1.
Whole Genome Sequencing:
How significant is it
for
food safety?
Technical Meeting on the impact of Whole Genome Sequencing
on food safety management within a One Health framework
GMI9
23 May 2016
Celine Nadon, PhD
Public Health Agency of Canada

2.
The Paper
Expert Workshop, December 2015, Rome
Frank Møller Aarestrup (Chair, Denmark)
Marc Allard (USA)
John Besser (USA)
Sabah Bidawid (Canada)
Tim Dallman (UK)
Stephanie Defibaugh-Chávez (USA)
John N. Kiiru (Kenya)
Ana Maria Maquieira (Uruguay)
Paula Mussio (Uruguay)
Celine Nadon (Vice-Chair, Canada)
Eva Møller Nielsen (Denmark)
Sophie Roussel (France)

3.
Outline
Background
Examples
BenePits & Drawbacks
Regulatory challenge
Resource Considerations
Discussion
Conclusions & Summary
Why WGS for food safety? Technical Paper sec.on 2
Real-life applicaEons Technical Paper Sec.on 3
Technical Paper Sec.on 4
Applying WGS within regulatory frameworks
Technical Paper Sec.on 5
Countries with limited capacity & resources Technical Paper Sec.on 6
One Health and needed global acEons Technical Paper Sec.on 7

4.
Background
600 000 000
WHO, 2015
420 000
foodborne illnesses
deaths
31
major food safety hazards

5.
Background
WGS will impact food safety worldwide
DISEASE SURVEILLANCE
FOOD INSPECTION
OUTBREAK INVESTIGATION
ATTRIBUTION FOOD TECHNOLOGY
Centre Image: Smithsonian InsEtuEon

6.
Background
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purpose$5$
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lab$1$
lab$2$
lab$3$
lab$4$
lab$5$
Courtesy of Aleisha Reimer

7.
Background
Sample collection
Bacterial Growth
DNA Extraction
Fragment
SequencingRaw Sequence Reads
Prep DNA
Library
DATA

8.
Background
Laboratory subtyping methods affect outbreak
detection and response
Adapted from John Besser, 2006

9.
Background
of food safety problems
from imprecise or incorrect product implicaEons
IdentiPication, mitigation and prevention
Reduced economic losses and waste
food security

10.
Examples
WGS is already being used for food safety
what can we learn?

11.
Examples
Available at cdc.gov
HIGHER RESOLUTION Listeriosis outbreak, United States 2014

12.
Examples
PFGE CLUSTER 1
PFGE CLUSTER 2
PFGE CLUSTER 3
Seasonal food
product
Seasonal food
product & other*
WGS
CLUSTER
WGS
CLUSTER
Seasonal food
product
Seasonal food product
not outbreak-associated
*ready-to-eat food product commonly associated with L. monocytogenes
Adapted from Besser, 2015
HIGHER RESOLUTION Listeriosis outbreak, United States 2014

13.
Examples
WGS
CLUSTER
WGS
CLUSTER
Seasonal food product
not outbreak-associated
Confirmed hypothesis quickly
Added strength to evidence
Resolved ambiguous lab-epi data
Accelerated response due to data sharing
Fueled research for prevenEon
What did WGS do?
HIGHER RESOLUTION Listeriosis outbreak, United States 2014

14.
Examples
REDEFINED “SPORADIC” Listeriosis cases, Denmark 2014-2015
TOTAL CASES
5-YEAR MOVING
AVERAGE
Sporadic case: any illnesses below expected levels?

15.
Examples
REDEFINED “SPORADIC” Listeriosis cases, Denmark 2014-2015
10 cases over 24 months
WGS CLUSTER
Environmental samples from
Company X, supplier to
Supermarket

16.
Examples
REDEFINED “SPORADIC” Listeriosis cases, Denmark 2014-2015
WGS CLUSTER
Detected and confirmed source of illnesses that would have
otherwise been “sporadic”
What did WGS do?
Enabled strong evidence from environmental and food sampling
Delineated outbreaks caused by the same product type from
different companies

17.
Examples
UNCOVERED ROOT CAUSE Salmonella EnteriEdis, UK 2014
EnteriEdis
phagetype 14b
Inns et al – Eurosurveillance 2015
Associated with
ea^ng at restaurants

18.
Examples
UNCOVERED ROOT CAUSE Salmonella EnteriEdis, UK 2014
Inns et al – Eurosurveillance 2015
Restaurant associa^on
was just the beginning:
WGS showed
• Outbreaks at different restaurants
were linked
• Egg distribuEon network correlated
with distribuEon of cases
• Traceback of eggs to single supplier in
another country, and linked to cases
outside of UK

19.
Examples
UNCOVERED ROOT CAUSE Salmonella EnteriEdis, UK 2014
Revealed the epidemiology behind the outbreak
What did WGS do?
IdenEfied true source – rather than implicaEng restaurant
business only, as the interface with the consumer
Enabled targeted intervenEon further upstream in food
producEon
Demonstrated benefits of global WGS sharing

20.
Examples
MOTIVATE ACTION Kenyan Experience
Vibrio
Salmonella
Campylobacter
E. coli

21.
Examples
MOTIVATE ACTION Kenyan Experience
Demonstrates value of mapping
disease hotspots, idenEfying high
risk foods, revising treatment
What did WGS do?
Increases consideraEon to
investments in food safety
Fuels interest in regulatory
intervenEons, food tesEng, AMR
Illuminates need for advocacy

22.
Examples
Why were these applications successful?
• FuncEoning naEonal food control system
• Inter-sectoral infrastructure & networks (including laboratory)
• Adequate volume of isolates (cost effecEve)
• Ability to isolate pathogens from all matrices
• Technical support: laboratory, bioinformaEcs
• Sufficient data storage and connecEvity
• InformaEcs capacity and infrastructure

23.
BenePits
Image: Chris Rinke, available at jgi.doe.gov
UNIVERSALITY
STRENGTH TO EVIDENCE

24.
Drawbacks
Image: Chris Rinke, available at jgi.doe.gov
SURVEILLANCE REQUIRED

25.
Global Data Sharing
Improves food safety sciences
Efficient use of resources
Enables trend analysis & rapid response
MiEgates health, social, economic impacts
InequiEes in capacity & resources
Data ownership & metadata access
Accountability & transparency
ValidaEon, standards & quality
Fear of being “scooped”
Technical trade barriers
Privacy law

26.
Regulatory Challenge
GUIDELINES
AND BEST
PRACTICES
ROLE OF WGS IN
EXISTING
STREAMS OF
EVIDENCE
DATA ACCESS &
TRANSPARENCY
Developed countries:
Factors to
consider for
using WGS in
regulatory
decisions
need to be
sorted out
legal issues
trade impacts
quality control
training
communication
sustainability
continuous
improvement

27.
Regulatory Challenge
ASSESS AND SENSITIZE
Developing countries:
(YES)
(NO)
STRENGTHEN NATIONAL FOOD SAFETY
DEVELOP AND EDUCATE
TRANSITION & FUND
Prepare policy makers, and assess: is your
country’s infrastructure ready for WGS?
Build/enhance human health surveillance, food
monitoring/testing, laboratories.
Decision-making guidance, rationale, cost-
benefit, leverage other countries’ experiences.
Educate & train.
Establish stakeholder engagement. Implement
national coordination mechanisms. Harmonize
SOPs. Sensitize. Sustainable funding.

28.
Resource Considerations
PERCEPTION
“WGS is too
advanced and
too difficult to
implement”
“WGS is the
perfect soluEon
to all our
problems”

29.
Resource Considerations
Feasibility Assessment
quesEons for fact-based answers
PRIORITIES Is food safety high priority? Are many people affected? Are
industry, trade and economy affected? Will WGS help with
the priority pathogens?
PREREQUISITES NaEonal food safety policy and integrated food control
system in place? FuncEonal naEonal health surveillance,
with naEonal clinical reporEng and databases? FuncEonal
naEonal food monitoring and tesEng?
READINESS Where is the appropriate place for naEonal coordinaEon?
How will the system work? Can other resources be
leveraged, e.g. WHO, FAO, PulseNet InternaEonal, Global
Microbial IdenEfier?

30.
One Health
Image: Nagasaki University
WGS can help bridge
inter-sectoral approaches
through a truly global
common dataset

31.
Global Action - Needs
FORUMS FOR
DISCUSSION
ASSISTANCE FOR
DEVELOPING
COUNTRY CAPACITY
INTERNATIONAL
OUTBREAK
INVESTIGATIONS
TECHNICAL
GUIDANCE AND
BEST PRACTICES
COORDINATION OF
GLOBAL ONE
HEALTH ACTIVITIES
LINK COUNTRIES
WITH EXTERNAL
PARTNERS
HARMONIZED
GUIDANCE TO
TRADE ISSUES
PUBLIC-PRIVATE
PARTNERSHIP
FACILITATION
Opportunity for international organizations

32.
Conclusion
Countries with existing effective food safety & health systems
well posiEoned for adopEng WGS
Others may need to develop or strengthen the basics Pirst
competent authoriEes, labs, food monitoring, human health surveillance
WGS will become standard methodology in food safety
Expected to be beneficial for all countries, with some challenges remaining
Greater role for international organizations
Neutral and transparent brokers?
WGS will not supplant epidemiology and basic good practices
WGS alone will not fix lacking or broken systems
Global sustained commitment and collaboration
Ensure technology advances do not contribute to further inequiEes

33.
Acknowledgements
Masami Takeuchi (FAO, Document Development Coordinator)
Markus Lipp (FAO), Renata Clarke (FAO)
Document Peer-Reviewers:
Saoud Al Habsi (Oman), Genevieve Baah-Mante (Ghana), Chris Braden (USA), Josefina
Campos (ArgenEna), Isabel Chinen (ArgenEna), Almueda C. David (Philippines), Joanne Edge
(UK), Mariam Eid (Lebanon), Dina El-Khishin (Egypt), Jeff Farber (Canada), Agaba Friday
(Uganda), Peter Gerner-Smidt (USA), Morag Graham (Canada), Kai Man Kam (China), Karen
Keddy (South Africa), Ernesto Liebana (EFSA), Virachnee Lohachoompol (Thailand), Kinley
Pelden (Bhutan), Jennifer Ronholm (Canada), Jorgen Shlundt (Denmark), MarEn Wiedmann
(USA), Seyoum Wolde (Ethiopia), and Mayren Zamora (Mexico)
Vanessa Jones, Sarah Cahill (FAO), Amy Louise Cawthorne (WHO), Gwenalaelle Dauphin
(FAO), Francisco Lopez (FAO)
Editing and Technical Contributions: