Pathogen subtyping tools for risk assessment and management of produce-borne outbreaks

There are numerous avenues for pathogenic contamination of produce along the cultivation, processing and retail chain, which presents major challenges for tracing the sources and routes of produce contamination. Over time, rapid, cost effective and flexible pathogen detection/subtyping methods that can yield ample diversity with portable data, have high discriminatory potential and possess a high level of epidemiological concordance have been developed and optimized. While this has not necessarily eliminated microbiological hazards, and produce-associated outbreaks continue to occur, sustained advancements in bacterial subtyping technologies together with better information technologies, have significantly improved the ability of regulators, public health laboratories and governments to identify food safety threats lurking in food supply chain(s). These evolutions and advancements have also dramatically improved the capacity of relevant authorities to identify and manage foodborne outbreaks. This overview explores contemporary pathogen subtyping approaches; PFGE, MLVA (the immediate previous gold standard for typing foodborne pathogens) together with WGS, the most recently adopted pathogen typing approach. Epidemiological findings illustrate that although PFGE can discern unique patterns in bacterial DNA, WGS is specific and can clarify inconclusive PFGE results. The quality and performance of pathogen subtyping is however, not sufficient and strong surveillance systems representative of all putative sources are required to identify the sources of human infection and adequately manage produce borne outbreaks and risks.