Distribution and Transfer Characteristics of antibiotic resistance genes in Bacterial Communities within Pig Farming Systems and Source Analysis of Key Antimicrobial-Resistant Bacteria

Objective To characterize the distribution and transmission of antibiotic resistance genes (ARGs) and antimicrobial-resistant bacteria (ARB) across pig farm environments in Shandong Province, China. Methods In June 2023, we collected 185 samples from two closed-system pig farms in Liaocheng and Dezhou, Shandong Province, China, including 28 metagenomes (manure, wastewater, soil) and 157 culture-based bacterial isolates. We applied metagenomic sequencing, whole-genome sequencing, antimicrobial susceptibility testing, and source tracking across pigpens, staff living areas, and surrounding soils. Results ARG and mobile genetic element (MGE) abundances peaked in wastewater, declined in manure and soil. Soil bacterial communities and ARG profiles exhibited a spatial gradient with increasing distance from farm boundaries. Transposases and integrases were the predominant MGEs driving ARG mobility. Multidrug-resistant Staphylococcus aureus (mecA-positive), Pseudomonas aeruginosa, and Bacillus cereus were detected across animal, environmental, and residential sites, indicating cross-compartment transmission. Conclusions Wastewater is the principal driver of environmental ARG dissemination in pig farming, facilitated by MGEs and ARB mobility.