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

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The indiscriminate and excessive use of antimicrobial agents in livestock production constitutes a significant contributor to antimicrobial resistance (AMR), posing substantial threats to global public health. Despite this critical concern, the genetic diversity and antibiotic resistance patterns of Escherichia coli (E. coli) in regional ecosystems remain insufficiently characterized. This study investigated the prevalence of antibiotic resistance, transmission mechanisms, and molecular epidemiology of E. coli strains 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 universal resistance to lincosamides and sulfonamides, with all isolates exhibiting multidrug resistance (MDR) to ≥9 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%). Eight aminoglycoside-modifying enzyme genes, 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 strains. These results emphasize the urgent need for implementing antimicrobial stewardship programs in livestock management to mitigate AMR proliferation.

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