Antimicrobial resistance of Escherichia coli isolated from retail whole chickens in Beijing and genomic analysis of cefotaxime-resistant MDR isolates

ObjectiveTo evaluate the antimicrobial resistance characteristics and molecular epidemiological features of Escherichia coli in retail whole chickens in Beijing， including resistance rates， resistance profiles， serotypes， sequence types （STs）， major resistance genes and plasmids distribution.MethodsFrom December 2017 to March 2023， Escherichia coli was isolated from whole chickens， and was subjected for antimicrobial susceptibility testing. Cefotaxime （CTX）-resistant isolates were selected for whole-genome sequencing， and bioinformatics methods were used to analyze the genomic characteristics of the isolates.ResultsThe prevalence of Escherichia coli in 87 retailed whole chickens samples was 87.4%， of which 84.2% of the strains showed varying degrees of resistance against detected antibiotics， with tetracycline （76.2%） as the most resistant antibiotic， and 71.8% of the strains were multidrug resistant. Genomic analysis of 38 CTX-resistant isolates showed that they belonged with 28 serotypes and 29 STs， and core genome multi-locus sequence typing （cgMLST） revealed even higher genetic diversity. The dominant antimicrobial resistance genes were the ESBL-encoding gene blaCTX-M-65 （44.7%， 17/38） for β-lactam resistance， the plasmid-mediated qnrS1 （60.0%， 18/30） and chromosomal mutation GyrA_S83L （96.7%， 29/30） for quinolones resistance. Additionally， 78.9% of the strains exhibited co-resistance to third-generation cephalosporins and quinolones. Plasmid analysis indicated that the IncFIB plasmid type was the most prevalent （81.6%， 31/38）.ConclusionThe contamination of multidrug resistant Escherichia coli in retail whole chickens in Beijing City was high. These strains carried multiple resistance genes， posing a potential risk of plasmid-mediated horizontal gene transfer. These findings highlight the need to strengthen food safety regulation and antibiotic usage supervision.