Opportunities and Challenges for Whole Genome Sequencing in Food - - PowerPoint PPT Presentation

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Opportunities and Challenges for Whole Genome Sequencing in Food - - PowerPoint PPT Presentation

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Opportunities and Challenges for Whole Genome Sequencing in Food Safety Assurance and Control Leon Gorris Unilever R&D Vlaardingen, The Netherlands 12 th CII Food Safety Summit 4 5 December 2017 Outline Next Generation Sequencing

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Opportunities and Challenges for Whole Genome Sequencing in Food Safety Assurance and Control

Leon Gorris

Unilever R&D Vlaardingen, The Netherlands

12th CII Food Safety Summit 4 – 5 December 2017

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Outline

  • Next Generation Sequencing approaches
  • WGS opportunities
  • WGS challenges

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https://www.genengnews.com/gen-articles/next-generation-sequencing-challenges/5953

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Amended from Frédéric René (2016)

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NGS / WGS - OVERVIEW

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Amended from Frédéric René (2016)

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NGS / WGS - OVERVIEW

FOOD PRODUCTS Water, RMs, Facilities, Environments HUMAN Microbiota Clinical samples

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Amended from Frédéric René (2016)

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NGS / WGS - OVERVIEW

Food Safety

Foodborne

  • utbreaks

Source tracking Food Authenticity & Food Fraud FOOD PRODUCTS Water, RMs, Facilities, Environments HUMAN Microbiota Clinical samples

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Conventional Microbiology Whole Genome Sequencing

1 day 1-2 days Weeks 1 day 12-18 hours Next Generation Sequencing Workshop

  • Sampling
  • Sequencing
  • Bioinf.analysis
  • Phylo.tree

takes ~ 1 week

WGS: “GAINING SPEED OVER CONVENTIONAL MICRO”

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Outline

  • Next Generation Sequencing approaches
  • WGS opportunities
  • WGS challenges

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https://www.genengnews.com/gen-articles/next-generation-sequencing-challenges/5953

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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

8 Molecular biology toolbox

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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
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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”

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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, PhD

FAO Headquarters, Rome, Italy (23-25 May 2016)

Simplifying laboratory analyses

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Steven M. Musser, PhD and Ruth Timme, PhD

Campden BRI, Chipping Campden UK (19 May 2016)

Potentially “preventative” (1)

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Steven M. Musser, PhD and Ruth Timme, PhD

Campden BRI, Chipping Campden UK (19 May 2016)

Potentially “preventative” (2)

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Christopher Braden

CFS-UnivGeorgia Annual meeting (1 March 2016)

Identifying more (small) clusters

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Ruth Timme, PhD

IAFP 2016, WGS Workshop (30 July 2016)

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Ruth Timme, PhD

IAFP 2016, WGS Workshop (30 July 2016)

GROWING THE DATABASE

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Ruth Timme, PhD

IAFP 2016, WGS Workshop (30 July 2016)

OPEN DATABASE

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Ruth Timme, PhD

IAFP 2016, WGS Workshop (30 July 2016)

GOING INTERNATIONAL

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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,……….”

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47th CCFH WGS Side event

Boston, 12 November 2015

http://www.icmsf.org/events/past_conferences.html

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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

  • perations?

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 event

Boston, 12 November 2015

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Steven M. Musser, PhD and Ruth Timme, PhD

Campden BRI, Chipping Campden UK (19 May 2016)

RESPONDING TO ASSOCIATIONS

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26 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!?

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27 http://www.fao.org/3/a-i5619e.pdf

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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 base

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WGS as a identification tool:

  • Identification of microorganisms…..
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Eva Møller Nielsen, PhD

FAO Headquarters, Rome, Italy (23-25 May 2016)

Investments needed

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Management consequences?

https://www.dashingd3js.com/about Data Generation Data Interpretation Management Action In house Outsource

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THANK YOU

leon.gorris@unilever.com