Plenary presentation by Vicky Lefevre (Acting Head of Surveillance and Response Support Unit, ECDC) at ESCAIDE 2018.

1. Whole Genome Sequencing in
EU Multi-country Foodborne Outbreak
Investigation
Vicky Lefevre, Acting Head of Surveillance and Response Support Unit, ECDC
ESCAIDE, Malta, 21 November 2018

2. EU Multi-country outbreaks
2

3. Whole Genome Sequencing: ECDC Vision 2020
By 2020, ECDC should have contributed to
establish standards and manage systems
enabling EU wide use of WGS as the
method of choice for typing microbial
pathogens for disease surveillance,
outbreak investigations and evaluation of
prevention policies.
3

4. Strategic Framework Priorities for 2019-2021
4

5. WGS-based typing use in national public health
reference laboratories
2015 2017
WGS-based typing used routinely for national surveillance - of at least 1 human pathogen
Not used for public health operations but planned by 2019
Not planned to implement within 3 years
Source: Revez J et al. Survey on the use of Whole Genome Sequencing for infectious diseases surveillance: rapid expansion of
European national capacities, 2015-2016 – Frontiers in Public Health, 2017 and NMFP 2017 survey 5

6. EU/EEA countries using WGS for surveillance or
outbreak investigations
Surveillance
Outbreak
Source: Revez J et al. Survey on the use of Whole Genome Sequencing for infectious diseases surveillance: rapid
expansion of European national capacities, 2015-2016 – Frontiers in Public Health, 2017 and NMFP 2017 survey. 6

7. Joint Molecular Typing for Enhanced Surveillance
2011 2012 2013 2014 2015 2016 2017 2018 2019
ECDC pilot molecular
typing data collection
PFGE and MLVA
EC vision on molecular
typing support for
outbreak preparedness
EC request to ECDC and EFSA
on establishment of molecular
typing databases
Pilot study WGS Listeria
STEC O104:H4
outbreak
First non-human isolate
submitted to the joint
database (PFGE)
Joint ECDC-EFSA Steering
Committee for a joint
molecular typing database
EC request to ECDC and EFSA to
upgrade joint molecular typing
database with WGS
Collaboration agreement: ECDC-EFSA- EURLs for
Listeria monocytogenes, Salmonella and VTEC
=> PFGE and MLVA
First joint cluster detections
PFGE and MLVA
EU-wide validation study
Listeria WGS
1st WGS support to multi-country
outbreak investigation
Upgrade Tessy database WGS

8. ECDC Molecular Typing Deployment
for Foodborne Diseases
8
Pathogen Status
Listeria monocytogenes
Salmonella enterica
STEC
PFGE/MLVA used for cluster detection (2013 )
PFGE/MLVA used for outbreak support/linking to food isolates (2013 )
WGS used for outbreak investigation support (2015 )
WGS used for cluster detection (2019 )
PFGE-based cluster detection stopped (2017-2018)

9. ECDC database PFGE, MLVA and WGS Isolates
Salmonella, Listeria and STEC
2012 - 2018
*for Salmonella Typhimurium and S. Enteritidis only
9
WGS for 5761 isolates
* as of 15 November 2018

10. PulseNet Bacteria Status
Listeria monocytogenes
Shiga toxin-producing E. coli (STEC)
Salmonella enterica
Clostridium botulinum
Shigella spp
Campylobacter
Vibrio spp
Yersinia spp
Chronobacter sakazaki
Other pathogenic E. coli (ETEC, EIEC,
EAEC, EPEC)
PulseNet WGS Deployment (US)
Outbreak
investigations
2018 deployment
cg/wgMLST
2019 deployment
cg/wgMLST
Current: WGS on
all US cases
PFGE ended
Source: John Besser, CDC, PulseNet

11. 0
20000
40000
60000
80000
100000
120000
1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017
PulseNet Isolates by PFGE and WGS (US)
1996-2017
Total Isolates, PFGE WGSSource: John Besser, CDC, PulseNet
Genomes:* 74,744
*as of June 13, 2018

12. WGS Improved Signal Detection and Response to
Multi-Country Foodborne Outbreaks
Whole genome
sequencing
support since 2015
MLVA1 + PFGE2
1MLVA=Multi-Locus Variable number tandem repeat Analysis
2PFGE=Pulsed-field gel electrophoresis
Weekly cluster
reports
Joint ECDC-EFSA
Rapid Outbreak
Assessments
Urgent Inquiry:
unusual increase of
cases at national
level

13. Urgent Inquiries related to Foodborne Diseases (n=277)
(2014 – 2018)
Diseases included:
anthrax, botulism,
brucellosis,
campylobacteriosis,
cholera, cryptosporidiosis,
food poisoning due to
toxins, hepatitis A,
hepatitis E, leptospirosis,
listeriosis, norovirus
infection, paratyphoid
fever, salmonellosis,
shigellosis, typhoid fever,
VTEC, vibriosis,
yersiniosis…

14. ECDC-EFSA multi-country outbreak
assessments and notifications for selected foodborne
diseases (2011 – 2018)
14*As of November 2018
0
2
4
6
8
10
12
14
16
18
2011 2012 2013 2014 2015 2016 2017 2018*
Noofoutputs
Year
Salmonella Listeria E.coli Salmonella notification Listeria notification
WGS support
since 2015

15. Data collection/analysis and WGS in Global Outbreak Investigation
15

16. Communication and WGS in Global Outbreak Investigation
16

17. 17

18. Listeria monocytogenes IVb, ST 6 confirmed outbreak
cases by month of symptom onset*, EU 2015–2018
(N=47)
FI reported the event in
an EPIS Urgent Inquiry
Following the request of EFSA and EC, the EURL
consulted the NRLs to identify possible food matches
RASFF alert FI,
other countries
followed reporting
withdrawal/recall
Interviews of patients confirmed exposure to frozen corn.
Some countries reported food matches related to frozen vegetable mix and frozen corn
Massive recall

19. 19

20. WGS: why is it revolutionary?
20
Discriminatory power of WGS much higher than that of other typing methods.
High ability to evaluate the “closeness” of strains.
High specificity, strength of association hypothesis from “matches”.
Early detection and delineation of multi-country outbreaks and dispersed
clusters.
More clusters detected (and ruled out).
More “sporadic” cases attributed to clusters.
Identification of persistent strains causing human infections in EU and likely
originating from continuous sources.
Laboratory work much less pathogen-specific and more amenable to automation.
Potential driver for policy and regulatory standards.

21. WGS: why is it not revolutionary?
The cost of WGS is still prohibitive for many countries.
Interpretation concerns, comparability between
different analysis, lack of standard bioinformatics
pipelines, definition of WGS-derived strain
nomenclature, need for trained staff with new skills
mixes.
“Matches” between cases and food/environmental
isolates provide a hypothesis but other data such as
epidemiological, exposure and trace-back information
are still needed.
More data to evaluate, and store and more
clusters to investigate.
Data sharing and availability of sequencing
results.
Food industry concerns, economic impact: what
is enough evidence for action?
21Source: The European Union summary report on trends and sources of zoonoses, zoonotic agents and food‐borne outbreaks in 2016

22. Is it Transformational….?
22
Whole Genome Sequencing in
EU Foodborne Outbreak Investigation