opportunities and challenges for whole genome sequencing in food safety...

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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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

9

• 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

10

Supporting Food safety risk assessments

11

“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

12

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

21

“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

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!?

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

THANK YOU

leon.gorris@unilever.com