a statement explaining their interest in attending the training, and how they anticipate benefiting from it in their daily work. The survey also includes inquiries about their current bioinformatics skills. Additionally, the National Focal Point for Microbiology/Observer National Focal Points for Microbiology should provide a short document (Word or PDF) justifying the selection of this individual for the training and how the host institute can benefit from their participation. The potential candidate can attach this document within the survey before submission.

Link: GenEpi-BioTrain nomination survey

As discussed in the meeting, we suggest that National Focal Points for Microbiology/Observer National Focal Points for Microbiology take the lead in the nomination process and coordinate with the NFPs for Surveillance/Observers, and the NFPs of the respective disease groups.

ECDC will then select candidates that best match the criteria to participate in the training course. Please bear in mind, that as there is a limited number of participants, nominating individuals does not guarantee their participation in the training.

Of note: there will be no costs for training participants or countries, all costs for training, per diem, accommodation and travel arrangements will be covered.

When selecting nominees, the following should apply:

Nominees must currently be employed in the public health sector in one of the EU/EEA countries/Western Balkans or Türkiye, and their work should include tasks to actively apply skills acquired as part of the training.
Nominees should be selected by the NFPs in an effort to ensure maximum impact of the training on the public health sector they serve, taking into consideration:

their projected period of implementation of skills at the institute
possibilities of cascading training nationally

direct use of the acquired skills

The deadline for nominations is the 26 November 2025, EOB.

We would also like to encourage you to send us specific topics which you would like to be addressed during the 1-day (or 1-half-days) virtual trainings.

If you have any further questions, please do not hesitate to reach out to us at [email protected].

Best regards,

the ECDC Microbiology & GenEpi-BioTrain teams

Attachments:

Presentations and meeting minutes from the information meeting 24 October 2025
Invitation letter to nominate candidates for the training programme
Annex 1 and 2: Information letter and overview of training blocks

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