Infokiri

Saatja: ECDC Microbiology <[email protected]>

Saadetud: 22.10.2024 19:27

Adressaat: Anastasia.Bilozor <[email protected]>; Hanna Sepp

<[email protected]>; TA Info <[email protected]>; Janne Pullat

<[email protected]>; Jevgenia Epštein

<[email protected]>; kadri.kermes

<[email protected]>; kadri.klaos <[email protected]>; Kärt

Sõber <[email protected]>; Kersti Villand

<[email protected]>; Liidia Dotsenko

<[email protected]>; Liisa Lilje

<[email protected]>; <[email protected]>; Piret Viiklepp

<[email protected]>; Regina Russanova

<[email protected]>; Signe Juhkam

<[email protected]>; tiina.kummik <[email protected]>

Teema: For action - Nomination process for the GenEpi-BioTrain (TB and

AMR) is open

Tähelepanu! Tegemist on väljastpoolt asutust saabunud kirjaga. Tundmatu

saatja korral palume linke ja faile mitte avada.

TO:

National Focal Points for Microbiology

National Focal Points for Surveillance, Tuberculosis, AMR, HAIs,

Training; Operational Contact Points for Bioinformatics, Operational

Contact Points (Microbiology and Epidemiology) for Tuberculosis,

Antimicrobial-resistant isolates (AMRISO), Diseases Caused by

Antimicrobial-Resistant Microorganisms (AMR), Healthcare-Associated

Infections: Clostridium difficile Infections (HAI-CDI), Healthcare-

Associated Infections: All (HAI-GEN); Contact Points for Operations for

EURGen-Net, ERLTB-Net members, 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, 18 October 2024.

Attached you can find the presentations and meeting minutes. The

recording of the information meeting is available on EVA ().

As promised, we would like to send you the official invitation letter to

nominate participants for training blocks one, two and three (attached).

Further information on the content and the target group for each training

block 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 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:

As discussed in the meeting, we suggest that National Focal Points for

Microbiology take the lead in the nomination process and coordinate with

the NFPs for Surveillance 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 29 November 2024, 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 .

Best regards,

the ECDC Microbiology &amp; GenEpi-BioTrain teams

Attachments:

* Presentations and meeting minutes from the information meeting 18

October 2024

* Invitation letter to nominate candidates for the training programme

European Centre for Disease Prevention and Control (ECDC)

Gustav III:s boulevard 40, 169 73 Solna, Sweden

Phone &#43;46 (0)8 58 60 10 00

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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

GenEpi-BioTrain

Minutes of the Information meeting held

on 18.10.2024

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

Introduction:

The third information meeting of the training program in Genomic Epidemiology and Public

Health Bioinformatics (GenEpi-BioTrain) was held on 18.10.2024.

The main objectives of this meeting were to provide a background for the initiation of the

training program and to inform about the upcoming training activities for Pathogen Wave 5

(Tuberculosis, TB) and Pathogen Wave 6 (Antimicrobial Resistance, AMR). The meeting

included presentations of the main activities planned for 2025, followed by a presentation of

the six partners involved in the GenEpi-BioTrain consortium, including Host institutes (SSI,

IP, RCB, THL, KUH) and Training institutes (SSI/DTU, RCB, IP). Lastly, the procedure for the

nomination process and the selection of the candidates was presented, and participants

were invited to ask questions in the Q&A session.

The agenda for the meeting is reported below.

Programme

13:00-13:05 Welcome (Anders Rhod Larsen, SSI)

o Adoption of the meeting agenda & Housekeeping

13:05-13:15 Presentation: Background of the training programme (Theresa Enkirch, ECDC)

13:15-13:25 Presentation: Training programme in genomic epidemiology and public health

bioinformatics – “GenEpi-BioTrain” (Valeria Bortolaia, SSI)

o Overview of the training programme and training activities

13:25-13:35 Presentation: “Bridging the gaps in bioinformatics” (Kirsten Ellegaard, SSI)

o Outline and learning outcomes of the course edition 2025

13:35-13:45 Presentation: Pathogen Wave 5 activities at Research Center Borstel (Christian Utpatel,

RCB)

o Overview of activities at RCB in 2025

13:45-13:50 Short break

13:50-14:10 Presentation: GenEpi-BioTrain consortium partners

o DTU o IP o RCB o SSI o THL o KUH

14:10-14:20 Presentation: Nomination and selection process (Theresa Enkirch, ECDC)

o Who did we invite and why o Who will be involved and how o Nomination and selection of training participants o Upcoming dates

14:20-14:30 Feedback and Q & A session; AOB (Anders Rhod Larsen, SSI)

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

Presentation: Background of the training program (Theresa Enkirch, ECDC)

• Theresa Enkirch welcomed new participants from the Western Balkans and Türkiye to a

training program initiated in response to the COVID-19 pandemic. The program’s origins

traced back to several EU investments aimed at enhancing biodefense preparedness and

rapid detection of SARS-CoV-2 variants. Key initiatives include the HERA incubator

launched in February 2021 and a €200 million investment announced by the EU to

bolster whole genome sequencing (WGS) capabilities.

• The European Commission and ECDC have been pivotal in providing short-term access

to high-capacity WGS services and supporting long-term national investments in WGS

infrastructure. These initiatives enhance public health laboratories, cross-border

networking, and bioinformatics standardization and training.

• ECDC’s expanded mandate in 2022 emphasized collecting molecular pathogen data to

detect and investigate serious cross-border health threats. ECDC also published a

strategy for integrated genomic typing to support multi-country outbreak investigations

and continuous surveillance through WGS.

• A training need assessment conducted in 2021 identified significant gaps in

bioinformatics knowledge and expertise among EU and Western Balkan countries. The

survey revealed a strong interest for training in evolutionary biology, metagenomics, and

phylogeny, highlighting the need for standardized data collection and multidisciplinary

team exercises.

• In response, the Genomic Epidemiology and Public Health Bioinformatics Training

Program (GenEpi-BioTrain) was launched as part of cross-border capacity-building

initiatives. With a budget of up to €5.2 million over four years, the program aims to

enhance genomic epidemiology capabilities beyond COVID-19. The program has

completed two years of training, with ongoing activities to further develop expertise in

genomic epidemiology and public health bioinformatics.

Presentation: Overview of the training program (Valeria Bortolaia, SSI)

• The program aims to train public health professionals to build capacity for the routine

use of genomic information for surveillance, preparedness, and outbreak response.

• Target participants for the training activities are public health professionals with and

without bioinformatic knowledge, depending on the type of training course.

• The concept of pathogen waves was explained: every year, the training activities will

mainly focus on two selected pathogens. Activities related to different pathogen waves

will occur at different training sites.

• The training institutes are: Statens Serum Institut (SSI) and Technical University of

Denmark (DTU), Denmark; Institut Pasteur (IP), France; Research Center Borstel (RCB),

Germany; Finnish Institute for Health and Welfare (THL), Finland; Karolinska University

Hospital (KUH), Sweden.

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

Five different types of training activities will be performed during the training program.

1) “Bridging the gaps in bioinformatics” workshop. 2) Interdisciplinary workshop in genomic epidemiology and public health bioinformatics. 3) Exchange visits for bioinformaticians. 4) Three-day training on specific topics in genomic epidemiology and/or public health

bioinformatics. 5) Virtual training in genomic epidemiology and/or public health bioinformatics on

various topics.

1) “Bridging the gaps in bioinformatics” workshop

• The aim is to strengthen programming knowledge and skills for using and developing

bioinformatics tools in the public health context.

• The participants are beginners in bioinformatics and interested in working in

bioinformatics.

• It is an in-person workshop that lasts two weeks. It is held once a year, and there are

ten trainees per course. For the year 2025, the event will be held at the SSI campus

from 24th February to 7th March 2025.

• The curriculum covers an overview of sequencing technologies, genome assembly and

analysis, QC, coding best practices, and pipeline development, among other topics.

2) Interdisciplinary workshops in genomic epidemiology and public health

bioinformatics

• This training aims to improve the knowledge and capacity for applied genomic

epidemiology and bioinformatics for public health action.

• The trainees are the ‘country teams’, where each team comprises a bioinformatician, a

microbiologist, and an epidemiologist from the same country.

• It is an in-person workshop that lasts two weeks. It is held twice a year, with 10 country

teams (30 trainees) per course.

• The curriculum is developed around cases, such as common outbreak scenarios, that

need to be solved by leveraging interdisciplinary collaboration.

• For 2025, Pathogen Wave 5 is scheduled to take place at RCB from 31st March 2025

to 11th April 2025, and Pathogen Wave 6 will be held at SSI from 27th October 2025

to 7th November 2025.

3) Exchange visits for bioinformaticians

• The aims are to learn the best practices of public health bioinformatics and build a

network of support. The visit is tailored to the individual needs of each trainee.

• It is an in-person activity, with three - five trainees per visit. Over the course of four

years, exchange visits will be held for a total of 60 trainees: 40 will attend one-week

visits, 15 will attend two-week visits, and five will attend three-week visits.

• For the one-week visits, the participants are bioinformaticians who have already

attended the ‘Bridging the gaps in bioinformatics’ workshop.

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

• A one-week exchange visit for Pathogen Wave 5 is scheduled at RCB from 15th to

19th September 2025, while another one-week exchange visit for Pathogen

Wave 6 will be held at IP from 16th June to 20th June 2025.

• The two-week and three-week visits will be announced separately.

4) Three-day specific training in genomic epidemiology and/or public health

bioinformatics

The aim is to train in specific topics selected depending upon the needs of the participants.

• The participants may have different skills, and the training curriculum can be modified to

accommodate different proficiency levels.

• It is a three-day, in-person course held three times a year. There are ten trainees per

course.

• The three-day course on SQL databases, attended by the trainees enrolled in the

‘Bridging the Gaps in Bioinformatics’ workshop, will take place at SSI from 20th to 22nd

May 2025.

• The three-day course specific to Pathogen Wave 5 will be held at RCB from 2nd to 4th

June 2025

• The three-day course specific to Pathogen Wave 6 will take place at SSI from 9th to 11th

December 2025.

5) Virtual training on genomic epidemiology and/or public health bioinformatics

• The aim is to train the interested trainees virtually for a full day or two half days.

• The topics can vary, and countries are welcome to express their needs for specific

topics.

• Virtual training is performed approximately once every month.

Information dissemination activities

• A virtual information session to present further details on the content of the training

activities to the appointed trainees is scheduled for January 2025.

• A quarterly newsletter is sent out regularly to inform about the ongoing and planned

activities of the GenEpi-BioTrain program.

• ECDC Virtual Academy (EVA) has a shared space open to everyone and course-specific

pages for the trainees.

Presentation: Bridging the gaps in bioinformatics (Kirsten Ellegaard, SSI)

• Kirsten Ellegaard introduced the third edition of the "Bridging the Gaps in Bioinformatics"

course, designed for Block 1 participants, i.e. trainees who attend this workshop, a three-

day course on SQL databases and a one-week exchange visit for bioinformaticians.

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

• The course is aimed at beginners in bioinformatics and is part of an annual training

initiative, with four planned editions in total. The course has been conducted twice already,

with positive feedback and a high number of applications.

• The course focuses on genome sequencing and analysis, helping participants to process

sequencing data from raw reads to genomes, as well as initiating basic genomic analysis.

• It is an intensive course that spans two weeks, packed with a comprehensive schedule

designed to cover both theoretical and practical aspects of bioinformatics.

• The course aims to teach participants how to handle and process sequencing data using

bioinformatics tools.

• Emphasis is placed on critically evaluating data at all stages of the analysis process and

understanding the importance of accuracy in genomic analysis.

• Participants will be introduced to the command line interface, Bash scripting, and Python

programming to equip them with the skills to handle data and build basic pipelines.

• While some genome analysis can be done without the command line, the course focuses

on providing bioinformatics skills that are critical for advanced work in the field:

• Week 1 focuses on command line basics, data quality assessment, and genome

assembly using Illumina and Nanopore data;

• Week 2 covers more advanced topics like phylogeny, pathogen-specific tools, pipeline

development, and sharing data in public repositories. The final day is reserved for

catch-up sessions and mentoring.

• The course is highly practical, with participants working on real sequence data using pre-

configured laptops (Ubuntu operating system). Approximately 90% of the course is

dedicated to hands-on exercises, with minimal lecture time (10%). Participants are

expected to be highly motivated and willing to continue their training and development

after the course.

Presentation: Overview of training activities at Research Center Borstel

(Christian Utpatel, RCB)

• Christian Utpatel briefly introduced the public health importance of TB, which causes

approximately 1.5 million deaths per year, with 10 million new infections reported

annually. TB was the deadliest infectious disease until surpassed by COVID-19 in 2022.

• Multidrug-resistant TB (MDR-TB) represents a serious threat, complicating treatment and

public health efforts. Efforts to combat TB include the WHO's End TB Strategy, which

aligns with the UN Sustainable Development Goals, aiming to eliminate TB by 2030.

• Three main training activities that will be conducted within GenEpi-BioTrain at RCB in

2025 are:

Interdisciplinary workshop in genomic epidemiology and public health

bioinformatics

• This two-week course will enhance participants' knowledge and skills in genomic

epidemiology and bioinformatics, focusing on using open-source tools for WGS, AMR,

and epidemiological data analysis.

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

• The course aims to deepen participants' understanding of how to interpret integrated

results for infectious disease prevention and control. Practical sessions will cover the

advantages and disadvantages of different diagnostics and national surveillance

sequencing strategies.

• Participants will engage in hands-on experience with targeted sequencing from primary

specimens and WGS for surveillance

One-Week Exchange Visit for Bioinformaticians

• This exchange visit will be tailored to the specific needs of five participants, focusing on

discussions before the visit to identify individual learning goals.

• Topics may include specific pipelines, cluster and outbreak detection, transmission

analysis, and the use of antibiotic resistance data.

Three-Day Course on Specific Topics

• This course will delve into advanced topics in genomic data analysis, including advanced

phylogenetic analysis and Bayesian modeling, to understand the evolution of AMR and

outbreak dynamics.

Additional presentations

• All the consortium partners (IP, RCB, SSI, THL, KUH) and the contractor, DTU, gave a

presentation explaining the organization and activities at their institutes.

• The last session was devoted to the explanation of the procedure for nomination and

selection of the participants for the GenEpi-BioTrain program. Nomination of the

participants should be done by the National Focal Points (NFP) for Microbiology.

Important dates to consider:

ECDC will send out invitation letters and the nomination template to the NFPs for

Microbiology, with the other NFPs and Operational Contact Points (OCPs) invited to this

meeting in copy, on 21st - 22nd October 2024. A survey link will be attached to the

nomination template. The invitation concerns Pathogen Wave 5 (Tb) and Pathogen Wave 6

(AMR). The deadline for nomination submission is 29th November 2024, and there will

be no extensions. The successful candidate will be notified by 20th December 2024 at

the latest. The selected candidates should confirm their acceptance of the program by 15th

January 2025.

The virtual training will take place throughout the year. All the national contact points will be

informed, and the information will be posted on EVA. No application is required to

participate in the virtual training, and the recorded sessions will be uploaded on EVA. It is

advisable to create a login on EVA so that the participants can receive automatic

notifications regarding these trainings.

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

Q & A sessions:

Q1: Will the slides/video recording be shared after the meeting?

A1: Yes, the minutes, video recordings, and slides will be uploaded to EVA and

accessible to all the participants.

Q2: Is it possible to nominate a candidate whose contract will end in April 2025 and will

likely be renewed but the information will not be available at the time of application?

A2: Yes, it is possible to nominate such a candidate; however, it is advisable to have

a backup in place if the primary candidate cannot attend.

Q3: Will the OCP for bioinformatics be informed about the nomination process?

A3: The OCP for bioinformatics will be informed, along with the National Focal Points

for Microbiology in each respective country.

Q4: Can a beginner in bioinformatics apply for an interdisciplinary workshop as part of a

country team?

A4: Yes, that is permissible.

Q5: Is applying for multiple training blocks from a single country possible?

A5: Yes, applications for multiple training blocks are permitted, as applying for one

does not exclude the possibility of applying for another.

Q6: Can a candidate re-apply if they have already applied or attended a workshop on

antimicrobial resistance (AMR)?

A6: Yes, candidates are welcome to re-apply if they haven’t been selected before;

they can also re-apply if they have already attended the course, however, it does not

make much sense to repeat the course because the content will be similar

Q7: Can a university team collaborating with public health institutions apply for the

workshop?

A7: Yes, that is permissible.

Classified as ECDC NORMAL

Anders Rhod Larsen ([email protected])

National Reference Laboratory for Antimicrobial Resistance

Statens Serum Institut

Denmark

Information meeting wave 5 & 6

Classified as ECDC NORMAL

Information meeting for ECDC contact points

ECDC Microbiology team

Contractors:

- Danish Technical University (DTU) and the consortium DTU & SSI (Statens Serum Institut, DK),

Institut Pasteur (FR), Research Centre Borstel (DE), Finnish Institute for Health and Welfare (FI) and

Karolinska University Hospital (SE)

Relevant stakeholders:

National Focal Points for Microbiology & Surveillance, Tuberculosis, AMR, HAIs, Training

Operational Contact Points for

- Bioinformatics, Tuberculosis, Antimicrobial-resistant isolates, Diseases Caused by Antimicrobial-

Resistant Microorganisms, Healthcare-Associated Infections: Clostridium difficile Infections,

Healthcare-Associated Infections

Observer National Focal Points for

- Microbiology & AMR

Contact Points for Operations for EURGen-Net, ERLTB-Net members

CC:

ECDC National Correspondents, National Coordinators of ECDC Coordinating Competent Bodies

Classified as ECDC NORMAL

Housekeeping rules

Mute your microphone

Disable camera

Post questions in the chat

Recording

Classified as ECDC NORMAL

Information meeting for ECDC contact points

ECDC NORMAL

Classified as ECDC NORMAL

ECDC team

5

Microbiology and Molecular Surveillance Group

Daniel Palm, Group leader

Theresa Enkirch, Microbiologist, project manager

Andreas Hoefer, Microbiologist

Luca Freschi, Bioinformatician

Rodrigo Filipe, Principal Expert Instructional Design/ E-Learning

Priyanka Nannapaneni, Bioinformatician

Training section

Jessica Beser, Microbiologist

Classified as ECDC NORMAL

The consortium

Contractor

National Food Institute, Technical University of Denmark (“DTU”)

Lead Rene Hendriksen

Host institutions

• Statens Serum Institut (“SSI”)- co-lead Anders Rhod Larsen

• Institut Pasteur (“IP”)-PI Sylvain Brisse

• Research Center Borstel, (“RCB”)-PI Stefan Nieman

Training institutions

• Karolinska University Hospital (“KUH”): PI Christian Giske

• Finnish Institute for Health and Welfare (“THL”):

PIs Carita Savolainen-Kopra, Saara Salmenlinna

ECDC NORMAL

Background of the training programme

Training programme in genomic epidemiology and public health bioinformatics –

“GenEpi-BioTrain”

Theresa Enkirch, ECDC (Microbiology and Molecular Surveillance Group)

18 October 2024

ECDC NORMAL

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

8

ECDC NORMAL

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 9

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)

ECDC NORMAL

10

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 NORMAL

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) 11

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 NORMAL

Whole Genome Sequencing in EpiPulse WGS surveillance expanded to new pathogens

12

ECDC NORMAL

ECDC Bioinformatic training needs assessment, November 2021

• Survey was sent to the NMFPs of all EU/EEA and Western Balkan countries (November 2021, January

2022)

• NMFPs were asked to identify 3 persons who can reply to the questions from the

institute’s bioinformatics, microbiology, and epidemiology perspective

Objectives of the survey:

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

deliver a genomic epidemiology training programme

• Assess how to promote the integration of experts with different backgrounds in multi-disciplinary

teams

13

ECDC NORMAL

Results training needs assessment (ECDC)

14

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

advanced training

• The great majority of the countries are interested in learning more about evolutionary biology

(89%) and metagenomics as a tool for surveillance (93%)

• Majority (>60%) of microbiologists would like to get more familiar with phylogenetic analysis

• All countries indicated that it would be important to know more about standards in data

collections/sharing (e.g. standardization of dates, ids, categories, etc.)

• The great majority of microbiologists (93%) and epidemiologists (89%) find it useful to

perform exercises in multi-disciplinary teams to improve the use of sequence information for

public health

ECDC NORMAL

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

15

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

Information meeting – 18 October 2024

Valeria Bortolaia, DVM, PhD

Overall Training Coordinator

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

17

GenEpi-BioTrain at a glance

18

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

19

TBD TBD

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

ECDC NORMAL

20

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

ECDC NORMAL

Bridging the gaps in bioinformatics (BTG)

21

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)

• It follows the pathogen waves (24 February - 7 March 2025)

Interdisciplinary genomic epidemiology and public health bioinformatics (InterD)

22

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”, whereby each team is

composed by a bioinformatician, a microbiologist and an

epidemiologist from a country

• It follows the pathogen waves

• Pathogen wave 5: 31 March – 11 April 2025

• Pathogen wave 6: 27 October – 7 November 2025

Exchange visits for bioinformaticians

23

In-person

3-5 trainees/visit

40 trainees x 1 week 15 trainees x 2 weeks 5 trainees x 3 weeks

• The aims are to learn best practices for public health

bioinformatics and to build a network for support

• Host institutions: IP, KUH, RCB, SSI, THL

• Trainee should express their training needs

• 1-week visits follow the pathogen waves:

• 1-week visit (Pathogen wave 5): 15 – 19 September 2025

(RCB)

• 1-week visit (Pathogen wave 6): 16 – 20 June 2025 (IP)

• 2- and 3-week visits will be announced separately

Specific topics in genomic epidemiology and/or public health bioinformatics

24

In-person

3 days

10 trainees/course

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

trainings can cover different proficiency levels

• Dates for 2025:

• SQL course (SSI): 20-22 May 2025

• Pathogen wave 5 (RCB): 2-4 June 2025

• Pathogen wave 6 (SSI): 9-11 December 2025

Virtual trainings on genomic epidemiology and public health bioinformatics

25

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

Information sharing activities

• Yearly virtual meeting with ECDC national contact points (18 October 2024)

• Yearly virtual information sessions with the appointed trainees (January 2025)

• Quarterly newsletter

• ECDC Virtual Academy (EVA) – open to everyone!

https://eva.ecdc.europa.eu/

26

27

Thank you!

We are looking forward to receiving applications from interested trainees!

Bridging the gaps in Bioinformatics Getting started on genome sequencing and analysis

Kirsten Ellegaard, PhD

Department of Bioinformatics Statens Serum Institut

Denmark

It’s the third edition of the course

❖We (the trainers) are also learning

❖Course continues to evolve, overall schedule is settled

This course is:

❖Popular

❖Much appreciated

❖Intense!

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)

Phylogenie

s

Pathogen-

wave tools*

Pipeline

develop-

ment

Data-

sharing

Wrap-

up/next

steps

Week 1

Week 2

* Brief! (Two pathogen-waves covered in one day)

It’s a “hands-on” course

❖ Laptops with data and software installed (Linux)

❖ Working on real data

❖ 90% practicals, 10% lectures

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

2025 Trainings at the Research Center Borstel

GenEpi-BioTrain Pathogen WAVE 5 Tuberculosis

18.10.2024

Tuberculosis

37

The causative agent:

• Member of the Mycobacterium tuberculosis complex (MTBC)

• 99,5 % sequence identity

• Genome: 4.4 million base pairs

• 4000 genes; 40 with known resistance mediating function

• More than 400 known resistance conferring mutations

Interdisciplinary genomic epidemiology and public health bioinformatics – Two Week course

Date: 31.3.25-11.4.25

• Enhance participants’ knowledge and skills in genomic epidemiology and bioinformatics

• Further participants’ knowledge and use of open source tools for integrated analysis and visualisation of WGS and resistance and epidemiological data

• Support participants’ deeper understanding of how the interdisciplinary interpretation of such integrated results can inform infectious disease prevention and control

38

One-week exchange visit for bioinformaticians

Date: 15.9.25-19.9.25

The content is tailored to individual learning needs and wishes.

39

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CAS E 1

CAS E 2

CAS E 4

CAS E 3

Three-day course on specific topics

Date: 2.6.25-4.6.25

The content can vary to cover different proficiency levels of the trainees.

• Advanced phylogenies including bayesian modeling*

• Detailed outbreak inspections for public health decision making*

40 *Examples only and content is to be decided

Classified as ECDC NORMAL

TRAINING PROGRAMME IN GENOMIC EPIDEMIOLOGY

AND PUBLIC HEALTH BIOINFORMATICS

“GENEPI-BIOTRAIN”

Consortium partners

DTU FoodSeptember 2022 Classified as ECDC NORMAL

Prof. René S. Hendriksen

National Food Institute,

Technical University of Denmark (DTU FOOD)

2

Information meeting for the training programme in

genomic epidemiology and public health

bioinformatics – “GenEpi-BioTrain”. 20 October 2023

Research Group for Global Capacity Building National Food Institute

Technical University of Denmark

DTU FoodSeptember 2022 Classified as ECDC NORMAL

Staff - students, Technical University of Denmark - DTU

3

Human resources – FTEs (incl. faculty)

5,824 13,414 Full-time students

18% 39%

43%

30% 30%

40%

PhD students

in support functions

researchers and educators (VIP)

BSc Eng

MSc Eng

BEng

Approx. 300 full-time staff under DTU Food

DTU FoodSeptember 2022 Classified as ECDC NORMAL

DTU National Food Institute conducts

research into and disseminates

sustainable and value-creating

solutions in the area of food and

health for the benefit of society.

DTU National Food Institute’s vision

is to make a difference by generating

future prosperity through research

into food and health.

DTU National Food Institute:

• Prevents disease and promotes

health

• Creates sustainable technological

solutions

• Develops new and better food

products for a growing population.

At the forefront of healthy, safe and sustainable solutions

DTU FoodSeptember 2022 Classified as ECDC NORMAL

Interdisciplinary cooperation

The National Food Institute’s tasks

are carried out in a unique

interdisciplinary cooperation between

the disciplines of:

5 5

Technology

Microbiology

Chemistry

Epidemiology

Modeling

Nutrition

Toxicology

DTU FoodSeptember 2022 Classified as ECDC NORMAL 6

Research at DTU Food

The Research Group for Global Capacity

Building is one of 14 units within the Institute

DTU FoodSeptember 2022 Classified as ECDC NORMAL

We work on a global scale building capacity for AMR

We are:

• FAO reference laboratory for Antimicrobial Resistance

• European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR)

• WHO Collaborating Centre for Antimicrobial Resistance and Foodborne Pathogens and

Genomics

• Program contractors for EC (HaDEA)/ European CDC

– EARS-net EQA provider

– EURGEN-RefLabCap

– FWD-AMR-RefLabCap

– GenEpi-BioTrain

• UK Aid Fleming Fund regional project grantee

– SeqAfrica

– EQAsia and SeqAsia (WGSAsia)

• UNSGM grantee

7

DTU FoodSeptember 2022 Classified as ECDC NORMAL

What we do in the Global Capacity Building

We work to:

• Strengthen the ability for and increase the quality of the global

monitoring of antimicrobial resistance (AMR) by implementing research

• Develop and implement methods and guidelines to support building the

capacity of AMR and WGS surveillance

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

UNEP, ECDC, EFSA, 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

8

Project size represents total grant amount

Collaboration

DTU FoodSeptember 2022 Classified as ECDC NORMAL

Whom we primarily work with and stakeholders

9

EURL

SeqAfrica

EQAsia

EURGEN

RefLabCap

FWD-AMR

RefLabCap

GenEpi

BioTrain UNSGM

FAO RL

WHO CC

EQAfrica

EARsNet

https://upload.wikimedia.org/wikipedia/en/thumb/5/5d/ECDC_logo.svg/1153px-ECDC_logo.svg.png

https://upload.wikimedia.org/wikipedia/en/thumb/5/5d/ECDC_logo.svg/1153px-ECDC_logo.svg.png

DTU FoodSeptember 2022 Classified as ECDC NORMAL

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

FAO Reference Center

for Antimicrobial Resistance

11 | Institut Pasteur –GenEpi-BioTrain Classified as ECDC NORMAL

The Institut Pasteur

Thierry LANG

International Relationships

Education Department

12 | Institut Pasteur –GenEpi-BioTrain Classified as ECDC NORMAL

 A non-profit foundation with

recognized charitable status, founded

by Louis Pasteur, 130 years ago/

 Staff 2500

 Our ambition is to advance research at

the service of human health and medical

progress for everyone.

 We have 4 missions:

1. Research

2. Public Health

3. Training

4. Research applications

Who We Are

13 | Institut Pasteur –GenEpi-BioTrain Classified as ECDC NORMAL

Strategic Priorities

Environmenta

l transitions

and Health

Infectious

diseases

threats

Origin of

diseases

Global ambition : to give new impetus to basic research and increase the

impact of research on health challenges

➢ 146 research units

➢ 13 Departments

➢ The Education Center

Basic research

Information

Knowledge

Translation/CR

Technology

Wealth

Health

➢ 16 Natl Reference Centers

➢ 7 WHO collaborative centers

➢

➢ Hub for bioinformatics

and BioStatistics

4 Priority Scientific Areas

➢ 35 Core technologies center

(Omics, microscopy, …) Biological Resources Center

Heath and

diseases at

the extremes

of life

14 | Institut Pasteur –GenEpi-BioTrain Classified as ECDC NORMAL

Education center at Institut Pasteur www.pasteur.fr/education

www.pasteur.fr/education

 Major focus on Public Health topics initial and

continuing education

 Out of the 40 courses

 20 courses on Public Health topics (Medical

Mycology, Tuberculosis, Vaccinology, Insect Vectors

and Pathogens, etc)

 14 courses are part of the Pasteur-Cnam-EHSP

Specialized Master in Public Health

 9 courses will be part of the NEW One Health –

Emerging Infectious Diseases (1H-EID) Graduate

School

MOOCs

 Theoretical

 Practical

face-to-face

Pasteur

COURSE

Pasteur

MOOCs

 Broadcasted on Fun platform

 Around 4 - 6 chapters

 25-30 videos (with MCQs)

 Online forum for scientific debates

 Live sessions

15 | Institut Pasteur –GenEpi-BioTrain Classified as ECDC NORMAL

Pasteur participants 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

Solène Cottis, Project Manager

Education Department Monica SALA, Director of Education Department

Thierry LANG, International teaching, Education Department

Hervé Waxin, Education Center

Murielle Almoussa, Education Center

Enteric Bacterial Pathogens Unit Natl Ref Centers for E. coli-Shigella-Salmonella,

WHO Collaborative Center for the typing and antibiotic resistance of Salmonella

François-Xavier WEILL, Head of Unit

Invasive Bacterial Infections Unit Hosts the National Reference Center for meningococci and Haemophilus influenza

WHO Collaborative Center for meningitis

Muhammed-Kheir TAHA, Head of Unit

Hub of Bioinformatics and Biostatistics Department of Computational Biology

Center for Computing Resources and Research

Marie-Agnès Dillies, Head of Platform

Hervé Menager, Head of Platform

Classified as ECDC NORMAL

GenEpi-BioTrain Tuberculosis: Introduction of the Host Institute

by Christiane Gerlach

| Forschungszentrum Borstel, Leibniz Lungenzentrum Classified as ECDC NORMAL22.10.2024

379

Forschungszentrum Borstel, Leibniz Lungenzentrum (1947)

Germany

Research Funding:

28 Mill Base Budget

8 Mill Third-Party

| Forschungszentrum Borstel, Leibniz Lungenzentrum Classified as ECDC NORMAL

RCB focuses on chronic

inflammatory lung diseases

such as asthma, chronic

obstructive pulmonary

disease (COPD) and

allergies, as well as

tuberculosis and other infection-related

inflammations of the lung. The overriding goal of the

basically interdisciplinary and translational research

activities is to elucidate the causes and

mechanisms of infectious and non-infectious

chronic inflammatory diseases of the lung in order

to derive new innovative concepts for their

prevention, diagnosis and therapy.

Nationally/Internationally involved in:

• The German Health Centers:

• German Center of Infectious

Diseases

• German Center of Lung Disease

• Large international Alliances:

• ERA4TB and UNITE4TB for the

development and clinical testing of

new TB drugs

| Forschungszentrum Borstel, Leibniz Lungenzentrum Classified as ECDC NORMAL

Genomics/Bioinformatics Experimental Mycobacteriology

Host –

Pathogen

Interaction

field studies

REM-Pictures: S. Homolka, T. Gutsmann

Experimental

evolution

Implementation team

field studies

22.10.2024

| Forschungszentrum Borstel, Leibniz Lungenzentrum Classified as ECDC NORMAL22.10.2024

EXCHANGE

Training in laboratories

Interdisciplinary work

Workshops

Continuing education

CAPACITY BUILDUNG

Wet lab and bioinformatic training courses

Maintaining and expanding competence • in diagnosis and therapy • in sequencing technology • In bioinformatic data analyses Documentation Transfer

| Forschungszentrum Borstel, Leibniz Lungenzentrum Classified as ECDC NORMAL22.10.2024

| Forschungszentrum Borstel, Leibniz Lungenzentrum Classified as ECDC NORMAL

Stefan Niemann:

Head of Molecular and Experimental Mycobacteriology Group

Director of the Program Area Infections

Head of the National and Supranational Reference Laboratory for Mycobacteria Borstel

Expertise: Molecular Biology, Molecular/Genome characterization of

M. tuberculosis complex strains and other pathogens

Christian Utpatel:

Research associate in Molecular and Experimental Mycobacteriology Group

Co-lead of NGS platform (1x Illumina NextSeq2000, 1x NextSeq100, 1x MiSeq,

1x MiniSeq, 1x iSeq100, 2x Oxford Nanopore MinION, 1x PacBio Sequel II)

with an annual sample throughput of ~10,000.

Expertise: Molecular Microbiology, Next Generation Sequencing (NGS) technology

and bioinformatics analysis to elucidate antibiotic resistance, transmission and

population structure of Mycobacterium tuberculosis complex isolates,

atypical mycobacteria and other selected pathogens Virtual training: “Introduction to bioinformatic analysis of SARS-CoV-2 amplicon sequencing data’’

Ivan Barilar:

Research associate in Molecular and Experimental Mycobacteriology Group

Expertise: Molecular Biology, Bioinformatics, NGS data analysis, Population Genetics Virtual training: “Introduction to bioinformatic analysis of SARS-CoV-2 amplicon sequencing data’’

22.10.2024

| Forschungszentrum Borstel, Leibniz Lungenzentrum Classified as ECDC NORMAL

Viola Dreyer:

Research associate in Molecular and Experimental Mycobacteriology Group

Expertise: Bioinformatics, implementation and developing of pipelines

for the analysis of NGS data for in-house analysis and development

of browser based pipelines for the automated analysis and resistance

prediction of MTBC strains (e.g. PhyResSE)

Matthias Merker:

Head of Evolution of the Resistome Group

Expertise: Exploration of drug interaction and bacterial genome evolution,

evolution of drug resistance, analysis of worldwide expansion of multidrug

resistant TB strains,TB strain identification, sequencing, genotyping

Christiane Gerlach

Scientific Project Manager in Molecular and Experimental Mycobacteriology Group

Expertise: Coordination of research and implementation projects

(application, contracting, reports, financing), worldwide management of the implementation

of modern genome-based diagnostics for the detection of multidrug-resistant tuberculosis,

establishing and expanding national and international partnerships and networks

22.10.2024

| Forschungszentrum Borstel, Leibniz Lungenzentrum Classified as ECDC NORMAL

Niemann and Merker groups

22.10.2024

| Forschungszentrum Borstel, Leibniz Lungenzentrum Classified as ECDC NORMAL

Thank you for your attention

22.10.2024

Classified as ECDC NORMAL

120 years of Statens Serum Institut

Statens Serum Institut (SSI) was established in 1902

▪ Governmental Public Health Institut under the Danish Ministry of Health

▪ The national center for infectious disease control and national

laboratory for both human and animal health

▪ Preparedness organisation - Infectious diseases

• Covid-19

• Foodborne disease outbreaks

• Antimicrobial resistance

• Vaccine program

▪ Danish National Biobank & Biomarkers

• Total 22 million biological samples

- screening of all newborns since 1982 (3 millions blood

samples)

Classified as ECDC NORMAL

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. 11,000 bacterial genomes in 2022

• Up to 15,000 SARS-CoV-2 genomes per week- > 800,000 in total

Classified as ECDC NORMAL

Optimized bioinformatic work flow

Team of 11

bioinformatician/computerscience

people servicing all surveillance

/diagnostic/research units

Bug A

B u

g C

Bug E

Classified as ECDC NORMAL

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

Classified as ECDC NORMAL

Capacity building programs

HERA Incubator: Direct grants for National WGS and RT-PCR

infrastructure projects: “SSI-SEQ”

EURGen-RefLabCap and FWD AMR-RefLabCap: Increasing capacity in

NRL functions, focus on implementing WGS for specific organisms

colistin and carbapenem resistant Enterobacterales, P. aeruginosa, A.

baumanii and Salmonella and Campylobacter

GenEpi-BioTrain: Improving bioinformatic capacity and make WGS data

useful in public health

Fleming Fund

- Fellows program in Bangladesh

- SEQ-Africa

Classified as ECDC NORMAL

Staff presentation at SSI and DTU

Valeria

Camilla Jette Lina Birgitte Lone

Camilla

AndersRene

Jette

Marianne Laila Deepak

KirstenHenrik Marc

Susanne

Finnish Institute for Health and Welfare

GenEpi- BioTrain

Site visit possibilities in Finland

22/10/2024 32

Classified as ECDC NORMAL

Duties and roles • 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

22/10/2024 33

Classified as ECDC NORMAL

22/10/2024 34

Classified as ECDC NORMAL

WGS-based surveillance • WGS started in 2014 for bacteria

• ̴ 2200 sequenced strains/year

• Sequencing in-house and outsourced

• WGS started in 2021-22 for viruses • Influenza A and B, since 2022, ∼ 60-240

genomes /year

• SARS-Cov2

• 2022, previously outsourced, ∼ 12 000 genomes

• week 40/2023-20/2024, >3000 genomes • Enterovirus, incl. polio, ∼ 20, since 2023

• Adeno outbreak investigation, ∼ 30, 2024

• MiSeq, NextSeq, MinIon 22/10/2024 Anni Vainio, Niina Ikonen 35

WGS, Bacteria

Classified as ECDC NORMAL

WGS based surveillance (or outbreak investigation) • Listeria, STEC, Salmonella, Vibrio, (Yersinia, Campylobacter, C. perfringens,

Shigella)

• MRSA, VRE, CPE, (ESBL)

• N. meningitidis, H. influenzae, S. pneumoniae

• (S. pyogenes)

• Legionella

• C. difficile

• M. tuberculosis

22/10/2024 Firstname Lastname 36

Classified as ECDC NORMAL

Viral WGS-based surveillance and outbreak investigation • Influenza A and B amplicon sequencing

• SARS-CoV-2 amplicon sequencing

• Polio- and other enterovirus sequencing

• Target enrichment sequencing for respiratory and emerging viruses

• Metagenomics

• Waste water surveillance for SARS-CoV-2, influenza A and B, RSV

22/10/2024 37

Classified as ECDC NORMAL

Site-visits at THL • August 2023

• Bioinformaticians, 5 persons, one week

• Focus on influenza, SARS-CoV2, waste water

• Also covered: WGS-surveillance for bacteriology and virology, reporting, standardization, laboratory infrastructure

• Possibilities • FWD, VPD, AMR, respiratory viruses, waste-water

• Program to be adjusted according to needs

22/10/2024 38

Classified as ECDC NORMAL

Experts

22/10/2024 39

Virology Niina Ikonen Erika Lindh Niko Tervo

Bacteriology Anni Vainio Ulla-Maija Nakari Saara Salmenlinna

Bioinformatics Pilvi Hepo-oja Jani Halkilahti

Classified as ECDC NORMAL

Karolinska University Hospital

Christian G. Giske, Professor Clinical Bacteriology

Jan Albert, Professor Clinical Virology

Annika Tiveljung Lindell, Head of Department

24 February 2023

Classified as ECDC NORMAL

Karolinska University Hospital

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

• The population of the Stockholm region is 2.4 million, almost a quarter of the population of Sweden, and the laboratory catchment area includes six of the seven emergency hospitals in the region and approximately half of the general practitioners

• Clinical microbiology is one of the departments belonging to Medical Diagnostics Karolinska (MDK)

• 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, respiratory viruses (except influenza), M. tuberculosis (primary diagnostics), atypical bacterial pneumonia, susceptibility testing of anaerobes, and mycology

Classified as ECDC NORMAL

Bioinformatics capacity

• Among trainers available in this project are • Sofia Stamouli, bioinformatician with expertise on viruses and metagenomics

• Lili Li, bioinformatician with expertise on viruses

• 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

Classified as ECDC NORMAL

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

• Subtyping of SARS CoV-2

• Metagenomics (16S, ITS, shotgun metagenomics)

Classified as ECDC NORMAL

Karolinska University Hospital Solna and Huddinge

ECDC NORMAL

Nomination and selection of training participants

Training programme in genomic epidemiology and public health bioinformatics –

“GenEpi-BioTrain”

Theresa Enkirch, ECDC (Microbiology and Molecular Surveillance Group) 18 October 2024

ECDC NORMAL

Who did we invite for this meeting and why

• National Focal Points for

• Microbiology

• Surveillance

• Tuberculosis

• AMR

• HAIs

• Training

• Observer National Focal Points for

• Microbiology

• AMR

• Contact Points for Operations for EURGen-Net

• ERLTB-Net members

• ECDC National Correspondents

• National Coordinators

2

• Operational Contact Points for Bioinformatics

• Operational Contact Points (Microbiology & Epidemiology) for

• Tuberculosis

• Antimicrobial-resistant isolates

• Diseases Caused by Antimicrobial-Resistant Microorganisms

• Healthcare-Associated Infections: Clostridium difficile Infections

• Healthcare-Associated Infections: All

→ To ensure the information reaches ALL relevant stakeholders

ECDC NORMAL

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

3

NFPs for Microbiology

Disease- specific NFPs

NFPs for Surveillance

Microbiologists, bioinformaticians,… Epidemiologists,…

Other potential candidates,…

Nomination of training

participants

ECDC NORMAL

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

4

ECDC NORMAL

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

5

ECDC NORMAL

Example: Survey for nomination

6

ECDC NORMAL

Example: Survey for nomination

7

(10 questions in total)

Choose the pathogen wave(s) and training block of interest

ECDC NORMAL

8

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

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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

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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

• F2F workshop “Interdisciplinary genomic epidemiology

and public health bioinformatics” (Block 2)

• For each pathogen waves, two country teams can be nominated

• Each country team should consist of one bioinformatician, one microbiologist, one epidemiologist

• Only complete country teams will be considered!

• Epidemiologists should be nominated in coordination with the NFPs for Surveillance/Disease-specific NFPs

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Country team

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Nominations per country

• 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

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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

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Further information on the nomination and selection process

• ECDC will send out invitations to the NFPs to select nominees on 21/22 October 2023

• Deadline for nominations/submitting the survey is 29 November 2024

• 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: 2 December – 13 December 2024

• Notification letter to successful candidates latest 20 December 2024 (Please send your acknowledgement and confirmation of attendance by 15 January 2024)

• 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

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Additional information

• There is a dedicated space on EVA (ECDC Virtual Academy) for the GenEpi-BioTrain: GenEpi-BioTrain Common (europa.eu)

• 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]

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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

Stockholm, 16/10/2024

Internal Reference: CS0004288

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

CC: National Focal Points for Surveillance, Tuberculosis, AMR, HAIs, Training; Operational Contact Points for Bioinformatics, Operational Contact Points (Microbiology and Epidemiology) for Tuberculosis, Antimicrobial-resistant isolates (AMRISO), Diseases Caused by Antimicrobial-Resistant Microorganisms (AMR), Healthcare-Associated Infections: Clostridium difficile Infections (HAI-CDI), Healthcare- Associated Infections: All (HAI-GEN); Observer National Focal Points for AMR, Contact Points for Operations for EURGen-Net, ERLTB-Net members, ECDC National Correspondents, National Coordinators of ECDC Coordinating Competent Bodies

Subject: Nomination of participants for the ECDC training programme in genomic epidemiology and public health bioinformatics - - Pathogen wave 5 (TB) and 6 (AMR)

Dear Colleagues,

I am pleased to invite you to nominate candidates for the third year of the training programme in genomic epidemiology and public health bioinformatics - - The trainings in 2025 will focus on two pathogen tuberculosis (TB) and antimicrobial-resistant pathogens (AMR; CCRE, MRSA, ). To some extent, wave 6 will be similar in content and format to wave 2. The decision to repeat this pathogen wave was triggered by the high number of requests we received from Member States. Each wave consists of several training blocks with different activities and durations (Annex 1). 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 20 September 2024 (Annex 2).

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).

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

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.

Listed training candidates should complete their applications by filling out the GenEpi-BioTrain nomination survey by Friday 29 November 2024. 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 20 December 2024 and will receive an invitation to an information meeting scheduled for January 2024. Yours sincerely,

21/10/2024

X Vicky Lefevre Vicky Lefevre Head of Unit Public Health Functions 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

Annex 1: Overview of the training blocks per pathogen wave

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

Training programme in genomic epidemiology and public health bioinformatics, the GenEpi-BioTrain

Background: ECDC and the European Commission have launched a number of activities to help strengthen EU/EEA

-CoV-2 variants, including a 83 Mio EUR national infrastructure programme. In addition, the new Regulation on serious cross-border threats to

serious cross-border t

Currently, 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 GenEpi- BioTrain

We will host a meeting on 18 October 2024, 13:00-14:30 CEST, with all relevant stakeholders to further outline training activities and provide more detailed information. A meeting invitation will be sent out soon.

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).

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

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 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-

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

Face-to-

o one bioinformatician, one microbiologist, and one epidemiologist to promote the collaboration of inter-disciplinary teams within the public health sector

Face-to-face training on specific topics in genomic epidemiology and/or public health bioinformatics (16 x 3 days; i.e. 3-4 times per year)

Exchange visits for bioinformaticians from the public health sector in EU/EEA countries//Western Balkans/Türkiye to one of the consortium partners (40 x 1 week (10 x per year), 15 x 2 weeks (3-4 x per year), 5 x 3 weeks (1-2 x per year))

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

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

Structure of the training: The overall training activities will be over a period of four years

The planned pathogen waves are as follows:

o Respiratory viruses (2023/1) and antimicrobial resistant pathogens (2023/2)

o Food- and waterborne diseases (2024/1; Listeria, Salmonella, STEC) and vaccine- preventable diseases (2024/2; N. meningitidis, B. pertussis)

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 Depending on training needs and demands, other pathogen waves can be repeated on 2026/1 and 2026/2 and/or additional pathogen waves can be included (e.g. STIs)

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 -to-

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/Observer National Focal Points for

Microbiology in coordination with National Focal Points/Observer of relevant disease groups are kindly invited to select nominees for the training activities described above.

o For the face-to-

National Focal Points/Observer 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/Observer specified above, and countries should nominate and rank up to two individuals per training

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/Western Balkans/Türkiye, and their work should include tasks to actively apply skills acquired as part of the training.

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

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, 18 October 2024 to relevant stakeholders to select nominees. After that, nominees can submit their applications via a survey link until Friday, 29 November 2024

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 20 December 2024

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 18 October 2024, 13:00-14:30 CEST.

Best regards,

the ECDC Microbiology & GenEpi-BioTrain teams