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

1. ECDC WGS strategy and Roadmap
for molecular and genomic
surveillance V2.1
14th National Microbiology Focal Points meeting
Marc Struelens, Chief Microbiologist, Office of the Chief Scientist,
European Centre for Disease Prevention and Control
14th NMFP, Stockholm, 12-13 May 2016

2. Roadmap - V1.2, 2013 for
integration of molecular and
genomic typing into European
level surveillance and
epidemic preparedness
2013
Concept paper: Surveillance
of communicable diseases in
Europe – a concept to
integrate molecular typing
data into EU-level
surveillance. Stockholm ECDC;
2013.
2007
2016WGS Strategy and
Roadmap - V2.1, 2016-19

3. • Drafted by ECDC cross-unit working group, October
2015
• Peer-reviewed by external experts and the Molecular
typing for Surveillance Task Force (MSTF) and revised
with minor modifications, November- December 2015
• Approved internally on January 2016
• Expected publication (June 2016)
ECDC strategy to harness whole genome
sequencing to strengthen EU outbreak
investigations and public health surveillance

4. ECDC vision on whole genome sequencing
• In five years’ time, ECDC will have contributed to
establish standards and manage systems enabling the EU
wide use of whole genome sequencing (WGS) as the
method of choice for typing of microbial pathogens,
replacing other methods.
• This will improve the accuracy and effectiveness of
disease surveillance, outbreak investigation and
evaluation of prevention policies by enhanced assessment
of disease and drug resistance transmission dynamics.
Source: ECDC Strategy to harness whole genome sequencing for strengthening EU outbreak investigations and
public health surveillance, 2016 – in press.

5. • To map the WGS-based public health initiatives and
engage partnerships;
• To promote integrated analysis of microbiological data
and epidemiological data;
• To provide guidance on and validation of WGS-based
methods for surveillance;
• To support the Member States in performing the
transition to appropriate use of WGS;
• To develop, run and evaluate selected pilot
implementation studies.
ECDC strategy to harness whole genome sequencing
to strengthen EU outbreak investigations and public
health surveillance: objectives

6. Role of the Molecular Typing for Surveillance Task
Force (MSTF)
• Composed of multi-disciplinary public heath experts from
the National Focal Points for Microbiology and for
Surveillance
• Support the revision of the ECDC strategy and roadmap
for integration of molecular/WGS typing into EU level
surveillance:
– Evaluate the added value of molecular typing proposals
prepared by ECDC Disease Programmes
– Participate in Delphi process meeting in the process of
ranking the roadmap disease priorities.
– Review the final draft of updated strategy and
roadmap.

7. MSTF ranking of public health need and EU-
added value of molecular typing integration for
surveillance and outbreak investigations

8. Roadmap V2.1 top priorities 2016-19
• EU wide WGS-based surveillance systems in the
near term:
– Continuous surveillance:
 Listeria monocytogenes
 Neisseria meningitidis
– Multi-annual pan-EU surveys:
 Carbapenemase-producing Enterobacteriaceae
 Antibiotic-resistant Neisseria gonorrhoeae
• WGS–based typing for investigation of cross-
border foodborne outbreaks (Listeria, Salmonella,
VTEC)

9. ECDC roadmap– version 2.1, 2016-2019
• Operationalisation of WGS-based surveillance systems
deferred until the required technical capacity across the
EU/EEA is met: human influenza virus, Salmonella enterica,
Shiga-Toxin producing E. coli (STEC) and multidrug-resistant
Mycobacterium tuberculosis
• Further evidence of the opportunities and challenges: PCR-
ribotyping for Clostridium difficile surveillance, and sequence-
based surveillance of anti-viral drug resistance in human
immunodeficiency virus (HIV) and Hepatitis C virus (HCV)
• Postpone until next roadmap revision in 2018: West Nile
virus (WNV) and meticilin-resistant Staphylococcus aureus (MRSA)

10. - WGS strategy
- Roadmap 2.1
- Work plan
(annual)
- Business cases
(multiannual)
- Updated DP proposals
- (Post)-pilot indicators
- Surveillance system
- MS capacity
- Pilot or feasibility
studies
- Routine
REVISION
CONSULTATION

11. Next steps
• Publication of the ECDC WGS strategy and updated
roadmap – version 2.1: June 2016
• Infographics on WGS for Public Health
• Mapping Member States’ WGS capacity (Joana Revez
presentation)
• Finalisation of three business cases
– Neisseria meningitidis
– Carbapenemase-producing Enterobacteriaceae
– Antibiotic-resistant Neisseria gonorrhoeae
• Evaluation of the roadmap implementation- indicators

12. Thank you for listening,
ECDC.Microbiology@ecdc.europa.eu