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 and mortality 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 total of 200 E. coli bacteria were isolated from 780 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. Result The most common urologic clinical manifestation combinations in this study were dysuria, urine urgency and urgency incontinence. The frequent UPEC virulence gene identified was fim H 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 fim H, 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.

Antimicrobial resistant and virulence genes profiles of some Gram-negative bacteria from clinical isolates at Usmanu Danfodiyo University Teaching Hospital, Sokoto, Nigeria

“…There was a significant association between surface adhesion genes with resistance to non-beta-lactam antibiotics, as reported by [18], thereby suggesting the inhibitory role of adhesions in the infiltration of drugs in these organisms. The gene for adhesion (fimH) and iron chelation (iutA) were detected only in E.coli (38.9% and 27.8%) and P. mirabilis (5.6% and 16.7%), respectively.…”

“…The preponderance of E. coli, as seen from previous studies, caused their inclusion in this study, and because E. coli is the predominant facultative anaerobe and commensal microbiota in the mammalian gastrointestinal tract [15,16] that play a key role in hospital and community acquired infections [17]. Additionally, E. coli strains posses a store of virulence factors that contribute to their ability to overcome different defence mechanisms causing disease [18]. There are few reported studies on virulence factors related to K. pneumoniae and P. mirabilis.…”

Antibiotic resistance, phylogenetic typing, and virulence genes profile analysis of uropathogenic Escherichia coli isolated from patients in southern Iraq

“…Our outcomes showed the presence of UTIs in all age groups and an approximately two-fold prevalence in females compared to males (62 females versus 38 males). The anatomical differences in the urinary system between men and women increases the frequency of disease in women; E.coli is part of the normal ora of the gastrointestinal system and urethra is shorter and wider in women increasing the chances of bacterial entry and colonization, resulting in ascending UTI (Dadi et al, 2020). The highest prevalence of the disease was in the age range of 0-5 years, which is not matching with the results of Shah et al (2019) in Nepal.…”

“…), so strains with larger genomes will be more pathogenic (Hozzari et al, 2020). Identifying virulence factors, not only indicates the pathogenic process of bacteria, but also plays an important role in the development of vaccines and drugs (Dadi et al, 2020).…”

“…The present results also showed that 96% of the isolates had at least one variant of the genes encoding virulence factors, and the distribution of virulence genes were as follows: mH (96%), aer (47%), papC (36%), cnf1 (16%), hly (15%), and afa (8%), respectively. mH, due to its high percentage among UPEC strains and its role in bacterial binding to urinary tract cells and colonization, is considered as a potential candidate to develop vaccine preventing urinary tract infections (Dadi et al, 2020). Bacterial access to iron plays an important role in urinary tract infections (Wiles et al, 2008), and many strains in this study encode the aer gene, which is necessary for iron uptake.…”