Proposal for 2016 survey of WGS capacity in EU/EEA Member States
Proposal for 2016 survey of WGS
capacity in EU/EEA Member States
14th National Microbiology Focal Points meeting
Joana Revez, Scientific Officer Microbiology, Office of the Chief Scientist
European Centre for Disease Prevention and Control
14th NMFP, Stockholm, 12-13 May 2016
Purpose of annual WGS capacity surveys
1- Monitor national arrangements and
stages of development of the Next
Generation Sequencing/Whole Genome
Sequencing public health applications
across the EU/EEA, as advised in JSM
2- Inform the implementation of ECDC
genomic surveillance strategy and
roadmap and align pilot projects with
national surveillance programmes;
3- Identify the areas where ECDC can foster
capacity for use of NGS technology.
Tailored questions for pathogens
- ECDC roadmap 2016-19 first two priority categories
• Operationalisation of EU wide WGS-based surveillance
systems in the near term:
• Listeria monocytogenes
• Neisseria meningitidis
• Carbapenem-resistant Enterobacteriaceae
• Antibiotic-resistant Neisseria gonorrhoeae
• Operationalisation of WGS-based surveillance systems
deferred until the required technical capacity across the
EU/EEA is met for:
• Human influenza virus
• Salmonella enterica
• Shiga-Toxin producing Escherichia coli (STEC)
• Multidrug-resistant Mycobacterium tuberculosis
Areas to be covered by the 2016 survey
1. NRL access to NGS/WGS technology
2. NGS/WGS technology platform(s) used
3. Description of NGS/WGS use in your country by
disease/pathogen (i.e. outbreak investigation, surveillance for trend
monitoring, real-time surveillance for outbreak detection and alert)
4. For each of the priority pathogens for EU surveillance:
• In and/or outsourced: sequencing and subsequent bioinformatic analysis.
• WGS characterisation of isolates done as first line or complementary.
• Sampling frame and volume of isolates tested.
• Full or partial WGS funding.
• Data storage/ reference databases.
5. Training needs
• methods of public health applications of NGS/WGS.
• genomic-based nomenclature, integration/interpretation of WGS.
• Survey call: 1 September -
30 September, on data as of
• ECDC analysis and report:
15th NMFP meeting (13-14
• Frequency: annually
Thank you for listening,