Phenotypic and Genotypic Characterization of Uropathogenic Escherichia Coli Isolates from Patients in Selected Hospitals in Kenya

Abstract

Uropathogenic Escherichia coli (UPEC) is the major cause of community and hospital-acquired UTI cases.However,there is increasing resistance to antibiotics used in the treatment of UPEC infections. Escherichia coli can be classified into eight phylo-groups, which differ in antimicrobial resistance. Production of extended-spectrumβ-lactamases (ESBLs) and plasmidmediated AmpC (pAmpC) β-lactamases are important mechanisms of resistance toβ-lactams antibiotics. In Kenya, β-lactams are used increasingly in the treatment of UTIs, most without a sensitivity test, a practice that may result in increased resistance due to misuse of the drugs. In 2010,the occurrence of ESBL in UPEC isolates was 27%. Since then,few studies on genetic determinants of resistance to β-lactams have been carrying out in Kenya. Moreover, the phylogroups of UPEC in Kenya have not been determined due to lack of continuous surveillance studies. This study, therefore, undertook to determine the occurrence of Extended-Spectrum βlactamases (ESBLs) and plasmid-mediated β-lactamases (pAmpC), the genetic determinants of resistance to β-lactams, and phylo-grouping of UPEC isolates in Kenya. This retrospective, laboratory-based survey study is nested in a parent protocol (KEMRI# 2767/WRAIR#2089) that has been running from 2015 to date. In this study,95 archived UPEC isolates obtained from patients in different hospitals in Kenya were purposely selected from the database at the start of the study. Data were analyzed in the statistical package for social sciences (SPSS) version 20, where the frequencies and percentages for occurrence of ESBLs and pAmpC β-lactamases plus phylo-groups for UPEC isolates were obtained through cross-tabulation in descriptive statistics. In this study, Nairobi, Kisumu, Kericho, Kilifi, and Kisii had 39/95;(41.1)%, 28/95;(29.5)%, 14/95;(14.7)%, 10/95;(10.5)% and 4/95;(4.2)% UPEC isolates respectively. The ESBLs were characterized by phenotype and genotype using a combined disk diffusion test and real-time PCR for identification of the blaTEM, blaCTX-M, and blaSHVβ-lactamase genes. Twenty three out of 95 UPEC isolates were positive for ESBL production.Nairobi, Kisumu, Kilifi, Kericho, and Kisii Counties had 12/23;(52.2)%, 5/23;(21.7)%, 4/23;(17.4)%, 2/23;(8.7)% and zero ESBL producers respectively.AmpC screening was done using the cefoxitin disk diffusion test and screen positives phenotypically confirmed by the disk approximation test. Five out of 23 ESBL producers were cefoxitin resistant. However, all five isolates were negative for AmpC production by phenotypic and genotypic methods. The predominant ESBL genes were blaCTX-M, and blaTEM each with 95.6% followed by blaSHV21.7%. Sixteen isolates (69.6%) had both blaCTX-MandblaTEM genes, whereas five isolates (21.7%) had all three genes (blaTEM, blaCTX-M, and blaSHV. A total of 93 out of 95 UPEC isolates were assigned to 5 of the eight phylo-groups by the quadruplex PCR methods of which thephylo-groups B231/95; (32.6%) and D 30/95; (31.6%) predominated.The results of this study could guide clinicians in the identification of the correct antibiotics forpatients with UTIs. Further,the results canbe used in mapping the phylo-groups associated with ESBL resistance genes to prevent there spread.This study recommendscontinuous surveillance studies to monitor the genes associated with ESBL resistance, futher tests to identify novel and emerging phylo-types such as the unassigned isolate