Fluoroquinolone-resistant <i>Escherichia coli</i> carrying <i>quinolone efflux pump</i> ( <i>qepA</i> ) with L348–G349 duplication in the absence of V134I substitution

ABSTRACT We report on five clinical fluoroquinolone-resistant Escherichia coli strains carrying a unique variant of the quinolone efflux pump gene ( qepA ). The E. coli isolates were recovered from fecal samples of children under 5 years collected at hospital discharge from two referral hospitals in Kenya. Whole-genome sequencing revealed that the isolates belong to sequence types 46 and 354, carrying the qepA gene flanked by intI1 integrase and ISCR3 elements. Protein sequence comparison revealed a duplication of the L348–G349 insertion, similar to the qepA8 variant, but without the V134I substitution. The unique qepA variant had 14 transmembrane helices, with the additional LG amino acids located within the periplasmic loop connecting transmembrane helices 9 and 10. Additionally, multiple co-carriage of mutations in gyrA and parC , as well as antimicrobial resistance determinants to aminoglycosides and beta-lactams, were identified in the isolates. The isolates exhibited phenotypic multidrug resistance and reduced susceptibility to a number of other antibiotics, including ceftriaxone. Additionally, the isolates exhibited an elevated (≥32 µg/mL) minimum inhibitory concentration (MIC) to ciprofloxacin, indicative of high-level resistance. The evolution of qepA indicates the persistence and diversification of transferable quinolone resistance determinants conferring low-level resistance, which may be facilitating further selection and dissemination of high-level fluoroquinolone resistance, expanding the mutant selection window in E. coli strains found in sub-Saharan Africa (SSA). The identification of a unique qepA variant—characterized by a unique L348-G349 duplication and absence of the V134I mutation typical of qepA8 —demonstrates that the qepA locus is continuing to diversify in clinical settings. IMPORTANCE Fluoroquinolones remain critical antibiotics for the treatment of bacterial infections in low- and middle-income countries. The increasing prevalence of resistance threatens the effectiveness of these agents. This report describes the detection of a quinolone efflux pump ( qepA ) variant with a unique mutation combination among the qepA alleles in Escherichia coli clinical isolates from children being discharged from hospitals in Kenya. The plasmid-mediated resistance gene qepA contained the insertion of an L348–G349 amino acid duplication without the additional V134I substitution present in the qepA8 allele. The existence of this qepA variant underscores the persistence and ongoing diversification of plasmid-encoded resistance determinants, which may be playing a part in selection for high-level resistance in SSA. This study highlights the need for enhanced genomic surveillance of antimicrobial resistance, antimicrobial stewardship, and implementation of strategies to mitigate the spread of antibiotic resistance.