The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain

Abstract

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. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. 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. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.

Food Security: Microbiological and Chemical Risks

“…In recent years, next generation sequencing (NGS) including whole genome sequencing (WGS) and metagenomics testing have emerged with a great potential to revolutionize how microbiological food safety is managed. Particularly WGS has emerged as a new tool that has great potential within a One Health context [75][76][77][78][79]. WGS provides the highest possible microbial subtyping resolution available to public health authorities for the surveillance of and response to foodborne disease and AMR threats.…”

“…This approach, when sometimes utilised together with PCR-based genotypic detection of AMR genes has been and will continue to be widely used in molecular epidemiology for AMR surveillance. However, such combinatorial approaches are unable to provide information on the mechanisms and drivers of AMR, and on the presence and spread of AMR genes throughout the global food chain [76]. The use of WGS can overcome these limitations and this is evidenced by the increasing number of publications describing various WGS applications for AMR surveillance among isolates from animals, food, environment and humans.…”

“…Currently, WGS-based AMR surveillance has already been adopted nationwide by US public health surveillance system, known as the National Antimicrobial Resistance Monitoring System (NARMS) [116]. NARMS tracks changes in antimicrobial susceptibility and characterizes AMR in foodborne enteric bacteria found in ill people (CDC), retail meats (FDA), and food animals (USDA) [76,116]. NARMS monitors antibiotic resistance among the following four major foodborne bacteria: Salmonella spp., Campylobacter spp., E. coli, and Enterococcus spp.…”

“…In general, a global WGS-based AMR surveillance system has yet to be implemented and most countries still depend on phenotyping testing and PCR-based genotypic methods for AMR surveillance. Nevertheless, many studies on the use of WGS-based AMR surveillance of abovementioned bacteria have been published and some are already described in excellent review by [76].…”

“…food, water, fecal, soil, or environmental samples) in one analytical procedure (one sequencing run). It allows the genomes of difficult-toculture or non-culturable microorganisms to be analysed since the entire DNA content of a sample is sequenced, regardless of its origin [76]. Metagenomic data provides an in-depth taxonomic identification (i.e.…”