Antibiotic resistance, virulence gene, phylogenetic group and genetic diversity of Escherichia coli isolated from Tibetan pig farms in Garze Tibetan Autonomous Prefecture, Sichuan, China

Introduction To investigate the correlations among antibiotic resistance, virulence gene, phylogenetic group, and genetic diversity, providing essential data for Escherichia coli (E. coli) infection prevention and control in Tibetan pigs. Methods A total of 244 E. coli isolates were collected. Antimicrobial susceptibility was assessed using the microdilution method. PCR was used to detect antibiotic resistance genes (ARGs), virulence genes, and phylogenetic groups. Genetic diversity was analyzed using enterobacterial repetitive element sequence-based PCR. Enteroaggregative E. coli (EAEC) 5-12, a representative strain with multidrug resistance and strong biofilm-forming ability, harboring abundant virulence genes, was selected for whole-genome sequencing (WGS) to validate PCR results. Results Among the 244 isolates, 84.43% showed multidrug resistance (MDR), with the highest resistance rates for chloramphenicol (99.59%), sulfadiazine (96.31%), and sulfamethoxazole (93.85%). Twenty-five ARGs were detected, with ant(3’)-Ia , bla TEM , aac(3’)-II , floR , and qnrS exceeding 80% detection rates. Integrase genes intl1 and intl2 were found in 90.16% and 15.16% of isolates, respectively. Seventeen virulence genes were detected; bcsA (98.77%), fimC (89.75%), and agn43 (59.43%) were the most prevalent. A total of 106 virulence patterns were identified, with agn43/bcsA/fimC being predominant (17.92%). Most strains belonged to phylogenetic group A (45.90%), followed by B1 (34.43%), while 29 strains were unclassified. Sixty-four isolates were identified as diarrheagenic E. coli (DEC), predominantly enteroaggregative E. coli (EAEC, 90.63%). Biofilm-forming ability was categorized as strong (4.69%), moderate (21.88%), weak (59.38%), or absent (14.06%). Clustering based on 61.2% similarity grouped the 64 DEC into five clusters, with 84.38% in cluster II, which contained all strong biofilm producers. Discussion Antimicrobial resistance profiles of EAEC 5–12 confirmed that primarily confer resistance through antibiotic efflux, target alteration, and reduced permeability. These findings will contribute to further understanding the positive correlation between antibiotic resistance and pathogenicity in E. coli from Tibetan pig farms, shedding light on the rational use of antimicrobial agents and tackling the antibiotic resistance crisis in Tibetan pig breeding in Garze Tibetan Autonomous Prefecture, Sichuan, China.