Antibiotic resistance in the food supply chain: where can sequencing and metagenomics aid risk assessment?

•Food safety risk analysis should consider antibiotic resistance selection.•DNA sequencing can differentiate strains involved foodborne disease outbreaks.•Genome sequencing can identify antibiotic resistance factors carried by bacteria.•Metagenomics could monitor transmission of resistance in the food supply chain.•At present, the benefits of metagenomic screening may not justify its costs.

Antibiotic resistance is a rapidly growing threat to human health. The environment - including animals and plants - functions both as a transmission route for antibiotic resistant pathogens and a source of resistance genes. The food supply chain connects environmental habitats for bacteria with humans through a route that sometimes - due to use of antibiotics in both agriculture and aquaculture - includes substantial selection for resistance. According to international food standards, selection and dissemination of foodborne resistance should be considered in the risk analysis of food production. High-throughput sequencing and metagenomics could contribute to understanding these transmission and selection processes in the food supply chain.

Graphical abstractDownload high-res image (286KB)Download full-size image