Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce

Foodborne illnesses pose a significant global health threat, often caused by pathogens like <i>Escherichia coli</i>, <i>Listeria monocytogenes</i>, and <i>Salmonella</i> spp. The emergence of antibiotic-resistant strains further exacerbates food safety challenges. This study combines shotgun metagenomics and culture-based approaches to detect foodborne pathogens and antimicrobial resistance genes (ARGs) in Malaysian produce and meats from the Kinta Valley region. A total of 27 samples comprising vegetables, meats, and fruits were analyzed. Metagenomics provided comprehensive microbial profiles, revealing diverse bacterial communities with species-level taxonomic resolution. Culture-based methods complemented these findings by identifying viable pathogens. Key foodborne pathogens were detected, with <i>Listeria monocytogenes</i> identified in meats and vegetables and <i>Shigella flexneri</i> detected inconsistently between the methods. ARGs analysis highlighted significant resistance to cephalosporins and penams, particularly in raw chicken and vegetable samples, underscoring the potential public health risks. While deli meats and fruits exhibited a lower antimicrobial resistance prevalence, resistant genes linked to <i>E. coli</i> and <i>Salmonella</i> strains were identified. Discrepancies between the methods suggest the need for integrated approaches to improve the pathogen detection accuracy. This study demonstrates the potential of metagenomics in advancing food safety research and supports its adoption as a complementary tool alongside culture-based methods for comprehensive foodborne pathogen surveillance and ARG profiling in Malaysian food systems.