Edastuskiri
| Dokumendiregister | Terviseamet |
| Viit | 8-2/25/8774-1 |
| Registreeritud | 31.10.2025 |
| Sünkroonitud | 03.11.2025 |
| Liik | Sissetulev dokument |
| Funktsioon | 8 Nakkushaiguste seire, ennetuse ja tõrje korraldamine |
| Sari | 8-2 Nakkushaiguste epidemioloogiaalane riigiväline kirjavahetus |
| Toimik | 8-2/2025 |
| Juurdepääsupiirang | Avalik |
| Juurdepääsupiirang | |
| Adressaat | ECDC Microbiology |
| Saabumis/saatmisviis | ECDC Microbiology |
| Vastutaja | Kärt Sõber (TA, Peadirektori asetäitja (1) vastutusvaldkond, Nakkushaiguste epidemioloogia osakond) |
| Originaal | Ava uues aknas |
Failid
|
Tähelepanu! Tegemist on väljastpoolt asutust saabunud kirjaga. Tundmatu saatja korral palume linke ja faile mitte avada. |
Dear Colleagues,
Please find attached the eleventh GenEpi-BioTrain quarterly newsletter.
Last week, we held our annual information meeting to share key updates and information on the upcoming Pathogen Wave 7 with stakeholders from various European countries.
Following the meeting, nominations for the upcoming training are now open. In case you missed the meeting, you can find the recording on ECDCs Learning Portal: Course: GenEpi-BioTrain - Genetic Epidemiology and Bioinformatics Training Programme
We would also like to take this opportunity to remind everyone interested in longer-term training opportunities in public health microbiology or epidemiology that today is the final day to apply for ECDC’s Fellowship Programme. You can find more information and the application link at the end of this email.
Kind regards,
The ECDC Microbiology & GenEpi-BioTrain teams
---------------------------------------------------------------------------------------------------------------------------------------------------
Applications for the ECDC Fellowship now open!
Do you know anyone interested in a career in field epidemiology or public health microbiology? This is an incredible opportunity to gain hands-on training and experience in communicable disease prevention, outbreak investigation, and public health response across the EU/EEA and beyond. Please help in spreading the word about the call for applications for the ECDC Fellowship.
About the Fellowship:
The programme offers a two-year practical training with placement at one of the accredited EPIET or EUPHEM training sites outside the fellow’s country of nationality or citizenship. Fellows gain valuable skills in intervention epidemiology, public health microbiology, public health management, applied research, communication and teaching.
Which track is right for you or your contacts?
- Field Epidemiology (EPIET): Designed for health professionals with a background in public health or epidemiology who want to work in national or regional surveillance and control centres.
- Public Health Microbiology (EUPHEM): For microbiologists with a medical, veterinary, or environmental background interested in applying epidemiological methods to microbiological data for disease prevention and control.
Important details:
- Fellowship start date: 7 September 2026
- Applicants must be nationals of an EU/EEA country with experience in public health, epidemiology, or microbiology.
- Application deadline: 30 October 2025, 24:00 CEST
Read all the details about the Call for application here.
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Classified as ECDC NORMAL
1
Newsletter#11 – Autumn 2025
GenEpi-BioTrain Newsletter #11 - Autumn 2025
Genomic Epidemiology and Public Health Bioinformatics Training in the EU/EEA, the
Western Balkan, and Türkiye
Dive into the latest updates with the GenEpi-BioTrain Quarterly
Newsletter!
In this issue, we highlight GenEpi-BioTrain’s achievements, key moments, and
upcoming opportunities in genomic epidemiology and bioinformatics. Our training
helps public health professionals, microbiologists, epidemiologists, and
bioinformaticians build practical skills and stay at the forefront of this exciting field.
Together, we celebrate milestones, reflect on our journey, and share exciting plans for
the near future.
On 24 October 2025 we had our yearly information meeting where we
shared important information and updates on the upcoming Pathogen
Wave 7 with relevant stakeholders from various European countries. In
case you missed the meeting, you can find the recording on ECDCs
Learning Portal: Course: GenEpi-BioTrain - Genetic Epidemiology and
Bioinformatics Training Programme
A one-week exchange visit for five Block 1 trainees working with Tuberculosis D
(Pathogen Wave 5) was held at the Research Centre Borstel (RCB) in Germany from
15th to 19th September, 2025.
Trainees dived into the world of Mycobacterium
tuberculosis genomics, gaining hands-on experience
with whole-genome sequencing analysis tailored to
their individual learning goals. Through lectures,
practical sessions, and lab visits, they explored the
fundamentals of NGS, analyzed MTB pipelines such as
MTBseq and PhyResSE, predicted resistance, studied
phylogenetics, and interpreted data—strengthening
their skills to track resistance and transmission for
informed public health action.
The programme also sparked lively networking and discussions among peers and
experts at the RCB, sharing insights on surveillance strategies and the latest
epidemiological trends.
1-week exchange visit for bioinformaticians
2
Join us online! Our virtual training sessions are open to all, no prior experience required. Register on the ECDC Learning Portal and revisit our training sessions at your convenience—recordings remain available.
The Technical University of Denmark (DTU) hosted the 19th virtual training, "Genomic
Tools in Outbreak Investigations - Case Study Cholera Outbreak,” on 27th August and
3rd September 2025. Around 599 participants enrolled for this training.
During this training, participants explored molecular
and genomic data and compared traditional typing
methods, such as Pulsed-Field Gel Electrophoresis
(PFGE), with modern Whole-Genome Sequencing-
Based Typing (WGST).
They honed skills in interpreting phylogenetic
relationships, antimicrobial resistance (AMR) and
virulence profiles, and applying genomic
epidemiology to real-world scenarios. A hands-on simulation exercise, conducted
between the two sessions, brought these concepts to life, reinforcing a practical
understanding in real-world scenarios.
For detailed information about this workshop and to access the recordings, please visit
the ECDC Learning Portal under GenEpi-BioTrain - Virtual training 19 - Genomic
Tools in Outbreak Investigations - Case Study Cholera Outbreak
The Institut Pasteur (IP) hosted the 20th virtual
training on "Klebsiella pneumoniae genomic
epidemiology and antimicrobial resistance” on
9th and 11th September 2025. Around 588 participants
enrolled for this training.
The virtual training provided participants with an
opportunity to have a closer look at Klebsiella
pneumoniae, covering its biology, genetic makeup,
diversity, and antibiotic resistance. The workshop demonstrated how studying this
important pathogen can inform public health actions, including vaccine development
strategies. It also introduced Life Identification Number (LIN) codes for tracking
strains, examined One Health research, and highlighted international efforts, such as
KlebN.
Virtual trainings
3
For detailed information and to access the recordings, please visit the ECDC Learning
Portal under GenEpi-BioTrain - Virtual training 20 - Klebsiella pneumoniae genomic
epidemiology and antimicrobial resistance
The IP organized the 21st virtual training as well, the
topic was “Bacterial strain Taxonomy for
Genomic Surveillance” and it was held on 22nd and
23rd September 2025 from 9:o0 to 12:00 CEST.
Around 616 participants enrolled.
This virtual training provided participants with a clear
understanding of bacterial classification and naming
systems, including MLST, cgMLST, SNP-based
taxonomies, LIN codes, and k-mer clustering, as well as an explanation of how these
methods support outbreak tracking and global public health. Participants also gained
hands-on experience with tools like BIGSdb, EnteroBase, MyKrobe, and PopPUNK,
enabling them to apply these approaches in genomic surveillance.
For detailed information and to access the recordings, please visit the ECDC Learning
Portal under Course: GenEpi-BioTrain - Virtual training 21 - Bacterial Strain
Taxonomy for Genomic Surveillance
The planned activities for Q4 in 2025 and Q1 in 2026 are outlined in chronological
order.
A 2-week “Interdisciplinary genomic epidemiology and public health
bioinformatics” workshop will be held at the Statens Serum Institut (SSI) from 27th
October to 7th November 2025, for 30 Block 2/Pathogen Wave 6 (AMR) trainees.
The training will focus on applied genomic epidemiology of methicillin-resistant
Staphylococcus aureus (MRSA), carbapenem-resistant Enterobacterales (CRE), and
Clostridioides difficile infections (CDI). The overall objective is to enhance
coordination and collaboration among bioinformaticians, epidemiologists, and
microbiologists to support public health action. Trainees will gain advanced
theoretical and practical expertise in outbreak detection, genomic epidemiology, AMR
surveillance, and One Health approaches through lectures, case-based learning,
hands-on exercises, and collaborative discussions.
A three-day workshop on Specific Topics on AMR will be held at the SSI from 9th
to 11th December 2025 for 10 Block 3/Pathogen Wave 6 trainees. This course is
designed to enhance participants’ understanding of the roles and responsibilities of
bioinformaticians in NGS-based surveillance and outbreak investigations of hospital-
acquired infections (HAI) caused by MRSA, CRE and C. difficile.
Upcoming activities
4
A virtual information meeting with all the selected candidates for Pathogen Wave
7 (focusing on One Health approach) will take place in January 2026 to introduce
training activities and answer questions from the trainees.
The fourth edition of “Bridging the Gaps in Bioinformatics” workshop will take
place at SSI from 23rd February to 6th March 2025 for trainees of block 1 /
Pathogen Wave 7 and 8. This popular course provides beginners with a solid
foundation in bioinformatics. Participants are introduced to key concepts and gain the
skills needed to work independently. With a strong focus on hands-on training,
trainees receive practical experience throughout the course, culminating in the
creation of a basic pipeline for processing genome assemblies, which equips them with
essential bioinformatics skills.
Additional activities within the GenEpi-BioTrain programme will be communicated in
due course.
1
Newsletter#11 – Autumn 2025
GenEpi-BioTrain Newsletter #11 - Autumn 2025
Genomic Epidemiology and Public Health Bioinformatics Training in the EU/EEA, the
Western Balkan, and Türkiye
Dive into the latest updates with the GenEpi-BioTrain Quarterly
Newsletter!
In this issue, we highlight GenEpi-BioTrain’s achievements, key moments, and
upcoming opportunities in genomic epidemiology and bioinformatics. Our training
helps public health professionals, microbiologists, epidemiologists, and
bioinformaticians build practical skills and stay at the forefront of this exciting field.
Together, we celebrate milestones, reflect on our journey, and share exciting plans for
the near future.
On 24 October 2025 we had our yearly information meeting where we
shared important information and updates on the upcoming Pathogen
Wave 7 with relevant stakeholders from various European countries. In
case you missed the meeting, you can find the recording on ECDCs
Learning Portal: Course: GenEpi-BioTrain - Genetic Epidemiology and
Bioinformatics Training Programme
A one-week exchange visit for five Block 1 trainees working with Tuberculosis D
(Pathogen Wave 5) was held at the Research Centre Borstel (RCB) in Germany from
15th to 19th September, 2025.
Trainees dived into the world of Mycobacterium
tuberculosis genomics, gaining hands-on experience
with whole-genome sequencing analysis tailored to
their individual learning goals. Through lectures,
practical sessions, and lab visits, they explored the
fundamentals of NGS, analyzed MTB pipelines such as
MTBseq and PhyResSE, predicted resistance, studied
phylogenetics, and interpreted data—strengthening
their skills to track resistance and transmission for
informed public health action.
The programme also sparked lively networking and discussions among peers and
experts at the RCB, sharing insights on surveillance strategies and the latest
epidemiological trends.
1-week exchange visit for bioinformaticians
2
Join us online! Our virtual training sessions are open to all, no prior experience required. Register on the ECDC Learning Portal and revisit our training sessions at your convenience—recordings remain available.
The Technical University of Denmark (DTU) hosted the 19th virtual training, "Genomic
Tools in Outbreak Investigations - Case Study Cholera Outbreak,” on 27th August and
3rd September 2025. Around 599 participants enrolled for this training.
During this training, participants explored molecular
and genomic data and compared traditional typing
methods, such as Pulsed-Field Gel Electrophoresis
(PFGE), with modern Whole-Genome Sequencing-
Based Typing (WGST).
They honed skills in interpreting phylogenetic
relationships, antimicrobial resistance (AMR) and
virulence profiles, and applying genomic
epidemiology to real-world scenarios. A hands-on simulation exercise, conducted
between the two sessions, brought these concepts to life, reinforcing a practical
understanding in real-world scenarios.
For detailed information about this workshop and to access the recordings, please visit
the ECDC Learning Portal under GenEpi-BioTrain - Virtual training 19 - Genomic
Tools in Outbreak Investigations - Case Study Cholera Outbreak
The Institut Pasteur (IP) hosted the 20th virtual
training on "Klebsiella pneumoniae genomic
epidemiology and antimicrobial resistance” on
9th and 11th September 2025. Around 588 participants
enrolled for this training.
The virtual training provided participants with an
opportunity to have a closer look at Klebsiella
pneumoniae, covering its biology, genetic makeup,
diversity, and antibiotic resistance. The workshop demonstrated how studying this
important pathogen can inform public health actions, including vaccine development
strategies. It also introduced Life Identification Number (LIN) codes for tracking
strains, examined One Health research, and highlighted international efforts, such as
KlebN.
Virtual trainings
3
For detailed information and to access the recordings, please visit the ECDC Learning
Portal under GenEpi-BioTrain - Virtual training 20 - Klebsiella pneumoniae genomic
epidemiology and antimicrobial resistance
The IP organized the 21st virtual training as well, the
topic was “Bacterial strain Taxonomy for
Genomic Surveillance” and it was held on 22nd and
23rd September 2025 from 9:o0 to 12:00 CEST.
Around 616 participants enrolled.
This virtual training provided participants with a clear
understanding of bacterial classification and naming
systems, including MLST, cgMLST, SNP-based
taxonomies, LIN codes, and k-mer clustering, as well as an explanation of how these
methods support outbreak tracking and global public health. Participants also gained
hands-on experience with tools like BIGSdb, EnteroBase, MyKrobe, and PopPUNK,
enabling them to apply these approaches in genomic surveillance.
For detailed information and to access the recordings, please visit the ECDC Learning
Portal under Course: GenEpi-BioTrain - Virtual training 21 - Bacterial Strain
Taxonomy for Genomic Surveillance
The planned activities for Q4 in 2025 and Q1 in 2026 are outlined in chronological
order.
A 2-week “Interdisciplinary genomic epidemiology and public health
bioinformatics” workshop will be held at the Statens Serum Institut (SSI) from 27th
October to 7th November 2025, for 30 Block 2/Pathogen Wave 6 (AMR) trainees.
The training will focus on applied genomic epidemiology of methicillin-resistant
Staphylococcus aureus (MRSA), carbapenem-resistant Enterobacterales (CRE), and
Clostridioides difficile infections (CDI). The overall objective is to enhance
coordination and collaboration among bioinformaticians, epidemiologists, and
microbiologists to support public health action. Trainees will gain advanced
theoretical and practical expertise in outbreak detection, genomic epidemiology, AMR
surveillance, and One Health approaches through lectures, case-based learning,
hands-on exercises, and collaborative discussions.
A three-day workshop on Specific Topics on AMR will be held at the SSI from 9th
to 11th December 2025 for 10 Block 3/Pathogen Wave 6 trainees. This course is
designed to enhance participants’ understanding of the roles and responsibilities of
bioinformaticians in NGS-based surveillance and outbreak investigations of hospital-
acquired infections (HAI) caused by MRSA, CRE and C. difficile.
Upcoming activities
4
A virtual information meeting with all the selected candidates for Pathogen Wave
7 (focusing on One Health approach) will take place in January 2026 to introduce
training activities and answer questions from the trainees.
The fourth edition of “Bridging the Gaps in Bioinformatics” workshop will take
place at SSI from 23rd February to 6th March 2025 for trainees of block 1 /
Pathogen Wave 7 and 8. This popular course provides beginners with a solid
foundation in bioinformatics. Participants are introduced to key concepts and gain the
skills needed to work independently. With a strong focus on hands-on training,
trainees receive practical experience throughout the course, culminating in the
creation of a basic pipeline for processing genome assemblies, which equips them with
essential bioinformatics skills.
Additional activities within the GenEpi-BioTrain programme will be communicated in
due course.