Whole-Genome Sequencing: Foodborne Illness Outbreaks in Exquisite Detail

One of the realities of living in an increasingly interconnected world is meeting the challenges of a globalized food system- namely, identifying the source of an outbreak of foodborne illness and establishing controls when food sources and producers span the globe. In a recent communication, Professor Guy Poppy, the Chief Scientific Advisor to the Food Standards Agency (FSA) addressed technology he described as “transforming the investigation of foodborne disease outbreaks” – whole-genome sequencing (WGS).¹

With next generation whole-genome sequencing, researchers and the food industry can “read” the few million nucleotides in suspect bacteria (or few thousand viral nucleotides) for around $100 and in just a few hours. In this way, they can quickly map differences and similarities between individual bacteria from the same species and identify related clusters of outbreaks that would go un-linked without this level of investigation.

Poppy illustrates the power of this technology with the example of the 2014 Salmonella outbreak in Europe. In that instance, the FSA investigated 287 cases of salmonellosis between May and September of 2014, eventually linking 69% of them to imported eggs infected with Salmonella Enteritidis PT14b. These cases spread from Northwest and South of England to France and Austria from infected eggs sourced from Germany. Although the investigative teams used traditional techniques to identify the strain, whole-genome sequencing produced detailed genetic data Poppy describes as “exquisite” that allowed investigators to prove that the geographically widespread S. Enteritidis PT14b isolates emerged from the same source and also to produce a clear picture of how the pathogen had spread.

The author further indicates that whole-genome sequencing is poised to move beyond confirming investigations to become the primary tool for identifying, characterizing, and comparing strains in suspected outbreaks involving a variety of foodborne bacteria, including Salmonella, Shiga toxin-producing E. coli, Campylobacter, and Listeria. In addition to its speed and cost-effectiveness, Poppy highlights the technique’s ability to trace evolutionary relationships, revealing linkages that might otherwise go unnoticed. He offers a 2012 listeriosis case to illustrate this. In that instance, whole-genome sequencing allowed investigators to re-examine data spanning two years and identify an additional 13 cases associated with a single food product, ultimately resulting in control measures.

Other potential applications of whole-genome sequencing include:

Emerging Pathogens- WGS would offer researchers access to genetic data useful for efficiently characterizing biological traits of variant or completely novel pathogens (e.g. virulence factors).
Routine Monitoring- Its precision-based utility for source tracking renders it ideal for regulatory monitoring. A pertinent example is a US-based 2013 Listeria outbreak that crossed multiple state lines and implicated three separate ice-cream production facilities run by the same producer.
Food Authentication- Untargeted WGS using next generation technology could offer unbiased detection of all species in a given sample and lead to identification of unexpected contaminants or adulterants, including cases of food fraud. The limitation here is that untargeted testing may be less sensitive than PCR-based testing.

The challenges inherent with whole-genome sequencing include the requirement for libraries of genome sequences and, with this, potential issues of intellectual property rights (e.g. who owns the data?) as well as patient confidentiality. Additionally, since investigations are often global, researchers would need standardized procedures as well as access to ways to store and interpret the data (e.g. bioinformatics).

On the whole, Poppy paints whole-genome sequencing as an emerging technology singularly capable of providing the “exquisite” detail suitable for making vital connections and tracking maneuvers during an investigation of foodborne illness, ultimately allowing for the implementation of control measures to prevent future outbreaks. For food producers who face the stark realities of potential outbreaks- both in terms of real finances and branding tarnishment- this news couldn’t be more welcome.

Learn more about designing custom molecular assays for outbreak tracking and tracing in our recent article: Designing Food Safety: Custom Assay Development for Salmonella

Reference

1 Poppy, Guy. (2016) ‘Issue Three: Whole-genome sequencing of Foodborne Pathogens.’ Chief Scientific Adviser’s Science Report, Food Standards Agency