Molecular epidemiology of Escherichia coli isolated from urinary tract infections in inpatients and outpatients in Gauteng, South Africa

Abstract

Urinary tract infections (UTIs) have the highest burden of disease worldwide and disproportionately affects female and elderly patients. The most common causative agent of UTIs is Escherichia coli. Escherichia coli that causes UTIs is classified as extraintestinal pathogenic E. coli (ExPEC) and more specifically uropathogenic E. coli (UPEC). Clear clonality exists amongst ExPEC isolates, and the most dominant clone is the multi-drug resistant sequence type (ST) 131. Between 20% to 30% of all UTIs are caused by ST131 UPEC. The aim of this study was to characterise ST131 and non-ST131 clones in E. coli isolated from urinary specimens in inpatients and outpatients in Gauteng, South Africa. Non-repeat E. coli isolates were collected from a private diagnostic laboratory over a one-week period. Isolate antimicrobial susceptibility results as well as corresponding patient information were collected. Isolates where screened for ST131 and its clades using two multiplex-PCR (M-PCR) assays. Non-ST131 were characterised using a seven single nucleotide polymorphisms RT-PCR (septatyping) assay. All isolates where further screened for colistin susceptibility using a resazurin reduction-based assay with a breakpoint concentration of 3.75 µg/mL. Non-susceptible isolates underwent minimum inhibitory concentration (MIC) determination by broth microdilution assay. Colistin resistant isolates underwent mcr-1 to mcr-5 screening using a M-PCR assay. Of the 428 E. coli isolates that were collected, 18% (n=77/428) were ST131. The proportional distribution of ST131 in outpatients was 20% (n= 54/274) and 18% in inpatients (n= 21/115). The most prevalent ST131 clade was C1 (32.5%; n=25/77) followed by C2 (23.4%; n= 18/77), A (19.5%; n= 15/77), B (13%; n= 10/77) and subclade C1-M27 (5.2%; n=4/77). Two septatypes, 271 and 620, are homogenous with ST69 and ST73 respectively, and were identified in both inpatients and outpatients. Sequence type 131 isolates showed high rates of resistance to ciprofloxacin (CIP) 79% (n= 19/24), levofloxacin (LEV) 84% (n= 16/19) and ciprofloxacin/levofloxacin combination (CIP/LEV), 57% (n= 30/53). Non-ST131 showed a resistance rate of 18% (n= 11/62), 15% (n= 6/40) and 20% (n= 47/239) for ciprofloxacin, levofloxacin, and ciprofloxacin/levofloxacin combination, respectively. The percentage of extended spectrum beta-lactamase (ESBL) producing isolates was 32% (n= 23/72) for ST131 isolates and 6% (n= 17/291) in non-ST131 isolates. Three isolates were resistant to colistin and had a MIC of 16 µg/mL. None of the colistin resistant isolates screened positive for mcr-1 to mcr 5 genotypes. This study was the first in South Africa to report the prevalence of ST131 and its clades from an ExPEC sample without an antibiotic resistance sampling bias. The prevalence of ST131 in UPEC limits the choice for effective antibiotic treatment. Better techniques for surveillance of ExPEC clones, such as a sequence-based methods, would effectively identify high-risk ExPEC clones, their associated antibiotic resistance genes, and the ability to perform horizontal gene transfer using mobile genetic vectors. This would allow for the implementation of better infection prevention and control strategies to stop the spread of these genes to environmental and or animal Enterobacteriaceae, contributing to the “One Health” model.