Distribution of virulence genes and phylogenetics of uropathogenic Escherichia coli among urinary tract infection patients in Addis Ababa, Ethiopia

Abstract

Background: Urinary tract infection (UTI) is a common cause of morbidity worldwide. Uropathogenic Escherichia coli (UPEC) bacteria are the major cause of urinary tract infections. UPEC strains derive from different phylogenetic groups and possess an arsenal of virulence factors that contribute to their ability to overcome different defense mechanisms and cause disease. The objective of this study was to identify phylogroup and virulence genes of UPEC among urinary tract infection patients.

Methods: A cross sectional study was conducted from January 1, 2017 to October 9, 2017. E. coli bacteria were isolated from UTI patients using culture and conventional biochemical tests. Identification of phylogroup and genes that encodes for virulence factors was done using multiplex polymerase chain reaction (PCR). Data was processed and analyzed with SPSS version16.0 and Epi-info version 3.4.1 software.

Results: The most common urologic clinical manifestation combinations in this study were dysuria, urine urgency and urgency incontinence. The frequent UPEC virulence gene identified was fimH 164 (82%), followed by aer 109 (54.5%), hly 103 (51.5%), pap 59 (29.5%), cnf 58 (29%), sfa 50 (25%) and afa 24 (12%).There was significant association between pap gene and urine urgency (p-0.016); sfa and dysuria and urine urgency (p-0.019 and p-0.043 respectively); hly and suprapubic pain (p-0.002); aer and suprapubic pain, flank pain and fever (p-0.017, p-0.040, p-0.029 respectively). Majority of E. coli isolates were phylogroup B2 60(30%) followed by D 55(27.5%), B1 48(24%) and A 37(18.5%). There was significant association between E. coli phylogroup B2 and three virulence genes namely afa, pap, and sfa (p-0.014, p-0.002, p-0.004 respectively).

Conclusion: In this study the most frequent E. coli virulence gene was fimH, followed by aer, hly, pap, cnf, sfa and afa respectively. There was significant association between E. coli virulence genes and clinical symptoms of UTI. The phylogenetic analysis indicates majority of uropathogenic E. coli isolates were phylogroup B2 followed by phylogroup D. Phylogroup B2 carries more virulence genes. Hence, targeting major UPEC phylogroup and virulence genes for potential vaccine candidates is essential for better management of UTI and further research has to be conducted in this area.

Keywords: Urinary tract infections; Uropathogenic Escherichia coli; Virulence genes and phylogroup.

Fig. 1

Virulence genes of uropathogenic Escherichia coli. (Proportion of uropathogenic E. coli virulence genes. The most frequent virulence gene was fim H, followed by aer, hly, pap, cnf, sfa and afa)

Fig. 2

Representative 1.2% agarose gel electrophoresis of uropathogenic Escherichia coli virulence genes isolated from urinary tract infection patients. (Lane M, 1-kb plus ladder; lane 1–15, amplified E. coli PCR products (sample 81–95) with the following virulence genes, pap (328 bp), fimH (456 bp) and afa (672 bp); lane 16, strain J96 positive control; lane 17, strain K10 positive control and lane 20, distilled water as negative control)

Fig. 3

Representative 1.2% agarose gel electrophoresis of uropathogenic Escherichia coli genes used to classify Escherichia coli into different phylogroup. (Lane M, 1-kb plus ladder; lane 1–15, amplified PCR products (sample 111–125) with the following Escherichia coli phylogrouping genes; arp A (400 bp), chu A (288 bp), yja A (211 bp) and TspE4C2 (152 bp); lane 16, strain CFT073 positive control; lane 17, strain J96 positive control and lane 20, strain K10 positive control)

Fig. 4

Phylogroup distribution of uropathogenic Escherichia coli isolates. (The most common phylogroup of uropathogenic Escherichia coli isolates was phylogroup B2 followed by phylogroup D, phylogroup B1 and phylogroup A)