Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics

Foodborne pathogens, particularly antimicrobial-resistant bacteria, pose a significant threat to global health. Metagenomic sequencing offers a fast and comprehensive method to detect pathogenic microbes and antimicrobial resistance genes. A study analyzed 260 food products, including raw meat, sashimi, and ready-to-eat vegetables. Clostridium botulinum, Acinetobacter baumannii, and Vibrio parahaemolyticus were identified as the top three foodborne pathogens in raw meat and sashimi. Chicken and RTE vegetables had higher percentages of carbapenem and cephalosporin resistance genes. Fresh, peeled, and minced foods had higher levels of pathogenic bacteria. This study provides valuable data for food safety assessments and quality indicators.