Antimicrobial resistance and characterization of ESBL-producing Escherichia coli from poultry and cattle in Isfahan, Iran

The rise of antimicrobial resistance (AMR), particularly from extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli, poses a global public health threat. This study investigated the prevalence, genetic characteristics, and antimicrobial resistance patterns of ESBL-producing E. coli isolated from free-range poultry and clinically healthy cattle in Isfahan, Iran. A total of 300 fecal samples were collected between May 2023 to May 2024, including 150 from smallholder poultry farms and 150 from a mix of dairy and beef cattle farms. Twenty privately owned farms (10 poultry and 10 cattle) were randomly selected using a stratified random sampling approach. All animals were clinically assessed by a licensed veterinarian and found to be healthy at the time of sampling. Samples were screened for ESBL production, and antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer disk diffusion method according to CLSI 2018 guidelines. Phenotypic confirmation of ESBLs was conducted using the double-disk synergy test (DDST). Genotypic analysis targeting blaCTX-M, blaTEM, blaAmpC, mcr-1, qnrS, qnrB, and aac(6’)-Ib-cr genes and Class 1 and 2 integrons was conducted via PCR. ESBL-producing E. coli was detected in 43.33% of poultry and 36.67% of cattle samples. The most common gene was blaCTX-M (30.77% poultry, 45.45% cattle). Multidrug resistance (MDR) occurred in 53.85% and 54.55% of poultry and cattle isolates, respectively. No statistically significant differences were observed between species (p > 0.05). The findings underscore the potential zoonotic risk of ESBL- and MDR-producing E. coli from livestock. Strengthened antibiotic stewardship and molecular surveillance in Iranian agriculture are essential.