Prevalence and mobile genetic element-mediated dissemination of antimicrobial resistance along the swine industry chain of Guizhou, China

Antimicrobial resistance (AMR) in livestock poses a significant threat to animal health, food safety, and public health. However, comprehensive data on AMR transmission across different stages of the swine industry chain in Guizhou Province, China, remain limited. Between 2022 and 2024, samples were collected from the breeding, slaughtering, and sales stages across major swine-producing areas of Guizhou Province. A total of 1,280 strains, including Escherichia coli, Salmonella and Staphylococcus epidermidis, were recovered from feces, wastewater, pork, and environmental samples. Antimicrobial susceptibility was tested against 18 antimicrobials by the agar dilution method. 37 resistance genes were screened by PCR, and 48 multidrug-resistant (MDR) strains were further characterized by whole-genome sequencing (WGS). The isolates showed high resistance to tetracycline (> 85%), ampicillin (> 80%),amoxicillin (79.6%), doxycycline(75.8%) and florfenicol (up to 88.7% in slaughtering stage). Among 37 targeted genes were detected, the most frequently detected were cmlA (52.3%), aadA1 (49.0%), qnrS (41.7%), aadA2 (40.6%), floR (37.1%) and blaTEM (32.2%). WGS showed that mobile genetic elements (MGEs), including class I integrons, Tn3-family transposons, and insertion sequences (ISs), playeda major role in resistance gene dissemination. Representative findings included the frequent co-localization of aadA gene family with class I integron gene cassettes, association of blaTEM−1 with Tn3-related structures and a pemI-pemK toxin-antitoxin system, disruption of the tetR-tet(A) regulatory unit by IS elements, and a conserved resistance core surrounding blaNDM. This study identified critical AMR hotspots and transmission patterns alongside the swine production chain in Guizhou and highlighted the important role of MGEs in the persistence and dissemination of resistance determinants. These findings provide baseline data for stage-specific AMR surveillance and for the development of targeted prevention and control strategies in the regional swine industry.