Antimicrobial resistance and molecular characterization of blaCTX-M-producing Escherichia coli isolated from broiler chickens in Peru

The misuse and overuse of antimicrobials in humans and animals contribute to the selection and dissemination of antimicrobial-resistant (AMR) bacteria. In animal production systems, antimicrobial use is a key driver of the emergence and spread of antimicrobial-resistant bacteria across humans, animals, and the environment within a One Health framework. A total of 300 cloacal swabs were collected from apparently healthy broiler chickens at two poultry collection centers in Lima, Peru. ESBL-producing Escherichia coli were isolated on CHROMagar™ ESBL and identified by conventional biochemical tests. Antimicrobial susceptibility testing was performed using the disk diffusion method according to CLSI guidelines, and ESBL production was phenotypically confirmed. CTX-M groups were detected by qPCR, and whole-genome sequencing (WGS) was performed on selected isolates. Seventy-nine ESBL-producing E. coli isolates were recovered (26.3%; 95% CI: 21.4–31.6). All isolates exhibited multidrug-resistant phenotypes. CTX-M group 1 was detected in 87.3% of isolates and group 9 in 12.7%. WGS analysis identified bla CTX-M-55 , bla CTX-M-65 , and bla CTX-M-3 distributed across multiple sequence types. Phylogenetic analysis revealed the presence of both closely related clonal clusters and genetically diverse isolates. These findings suggest that poultry production systems may serve as potential reservoirs of multidrug-resistant ESBL-producing E. coli in Peru. Given the study design and limited genomic sampling, the results should be interpreted as preliminary and highlight the need for expanded surveillance within a One Health framework.