Edastuskiri

Training programme in genomic epidemiology and public health bioinformatics – “GenEpi-BioTrain” Background of the training programme 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 Access to high-capacity, rapid turn-around time WGS services National WGS and RT-PCR National WGS and RT-PCR infrastructure projects (EU4Health) infrastructure projects Consolidation of national infrastructure (EU4Health) Cross-border capacity-building support programme 2021 2022 2023 2024 *: Either implemented directly by ECDC, or implemented by HERA/HaDEA with ECDC technical input and support 3  Updated EU regulations, November 2022 The Centre should broaden The national competent its collection and analysis of authorities ….shall data in terms of communicate the epidemiological surveillance following information…to and related special health the participating issues, progression of authorities of the epidemic situations, unusual network for epidemic phenomena or new epidemiological diseases of unknown origin, surveillance: including in third countries, molecular pathogen data and health systems data. …molecular pathogen Updated ECDC mandate Regulation on serious data, if required for cross-border threats detecting or to health and investigating serious repealing Decision No cross-border threats 1082/2013/EU to health 4 ECDC strategy for integrated genomic typing 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. ECDC strategic framework for the integration of molecular and genomic typing into European surveillance and multi-country outbreak investigations – 2019–2021 (europa.eu) 5 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 Support countries in building capacity for the routine use of WHY? genomic information for surveillance, preparedness and outbreak response Public health professionals: WHO? • w. background in computational biology/bioinformatics • w/o. specific background in bioinformatics (e.g. microbiologists and epidemiologists) WHERE? • SSI & DTU, Denmark; IP, France; RCB, Germany; HOW? THL, Finland; KUH, Sweden; WHEN? • In person & Online • 2023 - 2026 WHAT? Pathogen waves 11  Pathogen waves Year Site 1 Respiratory viruses (SARS-CoV-2, influenza) AMR (CCRE, MRSA and C. difficile) DK 2 FWD (Listeria, Salmonella, STEC) VPI (N. meningitidis, B. pertussis) FR DE 3 Tuberculosis AMR AMR DK/FR DK 4 One Health (bacteria) To be announced in 2026 FIN FR 12 Training activities per wave Interdisciplinary GenEpi and PH Exchange visits Bioinformatics Bridging the Gap Specific topics Country team 1x (2x) (3x) Virtual trainings 1 day 2 days 3 days 13 Bridging the gaps in bioinformatics (BTG) In-person • The aims are to strengthen programming knowledge and skills for use and development of bioinformatics tools 2 weeks in the public health context • Trainees have basic bioinformatics skills (beginners) 10 trainees/course • Dates: 23 February - 6 March 2026 14 Interdisciplinary genomic epidemiology and public health bioinformatics (InterD) In-person • 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 2 weeks the country team should be composed by: • three nominees from public health OR 30 trainees/course (10 country teams) • 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 15 Exchange visits for bioinformaticians In-person • The aims are to learn best practices for public health bioinformatics and to build a network for support 40 trainees x 1 week • Host institutions for 1-week visits for Block 1 trainees in 2026: 15 trainees x 2 weeks • IP – time to be decided, but no earlier than May 2026 3-5 trainees/visit • 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 16 Specific topics in genomic epidemiology and/or public health bioinformatics In-person • Topics to be defined based on trainees’ skills. Different trainings can cover different proficiency levels 3 days • Dates for 2026: • Course on SQL (or similar topic based on needs of Block 10 trainees/course 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) 17 Virtual trainings on genomic epidemiology and public health bioinformatics Virtual • Wide range of topics • Countries are welcome to express needs for specific topics 1 day • It does not need to follow the pathogen waves strictly • Approximately once per month Open to many trainees • Announced via the ECDC Learning Portal 18 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 Trainees' survey: long-term impact of GenEpi- BioTrain 67 respondents (45% response rate), one or two years after the training 20 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- • 1-week exchange visit to-face) • Topic adjusted to individual participants needs • “Crash-course” in bioinformatics • Possibilities for trainees to bring their own • 23 February – 6 March 2026 (2 weeks, data for analysis face-to-face) • Location ( participants on each): • At SSI (Copenhagen, Denmark) • Finnish institute for Health and Welfare (THL): Helsinki or Kuopio, Finland • 3-day specialized course (face-to-face) • Time to be decided, no earlier than May 2026 • Introduction to SQL (or similar topic, based on training needs of participants OR • Institut Pasteur (IP): Paris, France • Late May/early June 2026 • Autumn 2026 • At SSI (Copenhagen, Denmark) 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 Rawdata Genome assembly Command-line QC Week 1 (short/long reads Python (illumina/ & hybrid) nanopore) Pipeline Wrap- Pathogen- Data- Week 2 Phylogenies develop- up/next wave tools* sharing ment steps * Programme changes each year. Focused on methods. How the training is done Hands-on Team-work • Practicals with real data • Peer-to-peer learning • Minimal theory/lectures The trainers Each trainer team is We are responsible for 1-2 bioinformaticians days of the programme We work in teams of Experts in their fields two (minimum) 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) What participants will gain from this course: - Hands on experience for outbreak Practical experience on how investigations under a One Health approach interdisciplinary integration Enhanced knowledge and skills in the use of open source tools for integrated analysis of microbiology, and visualisation of WGS and epidemiology and epidemiological data bioinformatics can inform public health action 35 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 Generated by AI • Epidemiology of plasmids carrying carbapenemase-encoding genes 37 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 •GenEpi-BioTrain On-site course in Institut Pasteur — Wave 7 (2026) October 24th, 2025 Block 1 Wave 7 1-week exchange visits Wave 7: One Health approach 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. 40 Block 3 Wave 7 3-days face to face training Wave 7: One Health approach 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 41  Thank you for your attention! 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. Contact at Institut Pasteur: [email protected] 42  Research Group for Global Capacity Building National Food Institute Technical University of Denmark Prof. René S. Hendriksen National Food Institute, Technical University of Denmark (DTU FOOD) September 2022 DTU Food 43  Who we are ~ 30 employees; projects in Europe, Asia, Africa, … Subject matter experts in • Classical microbiology EURL- EURL-AR PH-AMR • Molecular microbiology FAO RL for AMR • Whole-genome sequencing EQAsia + WHO CC SeqAsia for AMR • Bioinformatics GenEpi • External quality assessments BioTrain SeqAfrica + • Capacity building UNSGM EQUAfrica • Among others… September 2022 DTU Food 44  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) September 2022 DTU Food 45  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 September 2022 DTU Food  Thank you for your attention 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] September 2022 DTU Food 24 OCTOBER 2025 Pasteur team Prof Sylvain Brisse & coll.  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 Research Center Borstel – Leibniz Lung Center Founded in 1947 ? Borstel Hamburg 368 Berlin Annual budget (Federal, State, Third Party) - ca. 36 Mio. Euro Member of the Leibniz Association - theoria cum praxi Nationally and internationally linked within networks 28.10.2025 | Forschungszentrum Borstel, Leibniz Lungenzentrum Research Center Borstel – Leibniz Lung Center 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 | Forschungszentrum Borstel, Leibniz Lungenzentrum RCB: Key competences Genomics/Bioinformatics Experimental Mycobacteriology Implementation team Host –Pathogen Interaction field studies Experimental field studies evolution REM-Pictures: S. Homolka, T. Gutsmann 28.10.2025 | Forschungszentrum Borstel, Leibniz Lungenzentrum RCB: Team Stefan Niemann Viola Dreyer Christian Utpatel Ivan Barilar Christiane Gerlach Matthias Merker Margo Diricks 28.10.2025 | Forschungszentrum Borstel, Leibniz Lungenzentrum THANK YOU 28.10.2025 | Forschungszentrum Borstel, Leibniz Lungenzentrum Statens Serum Institut 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) Implementation of WGS at Statens Serum Institut 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 Bug A Listeria Salmonella ESBL + CPO VRE Haemophilus VTEC Campylobacter Bioinformatic Meningococci Legionella department Bug C C. difficile supporting MRSA surveillance Gr A Streptococci Gonococci /diagnostic/research Virus units TB Covid-19 Bug E • Approx. 12,000 bacterial genomes in 2024 • Up to 15,000 SARS-CoV-2 genomes per week- > 1,100,000 in total Combining WGS with clinical and epidemiological data for surveillance and outbreak investigations Civil Registration System Key in all public health registers Whole Genome National Microbiology Sequencing National Patient Register Database • Typing • Primary care • Results of all • Resistance genes • Hospital care microbiological test • Clonal assembly performed in hospitals Surveillance and outbreak 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 GenEpi- Site visit possibilities in BioTrain Finland Finnish Institute for Health and Welfare 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 WGS, 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 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: o metagenomics: 16S and shotgun o HIV resistance typing • To provide knowledge on quality assurance and accreditation of bioinformatics pipelines Training programme in genomic epidemiology and public health bioinformatics – “GenEpi-BioTrain” Nomination and selection of training participants 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 • Operational Contact Points for Bioinformatics • Microbiology • Surveillance • Operational Contact Points (Microbiology & • FWDs and Zoonoses Epidemiology) for • AMR • Antimicrobial-resistant isolates • HAIs • Diseases Caused by Antimicrobial-Resistant • Legionnaires’ disease Microorganisms • Training • Healthcare-Associated Infections: Clostridium difficile Infections & All • National Coordinators • 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 71 How can I apply for the training programme? • Training participants should be nominated • Nomination of participants should be done by the NFPs for (Observer) National Focal Points for Microbiology (NMFPs) Microbiology ➢ GenEpi-BioTrain is a microbiology capacity building Disease- NFPs for activity specific NFPs Surveillance ➢ NMFPs have contacts to the National and sub-national laboratories Nomination of training ➢ NMFPs know where training and capacity building is participants needed most • Disease-specific NFPs and NFPs for Surveillance can contact Microbiologists, the NFPs for Microbiology to coordinate the nominations bioinformaticians,… Epidemiologists,… • NFPs for Microbiology lead the coordination of the nomination Other potential candidates,… process in their country 72 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 Choose the training block of interest (10 questions in total) 76 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 77  Training “blocks” per pathogen wave Block 1: Block 2: Block 3: Block 4: Block 5: • “Bridging the gaps” • Interdisciplinary training • Specific topics • Virtual training • Exchange visits • Exchange visits (“Country teams”) sessions • Specific topics Level: BEGINNER LEVEL BEGINNER/ BEGINNER/ BEGINNER/ BEGINNER/ ADVANCED LEVEL ADVANCED LEVEL ADVANCED LEVEL ADVANCED LEVEL Target Bioinformaticians or Per country: Bioinformaticians, Anyone who is TBD group: “bioinformaticians- 1 Bioinformatician others interested to-be” 1 Microbiologist (Microbiologists, 1 Epidemiologist epidemiologists,…) Further Candidates should Bioinformaticians should Candidates should These activities These activities info: work/plan to work have some experience; already have some will be announced will be announced directly with public No bioinformatic experience experience in separately separately health sequencing- needed for microbiologists bioinformatics related activities or epidemiologists 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 Country team • 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 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 Stockholm, 24/10/2025 Internal Reference: CS0008443 TO: National Focal Points for Microbiology, Observer National Focal Points for Microbiology CC: National Focal Points (Observer) for Surveillance, AMR, HAIs, FWD and Zoonoses, Legionnaires’ disease, Training; Operational Contact Points for Bioinformatics, Operational Contact Points (Microbiology and Epidemiology) for Antimicrobial-resistant isolates (AMRISO), Diseases Caused by Antimicrobial-Resistant Microorganisms (AMR), Healthcare-Associated Infections: All (HAI-GEN), Healthcare-Associated Infections: Clostridium difficile Infections (HAI-CDI), Campylobacter isolates, Campylobacteriosis, E. Coli isolates, Shigellosis, Verotoxigenic Escherichia Coli Infection (VTEC), Legionellosis, Listeria isolates, Listeriosis, Salmonella isolates, Salmonellosis, National Coordinators (Coordinating Competent Bodies) Subject: Nomination of participants for the ECDC training programme in genomic epidemiology and public health bioinformatics - “GenEpi-BioTrain”, Pathogen wave 7 (One Health) Dear Colleagues, I am pleased to invite you to nominate candidates for the fourth year of the training programme in genomic epidemiology and public health bioinformatics - “GenEpi-BioTrain”. The trainings in 2026 will focus on the topic of One Health (Wave 7) with a particular emphasis on antimicrobial resistance (AMR) and food- and waterborne (FWD) pathogens, including trainings on plasmid analysis and legionella. The topic for the subsequent wave (Wave 8) remains to be defined, based on need assessments and feedback from Member States and will be announced separately. Similar to previous pathogen waves, the One Health wave consists of several training blocks with different activities and durations (Annex 2). The overall objectives of the programme are to support countries strengthen their capacity in genomic epidemiology and bioinformatics for public health, while promoting interdisciplinary collaboration between bioinformaticians, epidemiologists and microbiologists. This will facilitate the routine use of genomic data in surveillance, preparedness, and outbreak response. Additionally, the trainings aim to foster cross-border collaborations and improve data sharing between countries and with ECDC. For more details, please refer to the information letter sent to EU/EEA countries, Western Balkans and Türkiye on 10 October 2025 (Annex 1). The training is designed for public health professionals with a background in computational biology and/or bioinformatics, as well as those without prior bioinformatics experience who are, or will be, involved in analysing, understanding and interpreting genomic data for public health surveillance (i.e. microbiologists, epidemiologists, professionals in public health response and surveillance). I would like to invite you as National Focal Point for Microbiology/Observer National Focal Points for Microbiology to nominate up to two participants per training block per pathogen wave from your country who could benefit from this activity. Due to limited training spaces available, nominations will not guarantee selection and participation in the course. European Centre for Disease Prevention and Control (ECDC) www.ecdc.europa.eu 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 Listed training candidates should complete their applications by filling out the GenEpi-BioTrain nomination survey by Wednesday, 26 November 2025. You as National Focal Points for Microbiology/Observer National Focal Points for Microbiology are kindly asked to provide a brief paragraph explaining the reason for selecting each candidate. This paragraph needs to be included in the candidate application. Of note: all costs for training, per diem, accommodation and travel arrangements will be covered and there will be no costs for training participants or countries. Successful participants will be notified by email no later than 19 December 2025 and will receive an invitation to an information meeting scheduled for January 2026. Yours sincerely, 28/10/2025 X Vicky Lefevre Vicky Lefevre Head of Unit SPR Signed by: Vicky Lefevre European Centre for Disease Prevention and Control (ECDC) www.ecdc.europa.eu 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 Saatja: "ECDC Microbiology" <[email protected]> Saaja: "Kairi Tõnsau" <[email protected]>, "Liisi Kink" <[email protected]> Teema: FOR ACTION - Nomination process for the Training programme in genomic epidemiology and public health bioinformatics is open – One Health wave Kuupäev: 2025-10-29 10:41 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 <https://learning.ecdc.europa.eu/enrol/index.php?id=787#section-0> 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: <https://ec.europa.eu/eusurvey/runner/GenEpiBioTrainOHWave> 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] <mailto:[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 European Centre for Disease Prevention and Control (ECDC) Gustav III:s boulevard 40, 169 73 Solna, Sweden Phone +46 (0)8 58 60 10 00 www.ecdc.europa.eu Follow ECDC on: Confidentiality Notice If you are not the intended recipient of this message, you are hereby kindly requested, to, consecutively, refrain from disclosing its content to any third party, delete it and inform its sender of the erroneous transmittal. Classified as ECDC NORMAL Annex 1: Information letter “Training programme in genomic epidemiology and public health bioinformatics GenEpi-BioTrain” 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 1/5 European Centre for Disease Prevention and Control (ECDC) Gustav den III:s Boulevard 40, 169 73 Solna, Sweden www.ecdc.europa.eu Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01 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 2/5 European Centre for Disease Prevention and Control (ECDC) Gustav den III:s Boulevard 40, 169 73 Solna, Sweden www.ecdc.europa.eu Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01 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. 3/5 European Centre for Disease Prevention and Control (ECDC) Gustav den III:s Boulevard 40, 169 73 Solna, Sweden www.ecdc.europa.eu Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01  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 4/5 European Centre for Disease Prevention and Control (ECDC) Gustav den III:s Boulevard 40, 169 73 Solna, Sweden www.ecdc.europa.eu Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01 Annex 2: Overview of the training blocks per pathogen wave 5/5 European Centre for Disease Prevention and Control (ECDC) Gustav den III:s Boulevard 40, 169 73 Solna, Sweden www.ecdc.europa.eu Phone: +46 (0)8 58 60 10 00 - Fax: +46 (0)8 58 60 10 01