A critical review of metagenomic approaches for foodborne pathogen surveillance

High-throughput sequencing methods (e.g., whole-genome sequencing and metagenomics) are rapidly changing multiple fields of microbiology, including food safety and pathogen surveillance. Current foodborne pathogen surveillance relies heavily on resource-intensive, isolate-based approaches, limiting large-scale implementation. To facilitate more efficient public health responses, innovative technologies that can rapidly and accurately identify diverse foodborne pathogens are essential. Metagenomics-based approaches represent a potential transformative advancement in food safety diagnostics. These techniques enable unbiased and comprehensive analysis of foodborne pathogen genetic material from clinical, food product, processing facility, and environmental samples, positioning metagenomics as a promising strategy for foodborne pathogen surveillance. Here, we explore how metagenomics can be applied to foodborne pathogen surveillance and outbreak detection, focusing on recent advances in both short- and long-read sequencing technologies. The challenges limiting potential applications are reviewed, including the detection and characterization of low-abundance pathogens, the complexity of assembly-based analysis, and the identification of antimicrobial resistance genes. Finally, we discuss a future outlook for metagenomics impacting public health response to foodborne pathogens. It is anticipated that through continuous improvements in sequencing and analytical technologies, that metagenomic approaches to foodborne pathogen detection and characterization will become routine, with the potential to reduce the foodborne illness burden.