Public Health Genomics: an introduction (2020 b-learning edition) (TBD)

Dates / duration  



Stockholm, Sweden 

Objectives /    Learning Outcomes  


Upon completion of the workshop, the participants should be able to: 

  • Understand the basics, strengths and limitations of microbial WGS and its applications for epidemiological and phenotypic inference in outbreak investigations and surveillance 
  • Generate, describe and interpret phylogenetic trees in the context of epidemiological investigations
  • Learn about and use online software tools available for WGS applications to national surveillance
  • Based on the content of the workshop, prepare a dissemination activity to cascade learning and prepare routine application of WGS in their institutions

The training course covers 8 key areas:

  • Basics of viral/bacterial genomics, genome structure and evolution
  • Next Generation Sequencing technology overview
  • Principles of sequence comparisons, SNP and MLST analysis
  • Phylogeny: different types of trees, how to read a tree, terminology for branches and leaves
  • Epidemiological and phenotypic inference from WGS data
  • Public health benefits of real-time WGS-enhanced surveillance for outbreak detection and response
  • How to establish a WGS-enhanced national surveillance system
  • Outbreak Case studies (FWD, AMR) using online WGS/epidemiological data integrated analysis and visualisation tools 

Target audience  

The target audience is a mix of 20 trainees including pairs of epidemiologists in charge of surveillance and National Reference Laboratory (NRL) microbiology experts in charge of molecular surveillance in the 10 Member States that lack  Whole Genome Sequencing (WGS) capability (NMFP 2017 survey) and/or have been asking specifically ECDC for opportunity to take WGS training (ECoSuM survey ...)


This training includes a review of the principles, applications and limits of WGS for surveillance of infectious diseases and antimicrobial resistance at national level and in related ECDC operational work. There will be practical sessions with exercises of online sequence data analysis and visualisation and interactive multidisciplinary discussions aiming at using integrated epidemiological analysis tools to contextualise and interpret WGS data for public health risk assessment. The training will also address the basics of viral/microbial genomics, structure and evolution analogised next Generation Sequencing (NGS), principles of sequence comparisons, Single Nucleotide Polymorphism (SNP) and Multilocus Sequence Typing (MLST) analysis. The principles of phylogeny (different types of trees, how to read a tree), epidemiological and phenotypic inference from WGS data and public health benefits of real-time WGS-enhanced surveillance for outbreak detection will also be covered. The course will also included surveillance and outbreak Case studies using online visualisation tools: Food and Waterborne Diseases (FWB), Tuberculosis (TB), Anti-Microbial Resistance (AMR). 

The course will be delivered using blended learning, with pre-course activities and face to face course. The course will be delivered in English.

Note: This course is not open for public enrolment. Participation is through invitation by the focal point of the respective disease programme or function areas which is guided by the framework of collaboration between ECDC and the Coordinating Competent Bodies of Member States.