Applying Genomics to Track Antimicrobial Resistance in the Food Chain

Abstract

Antimicrobial resistance (AMR) is one of the major challenges the world faces. The emergence and spread of AMR has been attributed to the misuse or indiscriminate use of antibiotics as therapeutic or prophylactic drugs in human and animal health care or in veterinary husbandry. In addition, there is a growing concern over the possibility of AMR transmission via the food chain. Strengthening AMR surveillance along the food chain is essential, in order to select intervention strategies, monitor their effectiveness and detect new trends and emerging threats. Classically, AMR surveillance has been based on the phenotypic characterization of isolates, mainly from zoonotic species, obtained from humans, animals or food, often also coupled to the execution of PCR-based genotypic tests for the detection of known AMR genes. Recent developments in the genomic field have prompted the use of whole genome sequencing (WGS) to analyze the isolates obtained in the frame of monitoring exercises and to characterize their repertoire of AMR determinants and mobile genetic elements. Moreover, the development of novel metagenomics approaches has opened up the possibility of undertaking culture-independent analyses of the pool of AMR genes, the resistome, in complex microbial communities. This book chapter describes the potential of both WGS and shotgun metagenomics to improve the tracking of AMR along the food chain.