Extended-spectrum β-lactamase-producing Escherichia coli in Chinese backyard animals: genetic diversity and public health implications

Abstract The emergence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) in food animals poses a significant public health concern. While the prevalence and genetic traits of ESBL-Ec in commercial farms have been widely studied, data from backyard farms remain limited. Herein, we investigated the occurrence of ESBL-Ec among backyard animals across 12 villages in Shandong province, China. Notable variations in ESBL-Ec prevalence were observed among animal species, ranging from 78.7% in pigs, 61.5% in cattle, 50.0% in sheep, 28.6% in ducks, 14.1% in dogs, 11.5% in chickens, and 5.3% in cats. In addition, 74 ESBL-Ec were recovered from 180 flies captured in household backyards. Genomic analysis revealed substantial genetic diversity, with dominant sequence types (STs) including ST10, ST48, ST206, and ST744 identified across multiple host species. Bayesian clustering showed that all seven lineages were distributed across at least two sources, suggesting frequent inter-host transmission. Several isolates from different animal species exhibited high similarity (0–65 single nucleotide polymorphisms), indicating potential clonal spread. The bla CTX-M-14, bla CTX-M-65, and bla CTX-M-55 genes were predominant, accounting for 79.1% of detected bla CTX-M variants, and were predicted to be located on IncFIB, IncHI2, IncFII, and IncX1 plasmids. Notably, isolates from backyard animals shared STs and bla CTX-M genotypes with previously reported human and environmental isolates from the same area, suggesting potential transmission across hosts and environmental niches. These findings highlight backyard farming systems as potential reservoirs of ESBL-Ec and emphasize the need for improved antimicrobial stewardship and management practices to limit resistance spread.