A Silver Lining of the Pandemic: Whole-Genome Sequencing and Food Safety

FAO

Zooming out and taking a broader perspective, WGS benefits are particularly visible in microbiology: WGS provides rapid identification and characterization of microorganisms with a level of precision that no tool has ever reached before. Through WGS, specific novel antibiotic targets (resistance genotypes) are being identified in the area of antimicrobial resistance (AMR)studies. It is a significant stepping-stone because more focused surveillance and more targeted diagnostics and drug development are made possible by identifying them and correlating them to the observed phenotypes. The level of detail provided by WGS makes it possible to refine case definitions precisely, which in turn allows for faster investigation of outbreak clusters, thus preventing additional cases of diseases sooner. For example, in 2014, a multinational Salmonella outbreak investigation was conducted in Europe where WGS was used to identify the root cause, and the data collected pointed to some egg farms in a specific location. While WGS was essential in the investigation, it was the international data-sharing efforts that made the investigation successful and conclusive. Another example is the outbreak investigation of Listeria linked to enoki mushrooms in Canada where the specific sequence of the Listeria strain was internationally shared, resulting in successfully tracing the multinational food safety outbreak and the rapid recall of the affected products.

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