Prevalence, Identification, and Antimicrobial Resistance of Bacterial Pathogens in Farm Animals from Western...

Data on the prevalence of bacteria and antimicrobial resistance (AMR) among food-producing animals in Kazakhstan remain limited in scope. As part of this regional cross-sectional descriptive study, specific bacterial taxa and AMR were characterized in farm animals in the West Kazakhstan Region. Between September 2025 and July 2026, samples were collected from 974 individual animals at 48 farms located in 12 administrative districts. Targeted bacteriological isolation was performed for Escherichia coli, presumptive Shigella spp., Salmonella spp., Yersinia enterocolitica, Campylobacter spp., and Staphylococcus aureus, followed by specific real-time PCR. Antimicrobial susceptibility was assessed in 214 E. coli isolates using the EUCAST disk diffusion method, and five selected isolates underwent exploratory screening by quantitative PCR (qPCR) for the presence of determinants associated with antimicrobial resistance. A total of 311 bacterial isolates were identified. The predominant taxon was E. coli, detected in 22.0% of the animals from which samples were collected and accounting for 68.8% of the isolates; followed by S. aureus (3.2% of animals), presumptive Shigella spp. (2.9%), Salmonella spp. (1.5%), Campylobacter spp. (1.5%), and Y. enterocolitica (0.8%). Corresponding molecular targets were detected in 303 of 311 presumptively identified isolates (97.4%). No clear age-related gradient in the prevalence of E. coli was observed, and this taxon was detected in all three study areas. Phenotypic resistance to at least one antimicrobial agent with an applicable clinical breakpoint according to EUCAST was detected in 2 of 214 E. coli isolates (0.9%), including resistance to ceftriaxone or amoxicillin with clavulanic acid. Molecular screening of five selected isolates revealed various determinants associated with antimicrobial resistance and mobile genetic elements, with blaCMY, mphA, qepA_1_2, catA1, and intI1F165_clinical being the most frequently detected. These results establish a regional baseline for comprehensive monitoring of bacteria associated with animal husbandry and antimicrobial resistance in Western Kazakhstan.