Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015

1. Overview of the ECDC whole genome
sequencing strategy
Marc Struelens on behalf of ECDC WGS drafting group
Microbiology Coordination Section, Office of the Chief Scientist
European Centre for Disease Prevention and Control
Expert consultation, Stockholm, 19 November 2015

2. ECDC Strategy to harness whole genome
sequencing for strengthening EU outbreak
investigations and public health surveillance
This paper states the ECDC vision for using whole genome
sequencing technology within the context of its agreed
strategy and roadmap for integration of typing data into EU
level surveillance. It addresses the following questions:
• What are the strengths and weaknesses of WGS-based
typing for multi-country outbreak detection, investigation
and disease surveillance?
• What is the current state and medium-term outlook for the
development, harmonisation and inter-laboratory portability
of WGS-based typing for epidemiological investigation?
• What is the strategy and proposed role of ECDC in
collaboration with the EU and global players?

3. ECDC vision
In five years’ time, ECDC will have contributed to establish
standards and manage systems enabling the EU wide use of
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. It will further
improve pathogen detection, identification, antimicrobial
resistance profiling and biological risk prediction.

4. ECDC roadmap for molecular typing integration in EU
surveillance, by disease, under revision for 2016-20.
Disease target Sampling Typing method(s) Status 2015
Salmonellosis Continuous PFGE, MLVA
In operation; WGS
planning
Listeriosis Continuous PFGE
In operation; WGS pilot
started
Shiga toxin/ producing E. coli
infection
Continuous PFGE
In operation; WGS
planning
Multidrug-resistant tuberculosis Continuous MIRU-VNTR
In operation; WGS
planning
Invasive meningococcal disease Continuous
Serogroup; 10 loci sequence;
WGS/cgMLST
Business case; WGS pilot
Antibiotic-resistant gonococcal
infection
Repeat surveys NG-MAST two loci sequence Business case; WGS pilot
Carpapenemase-producing
Enterobacteriaceae
Repeat surveys
WGS/cgMLST
/ resistome/ virulome
Business case; WGS pilot
Meticillin-resistant Staphylococcus
aureus (MRSA)
Repeat surveys
WGS/cgMLST
/ resistome/ virulome
Business case; WGS pilot
Human influenza Continuous, sentinel Gene sequence/ WGS pilot started
Human Immunodeficiency virus
(HIV) infection
Continuous Gene sequence/ WGS Strategy planning
Clostridium difficile infection Continuous, sentinel PCR-ribotyping pilot planned
Hepatitis C To be defined Gene sequence/ WGS Strategy planning
West Nile virus infection Seasonal, Sentinel Gene sequence/ WGS Strategy planning

5. Survey of EU/EEA countries use of WGS
for public health application for one or
more diseases, 2015.
Application for:
Current application
July 2015
(# countries)
Plan for application
in the next 3 years
(# countries)
Outbreak
investigations
18 17
Surveillance
programmes
10 18
Source: NMFP survey September 2015, N=28 respondents

6. Number of EU/EEA countries using WGS (and/or
planning within 3 yr. use ) for surveillance per
disease or AMR target
Source: NMFP survey September 2015, N=28 respondents

7. WGS data production, analysis and integration
with epidemiological data for public health
surveillance.

8. Technical requirements for multicentre sharing of
genomic information for public health use
• Quality assurance standards
• WGS analysis strategy and genotype nomenclature
• WGS data storage and exchange resources.
• Integration of WGS data with epidemiological data
• Epidemiological concordance validation
• Resource investment and expertise diffusion.

9. ECDC 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

10. Acknowledgments
• ECDC: Barbara Albiger, Mike Catchpole, Bruno Ciancio,
Denis Coulombier, Laura Espinosa, Karin Johansson, Csaba
Ködmön, Daniel Palm, Joana Revez, Ivo Van Walle and
Members of the Microbiology and Surveillance Steering
Committees
• National Focal Points for Microbiology and for Surveillance
• Participants to previous ECDC expert consultations and EFSA
colloquium on microbial genomics for health protection
• Disease network and laboratory network members and
coordinators (FWD, ERLTB-Net, ELI-Net, IBD-LabNet, Euro-
GASP,…)