Understanding of WGS varies between countries - FAO

By Joseph James Whitworth

- Last updated on GMT


Related tags Food safety management Food

Whole Genome Sequencing (WGS) has the potential to play a significant role in food safety but the level of understanding of concepts and potential vary among countries, according to FAO.

While WGS can significantly contribute to improving food safety management, it still relies on appropriate interpretation of laboratory data in the context of epidemiological evidence.

It provides rapid identification and characterization of microorganisms, including antimicrobial resistance (AMR), with precision not previously possible.

With the declining cost, applications in food safety management, including opportunities for enhanced integration of information from human and animal health, could contribute to better consumer protection, trade facilitation, nutrition and food security, said the Food and Agriculture Organization of the United Nations in the report​ with the World Health Organization.

Use in the field

WGS can be a powerful supplement to, but not a substitute of, basic good practices - such as strong public health surveillance systems, multidisciplinary investigations, good agriculture practices, good manufacturing and hygiene practices in the farm to table continuum.

The report presents four case studies to highlight key benefits and potential drawbacks of WGS in food safety management.

Possible partners for developing countries:

  • PulseNet International: a network of national and regional lab networks tracking enteric foodborne infections worldwide;
  • International Congress on Pathogens at the Human Animal Interface (ICOPHAI): a congress to bring together experts in One Health from Brazil, the US, Ethiopia, Kenya, Thailand, and other countries in South America, Asia, Africa, and Europe;
  • Global Microbial Identifier (GMI): a non-profit technical consortium on WGS for all microorganisms, including infectious diseases and food safety matters; and
  • CGIAR (formally known as the Consultative Group on International Agricultural Research): a global partnership addressing agricultural research for development.

On example was Public Health England beginning real-time sequencing of all presumptive Salmonella spp. from April 2014.

A statistical correlation between the UK egg distribution network and distribution of outbreak related patients was revealed by WGS. In June, a multi-national outbreak of Salmonella enterica serotype Enteritidis was linked to eggs.

“This case shows the power of WGS in revealing the epidemiology behind an outbreak, which allowed the definitive source of the outbreak - a single egg producer - to be identified and targeted for intervention, rather than just the restaurants where the contamination reached the population,” ​said FAO.

“Targeted intervention further up the food production chain can be additionally effective in reducing further risks.”

Another example, was the Kenya Medical Research Institute at the Centre for Microbiology Research, with the Welcome Trust Sanger Institute and the International Livestock Research Institute (ILRI), doing PFGE standard sequencing and WGS on Vibrio spp., Salmonella spp., Campylobacter spp. and E. coli strains for 15 years.

Data has assisted the government to understand potential benefit of WGS techniques in mapping disease hotspots, revising existing empiric treatment regimens and identifying high-risk foods during outbreaks.

WGS benefits – including universal application

WGS provides more precise information on pathogens than conventional methodologies enabling authorities to respond with a more targeted approach, limiting the number of implicated products (and those affected by recall) as well as the size of outbreaks (and number of human cases).

FAO cites an ECDC report​ which found: “WGS can be less expensive than current typing methods for pathogenic E. coli and Campylobacter spp. For Listeria, the cost is more or less the same, and for Salmonella, depending on the throughput, the cost can still be somewhat higher.”

WGS analyses are less costly than the myriad of standard subtyping methods necessary to characterize a single pathogen and results can are within a few days which is faster than current typing approaches.

WGS is universal across all pathogens while traditional methodologies often require laboratories to accredit species specific identification and typing methodologies and techniques are relatively easy to learn and apply compared to conventional methods such as serotyping or PFGE.

The drawbacks – including trade

Countries without established surveillance systems to supply isolates for sequencing may not see the cost benefit of adding WGS capability and implementation may divert essential resources from more pressing priorities, such as improved food security situations, development of basic monitoring and surveillance systems or improved water quality.

Even with access to basic bioinformatics/genomics software/online platforms, the interpretation of the data, especially in combination with epidemiological information, may not be easy.

Examples of voluntary databases that host WGS data

1. National Center for Biotechnology Information (NCBI)​: Part of the US National Library of Medicine (NLM), a branch of the National Institute of Health (NIH).

2. European Nucleotide Archive (ENA)​: Europe's primary nucleotide-sequence repository consisting of 3 databases: the Sequence Read Archive (SRA), the Trace Archive and European Molecular Biology Laboratory (EMBL) Bank. It provides a record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation.

3. DNA Data Bank of Japan (DDBJ)​: A biological database that collects DNA sequences, developed by Japan’s National Institute of Genetics (NIG). It is a member of the International Nucleotide Sequence Database Collaboration (INSDC). It exchanges data with EMBL at the European Bioinformatics Institute (EBI) and with GenBank at the NCBI.

If some countries implement WGS for food safety management, they are likely to apply the same system for imported food products.

However, some developing countries may not be able to provide the same level of WGS-based data on food products they export and may not be able to enter into mutual collaboration on an equal basis with trade partners who have more resources.

There is an issue around legal ownership of publicly available WGS data and applicable privacy laws and concerns from data producers, generators and collectors about ultimate use of their data.

Data sharing dilemma

FAO said there may be issues around liability and accountability that are legally binding in respect of WGS data use in a food safety regulatory framework.

There are concerns about data sharing around acknowledgement of owner, producer, generator or collector; and process of data sharing, including transparency, confidentiality and accountability.

Another challenge is scientists choosing to hold onto their WGS data to avoid others using it for publication as well as validation of reference materials and reference datasets for a global database.

If there are no harmonized techniques and interpretation standards, implementation of WGS in a regulatory framework may increase the risk of the methods being abused to create trade issues.

“For example, providing data showing that a given pathogen is present in food products in one country may result in technical barriers to trade from other countries. Another fear may be that Country A may identify a pathogen linked to specific food sources in Country B and act publicly on this, without engaging with Country B.”

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