Genotypic Diversity and Antimicrobial Resistance Profiles of Multidrug-Resistant Escherichia coli in Porcine Populations from Hubei, China

The indiscriminate and excessive use of antimicrobial agents in livestock production is a major driver of antimicrobial resistance (AMR), thereby posing a grave threat to global public health. Although several surveillance studies have documented antimicrobial resistance patterns of swine-derived E. coli in different regions of China, comprehensive investigations integrating multilocus sequence typing (MLST), resistance determinants, and virulence gene profiles have remained scarce for central China, particularly Hubei province, since 2018. This study investigated the prevalence of antibiotic resistance, and molecular epidemiology of E. coli isolated from swine farms in Hubei province, China, while simultaneously analyzing their clonal and genetic diversity. A total of 148 E. coli isolates were collected from porcine sources in central China, revealing distinct regional variations in genetic diversity. Multilocus sequence typing (MLST) analysis identified 38 sequence types (STs) distributed across 7 clonal complexes (CCs) and several unassigned clones. ST46 emerged as the predominant sequence type (19.6% prevalence), followed by ST23 and ST10. Antimicrobial susceptibility testing demonstrated 100% resistance to lincosamides and sulfonamides, with all isolates exhibiting multidrug resistance (MDR) to antimicrobial classes. Genetic characterization detected 16 resistance determinants, with individual isolates carrying 5–7 resistance genes on average. The resistance profile included seven β-lactamase genes: blaTEM (61.5%), blaCTX-M-1G (57.4%), blaDHA (46.6%), blaSHV (39.2%), blaCTX-M-9G (24.3%), blaOXA (13.5%), and blaCMY-2 (1.4%); and eight aminoglycoside-modifying enzyme genes, including polymyxin resistance gene mcr-1 (7.4%). Virulence factor screening through PCR detected nine associated genes, with EAST1, fyuA, STa, K88, STb, Irp2, and LT-1 present in 95.3% of isolates, while K99 and 987P were absent in all specimens. This investigation documents alarmingly high antimicrobial resistance rates in swine-derived E. coli populations while elucidating their genetic diversity. The findings suggest that intensive antibiotic use in porcine production systems has driven the evolution of extensively drug-resistant bacterial isolates. These results emphasize the urgent need to implement antimicrobial stewardship programs in livestock management to mitigate AMR proliferation.