Application of Whole Genome Sequencing (WGS) Approach Against Identification of Foodborne Bacteria

Abstract

Food quality and safety along with their associated hazards risks present a major concern worldwide associated with relative economical losses as well as potential danger to consumer’s health. In this context, antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. A lack of measures and reliable assays to evaluate and maintain a good control of antimicrobial resistance foodborne pathogens may affect the food industry economy and shatter consumer confidence. Hence, surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental, and food borne strains. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. It is imperative to establish fast and reliable analytical methods that allow a good and rapid analysis of food products during the whole food chain. This chapter summarizes the information on the method developed and application of the whole-genome sequencing (WGS) in the past few years focusing on surveillance of AMR in foodborne pathogenic bacteria. Emphasis is also posed with respect to the routine implementation of these next-generation sequencing methodologies on characterization of well-known food pathogens. Besides, potential advantages and disadvantages of the WGS have been discussed on the surveillance of AMR in foodborne pathogens.