Presentation of the 16th NMFP meeting held on 4-5 May 2017 in Stockholm

1. ECDC typing/WGS roadmap
revision plan, 2018
16th National Microbiology Focal Points meeting
Joana Revez, Scientific Officer Microbiology, Office of the Chef Scientist
European Centre for Disease Prevention and Control
16th NMFP, Stockholm, 4-5 May 2017

2. 1
ECDC Vision: Whole Genome Sequencing for
public health use by 2020
• 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.
European Centre for Disease Prevention and Control. Expert opinion on whole genome sequencing for public health
surveillance. Stockholm: ECDC; 2016.

3. 2
ECDC cross-disease WGS support strategy
1. Map the various WGS-based public health initiatives and
engage partnership.
2. Lead on the integrated analysis of the epidemiological and
WGS data.
3. Provide guidance and validation of WGS-based methods.
4. Support the Member States in performing the transition to
appropriate use of WGS.
5. Develop and run pilot implementation studies with disease
networks.
European Centre for Disease Prevention and Control. Expert opinion on whole genome sequencing for public health
surveillance. Stockholm: ECDC; 2016.

4. 3
ECDC Roadmap top disease priorities, 2016-18
WGS–based typing for investigation of cross-
border foodborne outbreaks
Listeria monocytogenes, Salmonella enterica, STEC/VTEC
EU wide WGS-based typing for surveillance
Continuous surveillance:
• Listeria monocytogenes
• Neisseria meningitidis
Multi-annual pan-EU surveys:
• Carbapenemase-producing Enterobacteriaceae
• Antibiotic-resistant Neisseria gonorrhoeae
ECDC roadmap for integration of molecular and genomic typing into European-level surveillance and epidemic
preparedness – Version 2.1, 2016-19. Stockholm: ECDC; 2016.

5. 4
ECDC Roadmap second priority diseases, 2016-18
WGS-based surveillance prepared but operations deferred
until technical capacity is met across the EU/EEA countries
for:
• Salmonella enterica
• Shiga-Toxin producing E. coli (STEC)
• Multidrug-resistant Mycobacterium tuberculosis
• Human influenza virus
European Centre for Disease Prevention and Control. ECDC roadmap for integration of molecular and genomic typing into
European-level surveillance and epidemic preparedness – Version 2.1, 2016-19. Stockholm: ECDC; 2016.

6. 5
- WGS strategy
- Roadmap 2.1
- Work plan
(annual)
- Business cases
(multiannual)
- Disease objectives
- Performance indicators
- Surveillance system
- MS capacity
- Pilot studies
- Routine operation
REVISION
CONSULTATION

7. 6
Timeline for the revision of the ECDC WGS
roadmap
European Centre for Disease Prevention and Control. ECDC roadmap for integration of molecular and genomic
typing into European-level surveillance and epidemic preparedness – Version 2.1, 2016-19.
2016 2017 2018 2019 2020
WGS- ELiTE II study WGS-based surveillanceL. monocytogenes
Roadmap V 2.1 Roadmap V 3
S. enterica/ STEC
WGS Data sharing/ analysis for outbreak
investigation including testing of analysis
platforms
PFGE-MLVA based surveillance
CPE and AR-N.
gonorrhoeae
BC
Case based-WGS data linkage
WGS-based EU survey
WGS-based surveillanceN. meningitidis BC
MDR-TB
No transition to WGS-based surveillance until
MS capacity increases; Maintenance of MIRU-VNTR
quality assurance and EU data collection and analysis
Monitor progress on international validation of WGS-based identification,
drug resistance prediction and typing nomenclature

8. 7
Timeline for the revision of the ECDC WGS
roadmap (cont’)
European Centre for Disease Prevention and Control. ECDC roadmap for integration of molecular and genomic
typing into European-level surveillance and epidemic preparedness – Version 2.1, 2016-19.
2016 2017 2018 2019 2020
Influenza
Roadmap V 2.1 Roadmap V 3
HIV/HCV
C. difficile
MRSA
No transition to WGS-based surveillance until
MS capacity increases
BC
Sequence-based
surveillance with
GISAID
WNV
Develop antiviral resistance surveillance strategy and map capacity
Evaluation of EU surveillance feasibility and utility
with PCR-ribotyping
BC
Strategy

9. 8
Thank you for listening,
ECDC.Microbiology@ecdc.europa.eu