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

Xing Zhao¹Jun Liang²Zhaobin Xia¹Chaoxi Chen^1*

• ¹College of Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
• ²Zhengzhou Inspection and Testing Center of Products Quality, Zhengzhou 450001, China, Zhengzhou, China

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. Microdilution and PCR were used to assess antimicrobial susceptibility, phylogenetic groups, antibiotic resistance genes, and virulence genes. Genetic diversity was analyzed using enterobacterial repetitive element sequence-based PCR. 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. The results revealed that 84.43% of the 244 isolated E. coli demonstrated varying resistance rates to 23 antibiotics and were highest for Chloramphenicol (99.59%), Sulfadiazine (96.31%), and Sulfamethoxazole (93.85%). Twenty-five antibiotic resistance genes, including ant (3')-Ia, blaTEM, aac (3')-II, floR, and qnrS, were detected and the detection rates were over 80%. Intl1 and intl2 were positively detected in 90.16% and 15.16% of strains, respectively. BcsA, fimC, and agn43 were the most prevalent (98.77%, 89.75%, and 59.43%, respectively) among 17 detected virulence genes. There existed 106 virulence patterns and the predominant one was agn43/bcsA/fimC, accounting for 17.92% (19/106). Most strains belonged to phylogenetic group A (45.90%), followed by B1 (34.43%), while 29 strains could not be classified into any group. Of the 64 diarrheagenic E. coli (DEC), enteroaggregative E. coli was the most prevalent pathotype (90.63%, 58/64). Biofilm-forming ability results verified that 4.69%, 21.88%, 59.38%, and 14.06% of the DEC were classed as strong, moderate, weak, and absent biofilm producers. Based on the 61.2% similarity, the 64 DEC were categorized into five clusters (I, II, III, IV, and V). 84.38% were classified into cluster II and the three strong biofilm-forming strains were all located in cluster II. Antimicrobial resistance (AMR) 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 a light on the rational use of antimicrobial agents and tackling the antibiotic resistance crisis in the Tibetan pig breeding in Garze Tibetan Autonomous Prefecture, Sichuan, China.