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.

Distribution of phylogenetic groups, adhesin genes, biofilm formation, and antimicrobial resistance of uropathogenic Escherichia coli isolated from hospitalized patients in Thailand

“…The most prevalent adhesin gene was fimH, followed by pap, sfa, and afa. In agreement with studies conducted in Ethiopia (Dadi et al, 2020) and Iran (Tajbakhsh et al, 2016), phylogenetic group B2 strains showed the highest frequency of the adhesin genes in our study. We found a coexistence of fimH and pap genes (69.2%), indicating a high presence of virulence genes among UPEC isolated from UTI patients in Thailand.…”

“…The P-independent, X-binding fimbrial adhesin encoded by the afa1 operon mediates specific binding to uroepithelial cells and human erythrocyte receptors ( Labigne-Roussel & Falkow, 1988 ). Different studies have investigated the presence of the adhesion-encoding genes pap (P fimbriae), sfa (S fimbriae), afa (afimbrial adhesin), and fimH (type 1 fimbriae) across UPEC strains using multiplex PCR ( Rahdar et al, 2015 ; Dadi et al, 2020 ; Tarchouna et al, 2013 ; Shetty et al, 2014 ).…”

Peer Review #1 of "Distribution of phylogenetic groups, adhesin genes, biofilm formation, and antimicrobial resistance of uropathogenic Escherichia coli isolated from hospitalized patients in Thailand (v0.2)"

“…The most prevalent adhesin gene was fimH, followed by pap, sfa, and afa. In agreement with studies conducted in Ethiopia (Dadi et al, 2020) and Iran (Tajbakhsh et al, 2016), phylogenetic group B2 strains showed the highest frequency of the adhesin genes in our study.…”

“…Our results are in accordance with several studies in which the dominant strain was found to be group B2. These studies were conducted in North America (45% prevalence of group B2) (Johnson et al, 2003), Denmark (67%) (Ejrnaes et al, 2011), Poland (35%) (Kot et al, 2016), South Korea (79%) (Lee et al, 2016), and Ethiopia (30%) (Dadi et al, 2020). Using a novel PCR-based method (Clermont et al, 2013), we could classify UPEC into groups C, E, and F and clade I, resulting in a lower percentage of strains in groups A, B1, and D than in earlier studies.…”

“…Manuscript to be reviewed Different studies have investigated the presence of the adhesion-encoding genes pap (P fimbriae), sfa (S fimbriae), afa (afimbrial adhesin), and fimH (type 1 fimbriae) across UPEC strains using multiplex PCR (Rahdar et al, 2015;Dadi et al, 2020;Tarchouna et al, 2013;Shetty et al, 2014).…”