Third-generation nanopore sequencing: advancing real-time pathogen detection and antimicrobial resistance surveillance in food safety applications

Foodborne diseases impact 600 million people annually, causing 420 000 deaths and over $110 billion in economic losses. Conventional pathogen detection methods take 3-7 days and lack sensitivity for low-abundance pathogens and antimicrobial resistance (AMR) genes. This review evaluates nanopore sequencing's potential in food microbiology, analyzing real-time pathogen detection, AMR surveillance, and performance <i>versus</i> traditional methods. A systematic review of 80 studies (2015-2025) revealed nanopore sequencing reduces detection time to <24 hours with 95-98% species identification accuracy and >90% AMR gene sensitivity, at $50-200 per sample <i>versus</i> $300-800 for traditional whole-genome sequencing. It enables multiplex pathogen detection, viable but non-culturable organism identification, and real-time AMR profiling. However, challenges include error rates of 8-15% in homopolymeric regions and the need for bioinformatics expertise. Addressing challenges, including error rates of 8-15% in homopolymeric regions and the need for bioinformatics expertise, requires strategic mitigation approaches. Despite limitations, advances in base-calling and workflows make nanopore sequencing a transformative tool for next-generation food safety surveillance.