| Summary: | We investigated the phenotypic and genotypic antibiotic resistance, and clonality of uropathogenic <i>Escherichia coli</i> (UPEC) implicated in community-acquired urinary tract infections (CA-UTIs) in KwaZulu-Natal, South Africa. Mid-stream urine samples (<i>n</i> = 143) were cultured on selective media. Isolates were identified using the API 20E kit and their susceptibility to 17 antibiotics tested using the disk diffusion method. Extended-spectrum β-lactamases (ESBLs) were detected using ROSCO kits. Polymerase chain reaction (PCR) was used to detect uropathogenic <i>E. coli</i> (targeting the <i>pap</i>C gene), and β-lactam (<i>bla</i><sub>TEM</sub><i>/bla</i><sub>SHV</sub>-like and <i>bla</i><sub>CTX-M</sub>) and fluoroquinolone (q<i>nr</i>A, q<i>nr</i>B, q<i>nr</i>S, <i>gyr</i>A, <i>par</i>C, a<i>ac(6’)-Ib-cr</i>, and q<i>ep</i>A) resistance genes. Clonality was ascertained using ERIC-PCR. The prevalence of UTIs of Gram-negative etiology among adults 18–60 years of age in the uMgungundlovu District was 19.6%. Twenty-six <i>E. coli</i> isolates were obtained from 28 positive UTI samples. All <i>E. coli</i> isolates were <i>pap</i>C-positive. The highest resistance was to ampicillin (76.9%) and the lowest (7.7%) to amoxicillin/clavulanic acid and gentamycin. Four isolates were multidrug-resistant and three were ESBL-positive, all being <i>CTX-M</i>-positive but <i>SHV</i>-negative. The a<i>ac(6’)-Ib-cr</i> and <i>gyr</i>A were the most detected fluoroquinolone resistance genes (75%). Isolates were clonally distinct, suggesting the spread of genetically diverse UPEC clones within the three communities. This study highlights the spread of genetically diverse antibiotic-resistant CA-UTI aetiologic agents, including multidrug-resistant ones, and suggests a revision of current treatment options for CA-UTIs in rural and urban settings.
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