July 26, 2024
Bulletin interne de l'Institut Pasteur
GenEpiBioTrain/ Genomic Epidemiology and Public Health Bioinformatics Training in the EU/EEA, the Western Balkans, and Türkiye
The Institut Pasteur is one of the 6 consortium members of GenEpi-BioTrain, an ECDC-funded interdisciplinary 4-year program to strengthen surveillance, preparedness, and response capabilities for outbreaks. This project includes others host institutes as consortium (Technical University of Denmark (Denmark), Statens Serum Institute (Denmark), Research Center Borstel (Germany), Karolinska University Hospital and Institutet (Sweden) and Finnish Institute for Health and Welfare (Finland)).
This project offers training in pathogen sequencing data interpretation, microbial genomics, bioinformatics, epidemiological surveillance, and more to European professionals from diverse backgrounds and fields of study linked to public health microbiology. A background in computational biology and bioinformatics is not required to apply to this training programme.
Through various training activities, including two-week workshops, three-day face-to-face sessions, exchange visits, and virtual training sessions, this project aimed at enhancing participants' knowledge and skills in public health bioinformatics and genomic epidemiology.
Details about the training are available on the Institut Pasteur website: GenEpi-BioTrain programme and on the ECDC Virtual Academy (EVA) platform: GenEpi-BioTrain Common. (To access the virtual training sessions, you can register for free on the ECDC virtual platform (EVA). Recordings of virtual trainings are available on the EVA platform and can be accessed even after the training is completed).
Many events have already been held since the programme was launched, and others are being prepared for the second half of 2024, which you can take part in. Focus on past and future highlights:
Past training activities
Since the beginning of this programme at Institut Pasteur, a 3-day training on “Phylogeny for Food- and Waterborne Diseases” and a 2-week workshop on “Interdisciplinary Genomic Epidemiology and Public Health Bioinformatics (Wave 3 – Food- and Waterborne Diseases)” have been held on campus.
A 3-day training “Phylogeny for Food- and Waterborne Diseases” was delivered to 10 bioinformaticians from European public health institutes in April 2024.
This workshop focused on conducting standard phylogenetic analyses in the context of FWD surveillance and outbreak investigation. Participants gained insights into the rationale behind phylogenetic analysis and acquired practical skills to perform, analyze, and interpret phylogenetic trees.
The course director was Julien Guglielmini, an expert in phylogenetic and comparative genomics, and speakers included Anna Zhukova (expert on new phylogenetic methods) and Alexandra Moura (expert on population genomics for Listeria). This training was rated 8.6 out of 10 by participants. All participants would highly recommend these training sessions to their colleagues.
Detailed information about this workshop can be found on EVA:
GenEpi-BioTrain - Topical training: Phylogeny for food- and waterborne diseases.
A 2-week workshop “Interdisciplinary Genomic Epidemiology and Public Health Bioinformatics (Wave 3 – Food- and Waterborne Diseases)” was held in May 2024 and delivered to 29 public health professionals from ten EU/EEA countries, representing collaborative country teams of epidemiologists, microbiologists and bioinformaticians.
This workshop focused on Listeria monocytogenes, Salmonella enterica, and other foodborne pathogens, including Escherichia coli and Klebsiella pneumoniae. Participants explored how interdisciplinary interpretation of integrated results can enhance efforts to effectively prevent and control the spread of infectious diseases.
The course director was Pr. Sylvain Brisse (head of NRC Diphteriae, head of NRC Whooping cough, expert on Klebsiella and bacterial strain taxonomy). Chiara Crestani (expert on bacterial strain taxonomy and Corynebacteria) was the course co-director and Carla Rodrigues (Deputy director of NRC Whooping cough) was the practical session coordinator. National and international speakers with renowned expertise were invited to this course, including Martin Maiden (Oxford University), Nabil Alikhan (Oxford University), Gabriele Arcari (Sapienza University), François Lebreton (Walter Reed Army Institute of Research), Alexandra Moura (Institut Pasteur), Julien Guglielmini (Institut Pasteur), François-Xavier Weill (head of NRC Salmonella, E. coli, and Shigella, Institut Pasteur), Marc Lecuit (head of NRC Listeria, Institut Pasteur), and many others.
Participants rated this course 7.4 out of 10. Out of 26 participants, 22 increased their skills between the first and last days of the workshop as shown by a pre- and post-course questionnaire. They highly recommend this course to their colleagues and were very satisfied with the training.
For detailed information about this workshop, please refer to EVA:
GenEpi-BioTrain - Interdisciplinary training in genomic epidemiology and public health bioinformatics on food- and waterborne diseases.
A virtual training on Waterborne Disease (Leptospirosis) and Water Surveillance was organized on July 22nd and 24th, 2024.
This virtual training was delivered by Mathieu Picardeau (head of NRC Leptospirosis), Jean-François Mariet (expert on molecular microbiology of leptospirosis, Institut Pasteur), Florence Ayral (expert on animal leptospirosis and surveillance in animals, VetAgro Sup), Laurent Moulin (head of R&D laboratory in Eau de Paris), and Sebastien Wurtzer (engineer expert in viral molecular detection tools for water surveillance in Eau de Paris).
At least 300 people registered for this virtual training, and between 150 and 200 attended the webinar. This virtual training was well-rated by participants and can be considered a success.
For detailed information about this workshop, please refer to EVA: GenEpi-BioTrain - Virtual training 8 - Waterborne disease and Water Surveillance.
Overview of all GenEpi-BioTrain virtual trainings on EVA:
Recording of the virtual trainings are available on the EVA platform and can be accessed even after the training is completed.
* GenEpi-BioTrain - Virtual training 02: From sequencer to polished reads for bacteria
* GenEpi-BioTrain - Virtual training 05: Bacterial genome assembly and quality control
* GenEpi-BioTrain - Virtual training 06: Introduction to SARS-CoV-2 wastewater analysis
* GenEpi-BioTrain - Virtual training 07: Phylogenetics and alignments
Upcoming training activities in the GenEpi-BioTrain project
Virtual training sessions directed by Institut Pasteur will be held frequently until summer 2025. After that, these sessions will continue to be organized by other consortium institutes included in this project.
At the beginning of September 2024, a virtual training on “Health Risks in Seafood Products” is planned and will be announced in August
At the beginning of October 2024, a one-week exchange visit with 5 participants will take place. The programme of these visits centers around analyses of trainees’ own data and is customized to meet individual trainees’ needs and align with GenEpi-BioTrain goals. These exchange visits also facilitated networking among participants and trainers, fostering valuable connections for future collaboration. It is expected that trainees will disseminate the knowledge gained during the exchange visits with colleagues in their respective countries.
Beginning of November 2024, a 3-day training on “Phylogeny for Vaccine-Preventable Diseases” is planned.
This training will be followed by a 2-week workshop beginning of December 2024 on “Interdisciplinary Genomic Epidemiology and Public Health Bioinformatics (Wave 4 – Vaccine-Preventable Diseases)”. This workshop will delve into surveillance and outbreak investigation techniques for pathogens such as Neisseria gonorrhoeae et N. meningitidis.
The project will continue into 2025 with a variety of training activities, including virtual sessions, 3-day trainings, and 1-week or 2-week exchange visits. Further details and announcements will be provided as the dates approach.
Registration and enrolment
To register for the 2-week workshops, 3-day face-to-face trainings, and exchange visits for bioinformaticians, you can contact Justine Schaeffer and/or Mathieu Tourdjman from the French national focal point and/or ECDC.Microbiology@ecdc.europa.eu.
Contacts
GenEpi-BioTrain team at Institut Pasteur: gebt@pasteur.fr
GenEpi-BioTrain team at ECDC: ECDC.Microbiology@ecdc.europa.eu