This study aimed to investigate the genetic characteristics, antibiotic resistance patterns and novel mechanisms involved in fluoroquinolone (FQ) resistance in commensal Escherichia coli (E. coli). The E. coli were recovered from a previous clinical study and subjected to antimicrobial susceptibility testing and molecular typing. Known mechanisms of FQ resistance (target sites mutation, plasmid-mediated quinolone resistance (PMQR) genes, relative expression levels of efflux pumps and porins) were detected using DNA sequencing of PCR products and real-time qPCR. Whole genome shotgun sequencing was performed on 11 representative strains to screen for SNPs. The function of a key SNP (A1541G) was investigated by site-directed mutagenesis and allelic exchange. Results showed that long term enrofloxacin treatment selected multidrug resistant (MDR) E. coli in chicken gut and these E. coli isolates had diverse genetic backgrounds. Multiple genetic alterations including double mutations on GyrA (S83L and D87N), single mutation on ParC (S80I) and ParE (S458E), activation of efflux pumps and QnrS1 protein contributed to the high-level FQ resistance (MICENR≥128 μg/mL), while the relative low-level FQ resistance (MICENR=8 or 16 μg/mL) was commonly mediated by decreased expression of the porin OmpF, besides enhancement of the efflux pumps. No significant relationship was observed between resistance mechanisms and virulence genes. Introduction of A1541G mutation on aegA was able to increase the FQ susceptibility by 2-fold. This study contributed to better understanding of the development of MDR and differences underlying mechanisms of high-level and low-level FQ resistance in E. coli.
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