Antibiotic Susceptibility and Molecular Characterization of Uropathogenic Escherichia coli Associated with Community-Acquired Urinary Tract Infections in Urban and Rural Settings in South Africa

Abstract

We investigated the phenotypic and genotypic antibiotic resistance, and clonality of uropathogenic Escherichia coli (UPEC) implicated in community-acquired urinary tract infections (CA-UTIs) in KwaZulu-Natal, South Africa. Mid-stream urine samples (n = 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 E. coli (targeting the papC gene), and β-lactam (blaTEM/blaSHV-like and blaCTX-M) and fluoroquinolone (qnrA, qnrB, qnrS, gyrA, parC, aac(6’)-Ib-cr, and qepA) 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 E. coli isolates were obtained from 28 positive UTI samples. All E. coli isolates were papC-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 CTX-M-positive but SHV-negative. The aac(6’)-Ib-cr and gyrA 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.