High-risk and virus-linked antibiotic resistome in swine farms: metagenomic profiling of cross-species transmission risks among humans, pigs, and soil

Abstract

The rapid acceleration of antimicrobial resistance (AMR) has emerged as a critical and pressing global threat. The role of viromes in disseminating antibiotic resistance genes (ARGs) across human-livestock-environment interfaces remains poorly characterized, despite its critical implications for AMR containment. In the present study, we conducted antibiotic resistome and viral metagenomic sequencing on paired samples from a swine farm ecosystem: pig feces, farm soil, worker stools, and non-exposed human controls, to outline the distribution characteristics of risk ARGs, viromes and virus-associated ARGs. Firstly, farmworkers exhibited significantly greater abundance of high-risk Rank 1 ARGs, particularly β-lactamase genes compared to controls, while soil displayed markedly lower ARG diversity. Next, we identified 138 viral OTUs carrying ARGs (predominantly Siphoviridae, Myoviridae and Podoviridae), with 67 % targeting pathogenic hosts including Escherichia coli. These viral carriers mediated resistance to clinically important antibiotics, such as tetracycline, aminocoumarin, and fosfomycin. Additionally, it was also found that occupational contact increases the diversity of ARGs in the viromes, suggesting phage-mediated ARG transfer is amplified by farm exposure. Collectively, this study provides a more comprehensive characterization of high-risk ARGs and virus-associated ARGs in swine farm systems, highlighting the incorporate virome surveillance in the spread of AMR.