The document summarizes the results of a 2015 survey on whole genome sequencing (WGS) capacity in European Union and European Economic Area Member States. Nineteen countries reported having national reference laboratories with access to next generation sequencing technologies like Illumina, and over half were applying WGS to surveillance and outbreak investigations of pathogens. While use of WGS is expanding rapidly, future annual surveys are needed to continued monitoring increasing capacity.

1. Results of the 2015 survey on WGS
capacity in EU/EEA Member States
14th National Microbiology Focal Points meeting
Barbara Albiger, Expert Microbiology, 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
2016
WGS Strategy and
Roadmap - V2.1, 2016-19
Survey on Member
States NGS capacity
(July 2015)

3. Survey on EU/EEA national plans and capacity for
WGS use for outbreak investigation and public
health surveillance, 2015
• Online survey (29 July 2015 to 13 October 2015,
anonymous)
• Target: National Microbiology Focal Points with the
support of colleagues from the National Public Health
Reference Laboratories
• Access, use or plans for Next Generation Sequencing
technology in the NRLs by July 2015
• Specification of the NGS technology platform(s) used
• Range of application in support to outbreak
investigations and/or surveillance by July 2015
• Sampling frame and volume of isolates tested in 2015

4. Results
• Completeness
Twenty-eight out of 30 NMFPs answered the
questionnaire on behalf of and in collaboration with
the national reference laboratories (NRL) for public
health in their country.
• NGS technology access
– Nineteen countries reported having NRL access to
one or more NGS technologies.
– Illumina technology platforms were the most
frequently used, and were available in 15 countries,
representing 62% of all platforms in use.

5. Results: surveillance by pathogen

6. Results: outbreak typing by pathogen

7. Trend in WGS use for national surveillance
EULabCap/ 2015 survey results, 2013-15
0
8
10
0
2
4
6
8
10
12
2013 2014 mid-2015
7
EULabCap Indicator 2.31. WGS use in national reference laboratories for
routine surveillance of one or more diseases/health issue.
NumberofEU/EEAcountries

8. Limitations of the survey
• Anonymity of answers: no follow up
• Missing data (2 countries)
• Timing of the survey

9. Conclusions and future plans
• Application of WGS for surveillance and
outbreak investigations is rapidly expanding in
the EU/EEA
• Over half of the countries having access to the
technology and NRLs were applying it in 2015
• Proposed annual surveys to monitor expanding
WGS capacity (September 2016, TBC)

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