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Proposal for 2016 survey of WGS capacity in EU/EEA Member States


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Presentation from the ECDC 14th NMFP meeting organised by the European Centre of Disease Prevention and Control - Stockholm, 12 - 13 May 2016

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Proposal for 2016 survey of WGS capacity in EU/EEA Member States

  1. 1. 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
  2. 2. 1 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 2015; 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.
  3. 3. 2 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
  4. 4. 3 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.
  5. 5. 4 Proposed timeline • Survey call: 1 September - 30 September, on data as of July 2016. • ECDC analysis and report: 15th NMFP meeting (13-14 October 2016) • Frequency: annually
  6. 6. 5 Thank you for listening,