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.

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