Whole Genome Sequencing and Food SafetyPotential relevance to the work of Codex

Whole-Genome Sequencing Expected to Revolutionize Outbreak Investigations By James Andrews | July 30, 2014

Whole genome sequencing – in the news

What is Whole Genome Sequencing?• A technology which allows us to reveal the complete DNA

(genetic) make-up of an organism• Allowing us to better understand variations both within and

between species – for food safety these are bacteria, viruses, parasites

• Allows us to differentiate between organisms with a precision that other technologies do not allow.

Another new technology – Do we need it?

• Every year foodborne diseases cause almost

• 1 in 10 people to fall ill

• 33 million healthy life years lost

Another new technology – Do we need it?• 2011 - E. coli O104:H4 centered on Northern Europe

• misidentification of cucumbers as the source ( Spanish growers estimated it cost them $200M/week)

• Farmers and industries lost $1.3 billion, and emergency aid provided to 22 European states cost another $236 million

• Number and cost of recalls increasing – Example from USA

National and Global Initiatives

Whole genome sequencing – how can it help?

WGS

Disease surveillan

ce

Source tracking

Food/Env monitorin

gIdentification of specific

traits, e.g. virulence, resistance

Outbreak investi - gation

Source attributi

on

Reality

WGS is already being used for food safety - what can we learn?

Applications of WGS in food safety management

• Current applications

• Benefits and drawbacks

• Challenges of applying WGS within a regulatory framework

• Considerations for countries with limited capacity and resources

Case 1: Real time WGS based health surveillance and food monitoring for Listeria monocytogenes• Listeriosis outbreak in USA

2014

Case 1: Real time WGS based health surveillance and food monitoring for Listeria monocytogenes

• What did WGS do?

• Confirmed hypothesis quickly

• Added strength to evidence

• Resolved ambiguous lab-epi data

• Accelerated response due to data shading

• Fuelled research on prevention

Case 2: Identifying and linking apparently sporadic cases over a long time period

• What did WGS do?

• Detected and linked illnesses that would otherwise have been categorized as sporadic

• Enabled strong evidence form environmental and food sampling

• Delineated outbreak caused by same product form different companies

Image developed and provided by Celine Nadon

Case 3: WGS based investigation uncovered root cause of Salmonella outbreak

• What did WGS do?• Initial link to restaurants was only the beginning

• Correlated case distribution to egg distribution and linked back to a single supplier in another country

• Identified cases in other countries

• Enable targeted intervention at source

• Demonstrated benefits of WGS data sharing

Inns et al, Eurosurveillance 2015

Case 4: Impact of WGS on food safety and public health policy in a developing country

• What did WGS do?

• Demonstrated value of mapping disease hotspots, revising treatment regimes, identifying high risk foods during outbreaks

• Greater consideration of investment in food safety

• Fuels interest in interventions

• Highlights need for advocacy

Benefits

Drawbacks

National/Global data sharing• Benefits• Efficient use of resources• Trend analysis • Rapid response• More targeted interventions

• Improved food safety• Improved mitigation of health, social and economic impacts

• Challenges• Data ownership and metadata access

• Accountability and transparency

• Validation, standards and quality

• Fear of being ‘ scooped’• Trade impacts• Privacy

Global Governance of data sharing• Nagoya protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity is a 2010 supplementary agreement to the 1992 Convention on Biological Diversity (CBD)• Entered into force on 12 October 2014• Over 70 parties

• Relevance for WGS data• Under discussion in WHO regarding sharing information on pathogens of high public health concern

• OIE discussed this at their most recent assembly• Convention on plant genetic resources – interpretation document

• Differing interpretations of relevance at country level• One of the aspects to be addressed in global data sharing efforts

Application of WGS within a regulatory framework

Image provided by Celine Nadon

Application of WGS within a regulatory framework

Image provided by Celine Nadon

Engaging countries• Meeting in Association with GMI 9 to provide countries with a platform to learn, share experiences and concerns

• Particular focus on developing countries• Benefits recognized but drawbacks = challenges

• Costs• Current level of food control systems

• Bioinformatics - key to appropriate and effective use of WGS

• Data sharing- cultural differences on what that means and what countries are willing to share

• One Health tool – transboundary technology• Raise awareness – enable informed decisions

What this technology means for Codex? • 2015 – side event at the Codex Committee on Food Hygiene

• Awareness of the technology and ongoing work• Sensitization to potential applications

• Recognition of molecular techniques in current Codex texts e.g. Guidelines on the Application of General Principles of Food Hygiene to the Control of Listeria monocytogenes in Foods – use in identifying source of organisms

• Application of Codex Texts e.g. Guidelines on the Application of General Principles of Food Hygiene to the Control of Pathogenic Vibrio Species in Seafood, sequencing starting to increase our understanding of pathogenic strains and target risk management measures accordingly

Future work – Scientific advice to Codex• VTEC and STEC – what

should Codex focus on?

• ILSI Europe - Next Generation MRA (Microbiological Risk Assessment) Integration of Omics Data into Assessment, Athens, Greece 13-14 May 2016

The Use of Whole Genome Sequencing and Metagenomics in Modelling and Risk Assessment 3 August 2016

Discrete traits analysis of S. aureus CC398.

Mark Woolhouse et al. Phil. Trans. R. Soc. B 2015;370:20140083

©2015 by The Royal Society

Antimicrobial resistance and movement from the food chain to humans

Diagram of the dissemination of S. Typhimurium DT104.

Pimlapas Leekitcharoenphon et al. Appl. Environ. Microbiol. 2016;82:2516-2526

International harmonization of methodology

• Standardization of protocols•Ongoing work of ISO

• Need for proficiency testing, lab accreditation•Ongoing efforts of GMI

• Bioinformatics• Greater

capacity, training from university onwards

Key points• This technology is becoming embedded in the food regulatory systems in a number of countries

• Provides a higher resolution of information than previously available – fewer hiding places

• Transition period – used to compliment existing technologies e.g. PFGE

• Benefits have already been demonstrated but challenges remain

• All countries may not be able to apply it for the foreseeable future but should be at least aware of its capability and potential implications – need to ensure that it does not contribute to inequities, trade barriers

• Data sharing key to unlock true potential but there are barriers to overcome to ensure this is fair and beneficial •Role of international organizations

Contributing to One Health – bridging intersectoral differences