Integrative Phenotypic and Genotypic Surveillance and Risk Assessment of Foodborne Antimicrobial Resistance in Meat–Environment Continuum

Foodborne antimicrobial resistance (AMR) poses a significant One Health challenge. However, the risk and transmission of AMR within the meat-environment continuum remain poorly understood. Here, we conducted an integrative AMR surveillance of meats and associated environments from three markets using culture-independent single-cell Raman spectroscopy for phenotypic profiling and metagenomics for genotypic analysis. We found that environments consistently harbored a higher abundance of metabolically active antibiotic-resistant bacteria than meats. By incorporation of phenotypic AMR (abundance and activity of antibiotic-resistant bacteria), genotypic AMR (percentage of high-risk antibiotic resistance genes), and transmission potential, a new risk assessment framework was established. The integrated assessment revealed that environments were critical AMR reservoirs with risk levels higher than or comparable to those in meats, underscoring the necessity of integrating multiple factors for accurate risk assessment. Moreover, source tracking analysis suggested reciprocal cross-contamination between the samples, which was further confirmed by 25 shared metagenome-assembled genomes (MAGs) hosting high-risk ARGs among samples. By bridging phenomic and genomic insights, this work advances precision AMR surveillance and provides a more accurate risk assessment framework, offering critical guidance for mitigating AMR in the environment and the food chain.