This article is A complementary article on WGS for food safety and on the Future of WGS is available here.
WGS for food safety
Thanks to its higher specificity, WGS is replacing identification and characterization methods such as serotyping, virulence profiling, antimicrobial resistance determination and previous molecular typing methods for outbreak investigation by public health authorities. As of 2021, WGS has been employed for regulatory purposes in food safety by more than 20 countries (Australia, Austria, Belgium, Canada, China, the Czech Republic, Denmark, Finland, France, Germany, Iceland, Ireland, Italy, Luxembourg, the Netherlands, Norway, Poland, Slovenia, Sweden, the United Kingdom, and the United States).
So far, the food industry mainly uses WGS to trace the introduction and transmission chains of pathogens and spoilage organisms in food production. Unlike food safety authorities, the food industry tends to use WGS in a less systematic way, mostly when other subtyping methods can’t discriminate strains. Only a few big companies can set-up such infrastructure internally, but smaller producers can rely on WGS services. The laboratory part tends to be frequently outsourced whereas the bioinformatics is more often done in-house to ensure a consistent approach and interpretation. Industry can compare isolates with entries in public databases to identify potential novel sources or geographic signals (and therefore indication on possible origin of contamination), association with human illness,…
| Use cases | User |
|---|---|
| Outbreak investigation. Retrospective or “vehicle-driven” comparisons to test epidemiological hypotheses regarding the source of an outbreak and include/exclude outbreak cases by matching (or not) a food isolate to clinical isolates.
WGS makes it possible to recognize persistent outbreaks with a small number of cases happening every year. WGS is a powerful tool for a food manufacturer to convincingly rule out its products from being the cause of an outbreak if the outbreak WGS profile is not found on its premises or products. |
Public health/Food safety authorities
Food Industry. Public Health England has been approached by the food industry on two separate occasions to compare pathogen WGS profiles with the outbreak profile |
| Prospective Surveillance (outbreak detection). Monitoring of cases of high burden diseases (listeriosis, salmonellosis,…) by public health laboratories, alerts are generated when clusters of pathogens with similar genomes are identified in a limited geographical area or time period | Public health/Food safety authorities. Implemented at least by 4 countries (US, Denmark, France, USA,..) |
| Improved root cause analysis for food safety management. It allows to distinguish contamination resulting from continuing independent sporadic introductions or reintroduction or persistence of a single strain in the production. | Food industry (most common use case for the food industry) |
Phenotypic prediction by aligning draft genomes to a gene database to predict traits such as the virulence profile, heat resistance, stress response, biofilm formation, resistance against antimicrobials and biocides.
The food industry can use these data to predict adaptation and survival of pathogens and spoilage organisms in the production environment |
Public health/Food safety authorities
Food industry (anecdotic) |
| Source attribution of sporadic contaminations by quantifying the relative contribution of different animal, environmental and food sources, including specific food commodity and production sources, to human illness. Comparing sequences of isolates from food, feed, and production environments can allow to identify genetic markers, which are specific for different food commodities. This information can be compared with sequences of human isolates and thereby identify the major sources of sporadic infections at the food-commodity level to identify intervention areas in food production that most likely will drive down the incidence of foodborne illness. | Public health/Food safety authorities
Food Industry (anecdotic) |
2/ Future of WGS in food safety
There are several limiting factors to the wide adoption of WGS by the food industry and public health authorities in low- and middle-income countries:
- Significant analytical costs compared to other subtyping methods.
- Complexity of analysis and lack of access to bioinformatic expertise
- Complexity of interpretation, the need of expertise in setting relevant single nucleotide polymorphism/allelic thresholds and additional data to get to a meaningful conclusion.
- Issues of privacy, ownership, and intellectual property rights which limits global open data-sharing of foodborne pathogen sequences.
- The need for further standardization to be able to compare data regardless of the sequencing platform, the bioinformatic approach and software used. The entire WGS process (sample preparation, sequencing and data analysis) need to be validated (performance specification) and verified.
- The requirement to sequence all historical isolates to set up a proactive sequencing which is not possible for most companies.
Since the use of WGS by public health authorities is likely to increase in the coming years, it is crucial for food businesses to get familiar with the terminology, methodologies, benefits and challenges of WGS.
Sources:
- A Silver Lining of the Pandemic: Whole-Genome Sequencing and Food Safety. Food Safety Magazine
- The Benefits and Barriers of Whole-Genome Sequencing for Pathogen Source Tracking: A Food Industry Perspective. Food safety Magazine. Amézquita et al.
- The Use of Next Generation Sequencing for Improving Food Safety: Translation into practice. Jagadeesan et al.
- Whole-Genome Sequencing for Food Safety. Food Safety Magazine. Peter Gerner-Smidt
- Whole genome sequencing for foodborne disease surveillance Landscape paper – WHO