Our project investigates the transmission dynamics of antimicrobial resistance (AMR) across the food chain, focusing on the dissemination of antibiotic resistance genes (ARGs) and resistant bacteria. We integrate whole metagenome sequencing with culture-based approaches to systematically characterize ARG reservoirs in environmental and food matrices and to evaluate potential connectivity between compartments.
Sampling encompasses manure, agricultural soils prior to manure application, post-fertilization soils, crop products, meat products, and dairy fermented products. For each sample type, we perform taxonomic profiling and quantify total ARG abundance and diversity. Metagenome-assembled genomes (MAGs) are reconstructed to identify ARG-carrying bacterial hosts within complex microbial communities and to guide targeted cultivation strategies. In parallel, antibiotic-resistant bacteria are recovered from all matrices using selective and non-selective approaches. Isolates are subjected to phenotypic antibiotic susceptibility testing to establish resistance profiles, followed by whole genome sequencing for detailed characterization of ARG content, genomic context, and associated mobile genetic elements. Comparative genomic analyses are conducted to assess genetic relatedness among isolates and to explore potential links between environmental, primary production, and food-associated compartments.
Preliminary analyses indicate overlapping ARG patterns between manure and fertilized soils, and in some cases similar genotypic contexts in isolates recovered from different matrices. We have also achieved the genomic-guided recovery of enterobacteria with diverse ARGs. However, the primary emphasis of this work lies in the establishment of a robust, integrative methodological framework that combines metagenomics, culturomics, resistance phenotyping, and high-resolution genomics and creates a specific database to facilitate the analysis of our findings.
By applying this coordinated One Health approach, the study provides a comprehensive platform for investigating AMR distribution and resistance profiles across the food chain, supporting future risk assessment and mitigation strategies grounded in harmonized multi-compartment data generation.
