GenEpi-BioTrain - Genetic Epidemiology and Bioinformatics Training Programme

This is a space to explain what the Genetic Epidemiology Training Programme (GenEpi-BioTrain)  is offering.

Information session 24 October 2025. 

   

Training activities for each pathogen wave

  • Face-to-face workshops “Bridging the gaps in bioinformatics” (2 weeks). 
    • The objective of this training is to strengthen programming knowledge and skills, database management, use and development of bioinformatic tools and increase awareness about application for use in the public health context
    • Trainees have basic/limited bioinformatics skills
    • The curriculum covers overview of sequencing technologies, genome assembly and analysis, QC, coding best practices, pipeline development, etc.​
  • Face-to-face workshops “Interdisciplinary genomic epidemiology and public health bioinformatics” (2 weeks)
    • The aim is to improve the knowledge of and capacity for applied genomic epidemiology and bioinformatics for public health action
    • Each workshop may include up to ten “country teams” of one bioinformatician, one microbiologist, one epidemiologist to promote the collaboration of inter-disciplinary teams within the public health institutions​
    • The curriculum will be developed around case studies (e.g. common outbreak scenarios) to be solved by leveraging on interdisciplinary collaboration
  • Exchange visits for bioinformaticians (either one, two or three weeks)
    • Participants from one EU/EEA country go to a public health institution of another EU/EEA country
    • The trainee shall have clearly defined public health bioinformatics-related learning needs and goals that the exchange visit is expected to address.
  • Face-to-face trainings on specific topics in genomic epidemiology and/or public health bioinformatics (3 days)
    • Specific topics (to be defined according to training needs and interests from Member States) in genomic epidemiology aimed at different proficiency levels.
  • Virtual training sessions/webinars (1 day or 2 half-days)
    • Specific topics (to be defined according to training needs and interests from Member States) in genomic epidemiology aimed at different proficiency levels.

Background

Since 2021, ECDC in collaboration with the European Commission has made substantial investments to increase the capacity of Member States public health laboratories to perform whole genome sequencing (WGS) and reverse transcription polymerase chain reaction (RT-PCR) (ECDC supports EU/EEA Member States in rapid detection of SARS-CoV-2 variants (europa.eu)).

To ensure efficient use of WGS infrastructure investments and to further strengthen Member States laboratory capacity, ECDC offers a training programme in genomic epidemiology and public health bioinformatics. The programme is launched in parallel to the WGS infrastructure support and should facilitate the use of genomic data in EU level surveillance and outbreak response.

The training programme, the “GenEpi-BioTrain”, was initiated in January 2023 and will continue over the next four years.

Objectives and aims of the training

The overall objectives of the trainings are to support countries in building up their capacity in genomic epidemiology and bioinformatics for public health purposes, and to increase the interdisciplinary collaboration between bioinformaticians, epidemiologists and microbiologists within a country to facilitate the routine use of genomic information for surveillance, preparedness, and outbreak response. Activities shall also enhance data sharing and collaborations between public health institutions and ECDC, and enhanced networking activities will foster cross-border collaborations.
  • To allow the professionals with a background in computational biology and bioinformatics to:
      - enhance and extend their skills to strengthen their capacity in the field of public health bioinformatics.
      - 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, professionals in public health surveillance and response) to take rapid and informed public health action.

  • To allow the professionals without a background in computational biology/bioinformatics to:
      - gain a better understanding of how genomic epidemiology can be applied in a public health context with special focus on how traditional and genomic data can be jointly analysed, interpreted and used for public health purposes.
      - 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.
      - 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
      - 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.

  • To allow professionals with a background in microbiology and epidemiology to:
      - enhance and extend their understanding of the field of public health bioinformatics.
      - better understand the needs and concepts of bioinformatics, with a focus on the inputs and outputs needed by these counterparts to take rapid and informed public health action.

Training target groups

  • Professionals working in public health institutions with a background in computational biology and bioinformatics who are/are going to 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 public health institutions 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).

Selection of participants

The ECDC will liaises with the National Focal points for Microbiology in coordination with National Focal Points of relevant disease groups are kindly invited to select participants.

Training materials

All training materials produced to deliver the training activities of this programme will be made available in the Library of Training Materials after events take place. Anyone can consult these materials, learn from them and share and adapt them to teach others. The materials are ECDC property and licenced as Creative Commons (CC BY 4.0). Read here more about licencing.