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 programme combines lectures and practical sessions delivered by multiple host institutions in order to enhance surveillance, preparedness, and readiness to respond to outbreaks.
This training programme 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 programme.
Several training activities will be delivered through this programme, 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 Virtual Academy (EVA) platform: GenEpi-BioTrain Common (europa.eu).
Courses delivered at Institut Pasteur, Paris:
The courses will follow two pathogen waves focusing first, on food- and waterborne pathogens (L. monocytogenes, S. enterica, E. coli, K. pneumoniae, …) and second, on pathogens of vaccine-preventable diseases (N. meningitidis, Haemophilus, C. diphtheriae, whooping cough, …).
Training activities scheduled at 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.
- 3-day face-to-face training sessions
- For 10 public health bioinformaticians
- Improvement of practical skills in bioinformatics
- One or two weeks
- Between 3 to 5 participants
- Public health bioinformatics-related learning needs and building a support network.
- 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:
Six virtual training sessions have been completed, and their recordings are available on the EVA platform at these links:
- “Whole-genome sequencing-based (WGS) detection of antimicrobial resistance (AMR) in bacteria”
- “From sequencer to polished reads for bacteria”
- “Introduction to bioinformatic analysis of SARS-CoV-2 amplicon sequencing data”
- “Introduction to avian influenza outbreak investigation using NGS data”,
- “Bacterial genome assembly and quality control"
- "Introduction to SARS-CoV-2 wastewater analysis"
- "Phylogenetics and alignments"
Announcement of others virtual trainings will be made on the EVA platform at this link.
Organizational team at 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.
Solène Cottis, Project Manager of the GenEpi-BioTrain programme at Institut Pasteur. She is responsible for the organization and the management of the training activities on site.
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 programme.
How to subscribe to the GenEpi-BioTrain programme ?
To access the virtual training sessions, you can register for free on the ECDC virtual platform (EVA). 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
Contact
GenEpi-BioTrain team at Pasteur: gebt@pasteur.fr.
GenEpi-BioTrain team at ECDC: ECDC.Microbiology@ecdc.europa.eu
The Institut Pasteur also proposes additional virtual trainings: for more details, please follow this link.
