opportunities and challenges for whole genome sequencing in food safety...
TRANSCRIPT
Opportunities and Challenges for Whole Genome Sequencing in Food Safety Assurance and Control
Leon GorrisUnilever R&D Vlaardingen, The Netherlands
12th CII Food Safety Summit4 – 5 December 2017
Outline
• Next Generation Sequencing approaches
• WGS opportunities
• WGS challenges
2
https://www.genengnews.com/gen-articles/next-generation-sequencing-challenges/5953
Amended from Frédéric René (2016) 3
NGS / WGS - OVERVIEW
Amended from Frédéric René (2016) 4
NGS / WGS - OVERVIEW
FOOD PRODUCTS
Water, RMs,Facilities,
Environments
HUMAN Microbiota
Clinicalsamples
Amended from Frédéric René (2016) 5
NGS / WGS - OVERVIEW
Food Safety
Foodborneoutbreaks
Source tracking
Food Authenticity
&
Food Fraud
FOOD PRODUCTS
Water, RMs,Facilities,
Environments
HUMAN Microbiota
Clinicalsamples
6
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Wh
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Gen
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1 day 1-2 days Weeks
1 day 12-18 hours
Next Generation
Sequencing
Workshop
-Sampling-Sequencing-Bioinf.analysis-Phylo.treetakes ~ 1 week
WGS: “GAINING SPEED OVER CONVENTIONAL MICRO”
Outline
• Next Generation Sequencing approaches
• WGS opportunities
• WGS challenges
7
https://www.genengnews.com/gen-articles/next-generation-sequencing-challenges/5953
Designing safe and stable products in a highly diverse product portfolio
Wide range of micro-organisms to understand in terms of ecology,
physiology & preservation/control
8Molecular biology toolbox
Molecular biology toolbox
metagenomics
meta-transcriptomics
transcriptomics
metabolic pathway modelling
genomic analysis
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• Eco-typing studies; microbiomes
• global gene expression profiling
• Single organism gene expression profiling
• identifying biomarkers/intervention targets
• genotype/phenotype correlations
Tools for innovation
• Mechanistic understanding of microbial properties, e.g.
- spoilage, safety
• Innovation of preservation systems
- preservation targets, resistance traits
• Validating safe product and process designs, e.g.
- challenge testing context
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Supporting Food safety risk assessments
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“Growth & Inactivation
kinetics”
“Pathogenicity, Virulence”
Trouble shooting
• Identifying micro-organisms / unravelling communities
- Phylogenetic and functional classification
• Investigational / root-cause analysis
- Targeted follow-up of traditional microbiology
- Tracing & tracking
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Eva Møller Nielsen, PhDFAO Headquarters, Rome, Italy (23-25 May 2016)
Simplifying laboratory analyses
Steven M. Musser, PhD and Ruth Timme, PhDCampden BRI, Chipping Campden UK (19 May 2016)
Potentially “preventative” (1)
Steven M. Musser, PhD and Ruth Timme, PhDCampden BRI, Chipping Campden UK (19 May 2016)
Potentially “preventative” (2)
Christopher BradenCFS-UnivGeorgia Annual meeting (1 March 2016)
Identifying more (small) clusters
Ruth Timme, PhDIAFP 2016, WGS Workshop (30 July 2016)
Ruth Timme, PhDIAFP 2016, WGS Workshop (30 July 2016)
GROWING THE DATABASE
Ruth Timme, PhDIAFP 2016, WGS Workshop (30 July 2016)
OPEN DATABASE
Ruth Timme, PhDIAFP 2016, WGS Workshop (30 July 2016)
GOING INTERNATIONAL
Outline
• Next Generation Sequence Interests
• WGS Opportunities
• WGS Challenges
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“WGS applications in food safety management, could contribute to greater consumer protection,trade facilitation, and food/nutrition security.”
“Countries around the world use WGS or consider using it for food safety: Argentina, Australia, Brazil, Canada, China, Denmark, Germany, Italy, Japan, Kenya, South-Africa, Spain, UK, USA,……….”
47th CCFH WGS Side eventBoston, 12 November 2015
http://www.icmsf.org/events/past_conferences.html
Whole Genome Sequencing (WGS)SCIENTIFIC ROBUSTNESS QUESTIONS
Are scientific studies available to validate the correct interpretation of finding particular genetic profiles in homes, environments or business operations?
Is the technology mature enough for us to understand the relationship between genotypic traits of isolates and actual risk to public health, rather than hazard presence?
What about quantification, given differences in regulatory limits of pathogens globally?
Is there clarity on the regulatory response when “interesting” or “suspect” WGS profiles are found to be associated between “field” & database profiles?
47th CCFH WGS Side eventBoston, 12 November 2015
Steven M. Musser, PhD and Ruth Timme, PhDCampden BRI, Chipping Campden UK (19 May 2016)
RESPONDING TO ASSOCIATIONS
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Value of information:
- Method standardization & protocol harmonization to maximize comparability.
- Quality Assurance challenge underestimated?
Validity of interpretation:
- Rather immature science area; demanding capability; genotype versus phenotypic expression/epidemiology; challenge to use data in risk-based food safety management
Legal matters:
- Ownership: 3rd Party data generation & storage, external collaborations; public storage/sharing
- Consequences: “false positive” associations in enforcement context; “legacy” cases raised; “risk communication during investigations”
- Governance: little involvement of legal experts in developments
Training and Education:
- A global and local challenge, less for technical skills then for operational application
JOBs TO BE DONE!?
27http://www.fao.org/3/a-i5619e.pdf
Utility of WGS – positive outlook
WGS as a new research tool / risk assessment input
- Microbial ecology, microbiome,….
- Preservations systems, tolerance, preservation targets,…..
- Resistance mechanisms, resistance anticipation/avoidance, AMR,…..
WGS as a investigational tool:
- Outbreak investigation, attributing cases to outbreaks,…..
- Root cause analysis, trouble shooting,….
WGS as an early warning tool:
- Identification of possible associations between illness cases and microorganisms…..
- Sharing of WGS data leverages resources to broaden the reference base28
WGS as a identification tool:
- Identification of microorganisms…..
Eva Møller Nielsen, PhDFAO Headquarters, Rome, Italy (23-25 May 2016)
Investments needed
Management consequences?
https://www.dashingd3js.com/about
Data Generation
Data Interpretation
Management Action
In house
Outsource
