GenEpi-BioTrain: Interdisciplinary Training in Genomic Epidemiology and Public Health Bioinformatics

Institut Pasteur (France), 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)

Date

From 2023 to 2026

This interdisciplinary program combines lectures and practical sessions delivered by multiple host institutions in order to enhance surveillance, preparedness, and readiness to respond to outbreaks.

This training program is intended for professionals from diverse backgrounds and fields of study linked to public health microbiology (e.g., bioinformatics, biology, computer science, biochemistry, microbial genomics, metagenomics, algorithm development, microbiology, molecular genetics, biomedical sciences, forensic biology, comparative and molecular bioscience, epidemiology, etc.) wishing to deepen their understanding and skills in public health bioinformatics and genomic epidemiology. Background in computational biology and bioinformatics is not required to apply to this training program.

Several training activities will be delivered through this program, including 2-weeks workshops, 3-days face-to-face training sessions, exchange visits for bioinformaticians, and virtual trainings.

Details about the training are available on the ECDC Learning Portal: GenEpi-BioTrain Program

Courses delivered at the Institut Pasteur, Paris:

The courses will follow various pathogen waves focusing on food- and waterborne pathogens (L. monocytogenes, S. enterica, E. coli, K. pneumoniae, …), on pathogens of vaccine-preventable diseases (N. meningitidis, Haemophilus, C. diphtheriae, whooping cough, …), on antimicrobial resistance and the notion of One Health applied to bacterial infections.

Training activities scheduled at the Institut Pasteur

Here are details of the training activities scheduled at Institut Pasteur:

Interdisciplinary Genomic Epidemiology and Public Health Bioinformatics

• 2-weeks workshops
• 30 participants divided into 10 “country teams” including one microbiologist, one epidemiologist, and one bioinformatician
• Theoretical courses and hands-on bioinformatics training
• Choice of themes and content will take trainees' needs into account.

Specific trainings in Genomic Epidemiology and/or Public Health Bioinformatics

• 3-day face-to-face training sessions
• For 10 public health bioinformaticians
• Improvement of practical skills in bioinformatics

Exchange Visits for Bioinformaticians

• One or two weeks
• Between 3 to 5 participants
• Public health bioinformatics-related learning needs and building a support network.

Virtual Trainings

• 1 day or 2 half-days
• Topics defined by the trainees' needs
• Open to all professionals
• Practical exercises will be included during these trainings
• Networking and discussion opportunities will be enhanced

Current virtual trainings available:

Virtual trainings are regularly organized as part of the GenEpi-BioTrain program. Recordings of completed sessions and information about upcoming trainings are available on the ECDC Learning Portal.

Organizational team at the Institut Pasteur

Sylvain Brisse, head of the Biodiversity and Epidemiology of Bacterial Pathogens Unit, head of the National Reference Center for diphtheria, head of the National Reference Center for Whooping cough and other Bordetella infections, and coordinator of the Genomic taxonomies of bacterial strains platform (BIGSdb-Pasteur). He is the GenEpi-BioTrain principal investigator at Institut Pasteur.

Anvita Bhargava, Project Manager of the GenEpi-BioTrain program at the Institut Pasteur. She is responsible for the organization and the management of the training activities.

Thierry Lang, International relationships officer of the Education Department of Institut Pasteur.

Experts in foodborne pathogens and vaccine-preventable bacterial pathogens, and bioinformaticians of the Hub of Bioinformatics and Biostatistics, will also be involved in this program. 

How to subscribe to the GenEpi-BioTrain program?

To access the virtual training sessions, you can register for free on the ECDC Learning Portal. To register for the 2-week workshops, 3-day face-to-face trainings, and exchange visits for bioinformaticians, you can contact Mathieu Tourdjman from the French national focal point  and/or ECDC.Microbiology@ecdc.europa.eu