Measurement and characterization of the foodborne resistome across the food matrices: current technologies, challenges, and food safety implications
摘要
Foodborne resistome, antimicrobial resistance genes (ARGs) of food-associated microbial communities, is a recently emergent theme in food safety surveillance. This study is mainly devoted to the methods currently available for the detection, quantification, and characterization of ARGs in food systems, with emphasis on their use across different food matrices. Compare analytical approaches: quantitative polymerase chain reaction (qPCR), digital PCR (dPCR), whole genome sequencing (WGS), shotgun metagenomics, targeted resistome sequencing, long-read sequencing, and functional metagenomics in terms of: sensitivity, quantification potential, host assignment, ARG discovery potential, and suitability for routine surveillance. Current research suggests that no single method can fully characterize the resistome, and the performance of the methods is strongly affected by the properties of the dietary matrix, the efficiencies of DNA extraction, the depth of sequencing, and bioinformatics operations. The study also points out major issues that hinder comparability across studies, for example, variations in sampling methodologies, normalization methods, ARG databases, and reporting metrics. Current research focuses on integrating targeted molecular tools with sequencing-based methodologies for enhancing resistome surveillance across the food chain. Future advances will require standard analytical methodologies, certified reference materials, standardized reporting systems, and coordinated farm-to-fork monitoring programs. The study highlights methodological strengths, limitations, and measurement issues to offer a characterization-oriented perspective for enhancing foodborne resistome assessment and surveillance.