http://tiny.cc/faowgsworkshop Potential usefulness of genome sequencing technology on food safety management - Canada. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.

1. Perspectives from Canada
Canadian Food Inspection Agency
Public Health Agency of Canada
Health Canada
Sabah Bidawid, PhD
Chief, Microbiology Research Division
Food Directorate, Bureau of Microbial Hazards
Health Canada
Celine Nadon, PhD
Chief, Enteric Diseases
National Microbiology Laboratory
Public Health Agency of Canada

2. 2
FOOD SAFETY IN CANADA

3. 3
Federal food safety responsibilities are shared
PRODUCTION PROCESSING/DISTRIBUTION/RETAIL/FOOD SERVICE CONSUMERS
On-farm Food
Safety Programs
Policy &
Standards
Monitoring/
Early Warning
Education &
Outreach
Inspection &
Enforcement
Public Health
Surveillance
AGRICULTURE &
AGRIFOOD CANADA
•Contributes to research
and development of on-
farm food safety
programs
HEALTH CANADA
•Establishes food safety policy and standards
•Conducts health risk assessments
•Informs Canadians about potential risk to
their health
•Safety of veterinary drugs and pesticides
• Research vis-a-vis policy development
CANADIAN FOOD INSPECTION
AGENCY
•Design and delivery of federal food
inspection programs
•Monitors industry’s compliance with
Acts and regulations
•Undertakes enforcement action as
necessary
PUBLIC HEALTH
AGENCY OF CANADA
•Public health
surveillance
•Leads outbreak
investigations with
P/T public health
officials
HEALTH CANADA
CFIA
PHAC
AAFC

4. 4
IMPLEMENTATION OF WGS – REGULATORY/INSPECTION
Outbreak
investigation
Monitoring
program
Isolated colony WGS Bioinformatics Report of
analysis
Health
Risk
Assessment
Regulatory
Action
(e.g., recall)
Map reads
Assembly
Identification
Typing/Signature sequences
Virulence profile
Quality metricsDesired outcomes:
• Comprehensive analysis
• Definitive identification
• Risk profiling
• Timely interventions
Canadian Food Inspection Agency
Approximately 12,500 food
samples analyzed annually for
compliance and investigation
Fresh Produce – 10%
Imported and Manufactured
Foods – 4%
2014-2015
SAMPLED PRODUCTS

5. 5
IMPLEMENTATION OF WGS - POLICY
NO
YES
YES
STRONG
EVIDENCE
PFGE ANALYSIS PHAC/
HC/CFIA Link cases to food
Section B
STRONG
EVIDENCE
NO
NO
HRA HC Section E
Appendix E NO
RISK ASSIGNED
TO FOOD HC
Section F
CHECK GMPs
and HACCP
CFIA
RISK MANAGEMENT ACTION
CFIA Section G
GMP, HACCP, QA, Investigation
Check additional products
LEGEND
STRONG EVIDENCE
NO
YES
NEXT
BACK AND FORTH
YES
CONTINUE
SURVEILLANCE
PHAC/CFIA
Continue epidemiological
investigation
NO MORE
LEADS
CLOSED
UNSOLVED
TRACEBACK/TRACEFORWARD
Products identified in distribution CFIA Section D
YES
STRONG
EVIDENCE
EPIDEMIOLOGICAL
ANALYSIS PHAC
(# cases, demographics, clinical presentation,
food history/exposures)
Section C
YES
CONTINUE PHAC
SURVEILLANCE
NO
CASES OF ILLNESS (food, # of cases, history, etc.) PHAC
Section C
FOOD SAMPLE (in-situ; for
pathogen ID) CFIA*
Section A
ISOLATE MATCH PHAC
(link between cases)
Section B

6. 6
IMPLEMENTATION OF WGS - POLICY

7. 7
IMPLEMENTATION OF WGS - POLICY
“While PFGE and MLVA are the gold standard subtyping methods for
foodborne bacterial pathogens, newer methods are being developed
for genetic profiling, including whole genome sequencing. This
research and development is done to ensure that the best
technology and most current science are available for foodborne
disease investigations and with the application of validated
interpretation criteria and assessment of weight of evidence. When
new tests are applied during outbreak investigations for this purpose,
they are applied in parallel to the primary tests and are carefully
interpreted on a case-by-case basis.”

8. 8
IMPLEMENTATION OF WGS POLICY:
 Foodborne Pathogens
• Canada is in the process of incorporating information from WGS
into Health Risk Assessments and Epidemiological Surveillance
– WGS is being performed on, Bacteria, Viruses, and Parasites from
Clinical, Environmental, and Food Sources
– WGS data: currently used to monitor trends in emerging
pathogens, AMR, to identify novel virulence factors, and as an
parallel/alternative to traditional analyses like MLST and serotyping
– HC is also working on Quality Assurance and Best Practices
Standards Guidelines for sequence analysis (Pightling et al., 2015;
2014).
– Working toward using WGS to support the development of policy/
standards/compliance.

9. 9
IMPLEMENTATION OF WGS:
SURVEILLANCE & OUTBREAKS
PulseNet Canada
Genomic
Epidemiology
Roadmap
Aleisha Reimer with contributions
from Drs Celine Nadon, Morag
Graham, and PulseNet Canada
members
October 16, 2013
Based on existing
PulseNet Canada
model
De-centralized
sequencing and
analysis
Parallel, centralized
storage & analysis of
national data sets
Continued NML
support in reference
testing, training,
certification &
proficiency
Continued method
development,
refinement, and KT

10. 10
IMPLEMENTATION OF WGS: SURVEILLANCE & OUTBREAKS
WGS initiated by
NML or member
and permission
granted by member
laboratory
Sequencing
performed by NML
Sequencing performed by
member laboratory, but part
of a multijurisdictional
cluster/outbreak
Member uploads raw
sequence to NML database
Multi-jurisdictional
bioinformatics analysis
performed by NML
Member can
download raw
sequences
Results & interpretations
are verified with the
submitting laboratories for
consensus
NML provides results
interpretations to PHAC
managers & epidemiologists,
OICC, and international
partners (as determined in
previous step).
Information Flow:
Whole Genome Sequencing
Challenges:
- Comfort level among partners on
appropriate use of data
- IP and isolate ownership: national
agreements to enable meta-data
sharing
- Paradigm shift about what should
be publicly available
Mitigations:
- Transparency
- Rigorous communications protocols
- Trust building
- MOU

11. 11
BIOINFORMATICS AND IT INFRASTRUCTURE
NML
IRIDA
BioNumerics
HPC
AB
BC
SK
MB
ON
QC
NL
NB
NS
PEI
NU
NT
Hub and Spoke Model
- High speed connections from FPT
partners to NML
- IRIDA and BioNumerics used for
data storage, management,
surveillance, analysis
- Centralised IT and bioinformatics
experts
- Intent – common platform for
federal partners

12. 12
CFIA
BIOINFORMATICS
HUB
NML
BIOINFORMATICS
HUB
Public Health Lab WGS Capacity
Food Lab WGS Capacity

13. 13
STANDARDS AND HARMONIZATION
International standards for Bioinformatics and Genomics for public health and
regulatory activities - currently under way. Government of Canada active in:
• Global Coalition for Regulatory Science Research Working Group on Bioinformatics
- developing Best Practices for bioinformatics for food regulatory application
• Global Microbial Identifier international consortium developing standards for
genomic epidemiology
• PulseNet International harmonization and standards for surveillance and outbreak
response
• International Standards Organization Technical Committee (ISO/TC 34/SC
9/WG25) – QA standards for genomics in food testing
• IRIDA platform incorporates ontologies, public APIs, data provenance, and a
flexible QA/QC system for WGS-based analyses
Approach: Harmonized, non-prescriptive
standards and best practices

14. 14
EDUCATION
NEED GOAL APPROACH TO DATE…
Lab capacity – data
analysis specialists to
perform genomic
analyses and
interpretation “frontline”
Knowledge of how
to interpret genomic
information by
partner laboratories
Hub and Spoke:
Expert computational
resources that
cascade skills to wider
users (hub); lab staff
receive training
appropriate to their
role (spokes)
Technical bioinformatics
workshops; genomics
wet lab training; practice
(repeated outbreak
analyses)
Stakeholders with
comfort &understanding
of the added value &
benefits offered by
WGS
Stakeholder fluency
in genomics-based
evidence
HUB & SPOKE model;
different audience than
for operational training
Educational webinars,
multi-jurisdictional task
groups, annual
meetings, briefing
notes, white papers
Knowledge translation activities critically important, tailored for audience

15. 15
CASE STUDIES
Organism Case or Outbreak Details (putative/confirmed vehicle)
L. monocytogenes Collaboration with USA (lettuce product)
L. monocytogenes Collaboration with USA (RTE meat product)
Salmonella Thompson National laboratory investigation to support outbreak
response in a single province (suspected chicken
products)
E. coli O157:H7 Large outbreak in a single province (pork products)
L. monocytogenes Ongoing cluster of common PFGE pattern
L. monocytogenes Collaboration with USA (caramel apples)
S. Enteritidis Collaboration with USA (bean sprouts)
Selected Investigations Supported Prospectively by
WGS, PulseNet Canada, 2014
Usefulness of WGS application to outbreaks in 2014:
- Increased resolution; ability to rule in/out matching PFGE patterns
- Provided confirmation of PFGE/MLVA findings
- Grouped unrelated PFGE patterns – large clusters that otherwise may have been missed
- Facilitated development of data sharing protocols for use in real time as well as
knowledge translation to lab and epi partners

16. 16
CASE STUDIES
In Canada, WGS is routinely applied during cluster investigation or
outbreak response in parallel to PFGE/MLVA. General findings:
WGS CONFIRMS MOLECULAR
RESULTS
WGS PROVIDES ADDITIONAL
INFORMATION
Example: beef-associated E.
coli O157:H7 outbreak (2012)
PFGE & MLVA used for case
definition; WGS in parallel gave
same results
Example: Canadian cases - US
outbreak of listeriosis
associated with caramel apples
Canada had 2 PFGE matches
One case reported apple
exposure, one did not
WGS confirmed that the case
with no exposure was not
outbreak-related, despite the
PFGE match
Only
molecular
results
“officially”
used

17. 17
CASE STUDIES
WGS CONFIRMS MOLECULAR
RESULTS
Example: beef-associated E.
coli O157:H7 outbreak (2012)
Example: Canadian cases - US
outbreak of listeriosis associated
with caramel apples
WGS used in parallel with
established molecular tests
enables database building &
increases knowledge transfer
activities while providing the
“comfort” of the gold standard
Independent analyses using two
pipelines (US and Canada) were
in agreement, thus increased
confidence in WGS results of a
higher resolution than PFGE
In Canada, WGS is routinely applied during cluster investigation or
outbreak response in parallel to PFGE/MLVA. General findings:
WGS PROVIDES ADDITIONAL
INFORMATION

18. 18
SUMMARY
Status: government-wide tiered approach; mostly
in parallel with traditional tests so far
Implementation challenges: what happens when
funding is insufficient? When volumes are low? How
long until traditional tests are phased out? What will
new interpretation criteria look like?
Primary issues present in Canada:
standardization/harmonization, IT and bioinformatics
infrastructure, data integration, sharing, and KT

19. 19
Co-Authors
Canadian Food
Inspection Agency (CFIA)
- Burton Blais
Health Canada (HC)
- Sabah Bidawid
- Franco Pagotto
- Nicholas Petronella
- Jennifer Ronholm
- Jennifer Holtzman
Public Health Agency
of Canada (PHAC)
- Celine Nadon
- Morag Graham
- John Nash
- Aleisha Reimer
- Gary Van Domselaar

20. 20
Additional Materials
- Discussion points on FAO questions
- GMO perspective on use of genomics

21. 21
INSIGHTS
Is WGS considered beneficial for food safety management in Canada?
What could be the drawbacks?
• Benefits
– Harmonize methodology (decrease lab to lab variability) – one test fits all approach
– Highly informative tests results (identification, characterization, risk assessment)
– Third party evaluation of results
– Cost effective and timely
• Drawbacks
– Still need an isolate
– Possible decline of culture collections
– Comparison to legacy data
What are the necessary conditions /infrastructure to employ WGS
technology for food safety management in Canada?
• Sequencing capacity
• High Capacity Storage and Data analysis
• Bioinformatics support in the form of tools, expertise, & databases
• Interpretation criteria/policy for data use
• Governance for sharing
If in the future this will be used for food safety management, what are
the key prerequisite activities?
• Database construction
• Validation experiments

22. 22
INSIGHTS
What agencies are/should be involved to make good results? How they are
(can be) working together on this topic? Are there any important stakeholders
(industry/company or academia/research) who should be involved?
• Health Canada (HC); Public Health Agency of Canada (PHAC); Canadian Food
Inspection Agency (CFIA).
• Provincial and territorial public health
• Food Industry
What could be the real challenges (overall and specific) in when actually
using WGS for food safety management?
• Sharing (databases, sequencing data, tools, results of validation experiments etc.)
• Food Industry outpacing regulatory and compliance agencies (CIFA, PHAC, HC)
• Predictive accuracy (e.g. predicting phenotype)
What roles do you expect/wish that international organisations would play
on this topic?
• Standardization/harmonization (not prescriptive though)
• Database

23. 23
Capacity building for pre-market assessment of genetically
modified organisms
• Mandated activity (Division 28 of the Food and Drug Regulations)
– molecular characterization, nutritional composition, chemical safety
number of DNA insertion sites in the genome, presence of complete or partial
copies, intact insert, absence of plasmid backbone
• Companies typically provide data generated by classical molecular biology
methods (Southern blot, PCR, Sanger sequencing), however there is interest from
industry to provide regulators with molecular characterization data generated
using WGS
• Approach
– Consultation with experts and stakeholders (CFIA lead, March 2015)
– Draft internal guidance by GoC expert working group (Health Canada lead,
Nov. 2015)
– External guidance will be developed by GoC working group (2016)