The overall aim of this workshop is to learn the basic concepts and methods of public health genomics and acquire basic skills for use of open- access tools for integrated analysis and visualisation of WGS and epidemiological data as well as participate in multidisciplinary interpretation of results to inform disease control.

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 Public health professionals with microbiology and/or epidemiology backgrounds who are conducting laboratory-based surveillance and using molecular typing data for surveillance of communicable diseases and who are planning to implement integration and use of WGS data for national surveillance in 2019 or later in their Member State.



Welcome to the Cross-sectoral biorisk awareness and mitigation training (3rd Edition, for training specialists) - BAM2019. The course is jointly organised by the European Centre for Disease Prevention and Control (ECDC) and the European Police Office (EUROPOL).

If you were nominated by your Country, you have received a password to participate in the selection of this course. Please complete the application form to submit your candidature. Thank you!

The overall aim of this course is to strengthen capacity in the application of scientific principles and concepts to inform and influence policy making decisions related to the prevention and control of communicable diseases among public health specialists in Member States of the European Union (EU) and of the European Economic Area (EEA). 

This includes knowledge of retrieval, analysis and appraisal of evidence from all data sources so that participants can make an informed decision about its quality and relevance for their work, and building participants’ skills in designing knowledge translation and exchange (KTE) strategies to support evidence-informed decision making (EIDM). 

The course will bring together country experts to exchange experiences, views and gain skills on how to inform policy makers in relation to detection, preparedness, assessment and control of public health threats with a cross-border dimension at the EU-level in the area of communicable disease prevention and control. It focuses primarily on the process of gathering and communicating a body of evidence, rather than the process of taking decisions based on this evidence.

The Senior Exchange Initiative provides the participants with the opportunity to familiarise themselves with working methods of other EU countries, and allows the host sites to share their experience, and build closer links to other institutions. The initiative aims at creating a network and trust among colleagues and supporting the European dimension in public health through cooperation and training.

The exchange visits are self-organised, meaning the visiting expert and the host site agree on topics, scope and objectives, and should be scheduled for about one week. ECDC funds travel, accommodation and per diem.