Circulation and Carriage of the Bacteriome and Resistome Among Animals, Handlers, and Farm Soil—A One Health Study

Background: AMR is a public health threat. Farms are key crossing points where animal handlers, livestock, and soil meet, potentially enabling cross-sector circulation of bacteria and antibiotic resistance genes. Objectives: This study evaluated a One Health approach to describe the bacteriome and resistome across farms. Methods: Shotgun metagenomic sequencing was performed on 44 samples collected from animal handlers, chickens, camels, cows, sheep, and soil across six farms. Taxonomic composition was profiled, and ARGs were identified. Beta-diversity ordination and ARG network analysis in each farm were used to assess cross-sector overlap. Results: Enterobacteriaceae was the most consistently dominant bacterial group across all farms, whereas soil samples had a taxonomically distinct community. A core resistome characterized by glycopeptide-resistance genes and multidrug efflux systems was observed across sampled sectors, with tetracycline-, fluoroquinolone-, and beta-lactam resistance genes also frequently detected. The extent of overlap in ARG profiles among animals, handlers, and soil varied substantially between farms, ranging from broad cross-sector overlap to patterns predominantly restricted to animal samples. Conclusions: To our knowledge, this is the first study in this region to apply shotgun metagenomics within a One Health framework. This study moves beyond single-host or single-compartment studies and provides a regional baseline. Escherichia coli was the most common bacterium found across these groups, highlighting its relevance for further exploration in the context of AMR surveillance. The degree of overlap in bacterial taxa and ARG profiles between animals and handlers varied by farm, indicating differences in microbial community and resistance-determinant distributions across farm settings. However, these similarities do not establish direct transmission or identify its direction. Overall, these findings highlight the importance of integrated One Health surveillance to better monitor and control AMR in farming systems.