{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T15:51:33Z","timestamp":1786117893233,"version":"build-2736575974"},"reference-count":25,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["1R01AI150978"],"award-info":[{"award-number":["1R01AI150978"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,8,4]]},"abstract":"ABSTRACT<\/jats:title>\n \n \n \n We report on five clinical fluoroquinolone-resistant\n Escherichia coli<\/jats:italic>\n strains carrying a unique variant of the quinolone efflux pump gene (\n qepA<\/jats:italic>\n ). The\n E. coli<\/jats:italic>\n 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\n qepA<\/jats:italic>\n gene flanked by intI1 integrase and ISCR3 elements. Protein sequence comparison revealed a duplication of the L348\u2013G349 insertion, similar to the\n qepA8<\/jats:italic>\n variant, but without the V134I substitution. The unique\n qepA<\/jats:italic>\n 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\n gyrA<\/jats:italic>\n and\n parC<\/jats:italic>\n , 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 (\u226532 \u00b5g\/mL) minimum inhibitory concentration (MIC) to ciprofloxacin, indicative of high-level resistance. The evolution of\n qepA<\/jats:italic>\n 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\n E. coli<\/jats:italic>\n strains found in sub-Saharan Africa (SSA). The identification of a unique\n qepA<\/jats:italic>\n variant\u2014characterized by a unique L348-G349 duplication and absence of the V134I mutation typical of\n qepA8<\/jats:italic>\n \u2014demonstrates that the\n qepA<\/jats:italic>\n locus is continuing to diversify in clinical settings.\n <\/jats:p>\n <\/jats:sec>\n \n IMPORTANCE<\/jats:title>\n \n 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 (\n qepA<\/jats:italic>\n ) variant with a unique mutation combination among the\n qepA<\/jats:italic>\n alleles in\n Escherichia coli<\/jats:italic>\n clinical isolates from children being discharged from hospitals in Kenya. The plasmid-mediated resistance gene\n qepA<\/jats:italic>\n contained the insertion of an L348\u2013G349 amino acid duplication without the additional V134I substitution present in the\n qepA8<\/jats:italic>\n allele. The existence of this\n qepA<\/jats:italic>\n 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.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.1128\/spectrum.00056-26","type":"journal-article","created":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T13:00:48Z","timestamp":1782738048000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Fluoroquinolone-resistant\n Escherichia coli<\/i>\n carrying\n quinolone efflux pump<\/i>\n (\n qepA<\/i>\n ) with L348\u2013G349 duplication in the absence of V134I substitution"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6586-1504","authenticated-orcid":true,"given":"Kevin","family":"Kariuki","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04r1cxt79","id-type":"ROR","asserted-by":"publisher"}],"name":"Centre for 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