Metagenomic analysis reveals resistome characteristics and high-risk resistance genes in the pig nasal cavities, feces, and farm dust

Antimicrobial resistance (AMR) poses a threat to global public health. Swine farms are critical AMR reservoirs. Comprehensive resistome profiling and risk assessment across pig-associated niches remain limited. Metagenomic analysis of antibiotic resistance genes (ARGs) in pig nasal cavities, feces, and farm dust was performed.

Nasal and dust samples exhibited significantly increased ARG diversity and abundance compared with feces. We identified 78 potentially hazardous ARGs and proposed an improved risk classification framework integrating host promiscuity, mobility, and human health risks. These ARGs were classified into four risk levels: 25 Level I (current high risk), 25 Level II (potential future threats), 18 Level III (host-promiscuous but nonmobile), and 10 Level IV (host-specific). High-risk ARGs mainly confer aminoglycoside, macrolide–lincosamide–streptogramin (MLS), and tetracycline resistance. Metagenome-assembled genome (MAG) analysis revealed that bacterial taxa enriched in ARGs were predominant in nasal and dust samples. Moreover, these environments presented higher mobile genetic element (MGE) abundance and similar ARG–MGE co-occurrence patterns. Notably, 74.12% of the mobile ARGs were predicted to be plasmid-borne, and these ARGs tended to be assigned higher health risk levels than chromosomal ARGs.

These findings provide a practical framework for ARG risk assessment and highlight the nasal cavity and dust as underappreciated but important AMR reservoirs in pig farms.