Clinical and non-clinical Escherichia coli from chickens reveal antimicrobial resistance patterns of one health concern.

Antimicrobial resistance in Escherichia coli from poultry production represents an increasing concern due to its impact on animal health and its potential implications for public health through the dissemination of clinically relevant antimicrobial resistance genes. This study assessed the prevalence of resistance to cefoxitin, ceftazidime, ciprofloxacin, imipenem, and colistin, together with the associated resistance genes, in Escherichia coli isolated from chickens with and without clinical signs of colibacillosis over a 24-year period. Colistin resistant isolates were further characterized using whole genome sequencing (WGS). A total of 196 isolates were subjected to antimicrobial susceptibility testing. Susceptibility to colistin was determined by minimum inhibitory concentration, whereas susceptibility to cefoxitin, ceftazidime, ciprofloxacin and imipenem was assessed by disk diffusion. The presence of resistance genes (blaTEM, blaCTX-M, blaSHV, qnrA, qnrB and qnrS) was investigated by polymerase chain reaction. Four colistin resistant isolates were further analyzed by WGS by using the Illumina MiSeq platform to characterize resistance determinants, virulence associated genes and Multilocus Sequence Type. Among the isolates, 42.9% were non susceptible to ciprofloxacin, 8.2% to cefoxitin, 6.6% to ceftazidime and 1.5% to imipenem. Multiple resistance genes were detected in 4.59% of isolates, with blaTEM and blaCTX-M being the most frequent. Colistin resistance was observed in 22.45% of isolates. Genomic analysis identified sequence types ST345, ST648 and ST23, previously associated with avian pathogenic E. coli, and one novel sequence type designated ST18020. These findings highlight the persistence and genetic diversity of antimicrobial resistant E. coli in poultry production and reinforce the importance of continuous molecular surveillance.