Molecular characterization and the virulence gene presence of uropathogenic Escherichia coli in the Indonesian community: the phylogeny groups and clinical manifestation

Background: Uropathogenic Escherichia coli (UPEC) is the most prevalent pathogen in Community -acquired Urinary Tract infections (Ca-UTI) with a divergent spectrum of clinical diseases. Molecular characterization of the virulence gene and the phylogeny group of UPEC could elucidate the broad spectrum of clinical manifestations associated with this pathogen, ranging from asymptomatic bacteriuria to urosepsis. Method: This study collected clean catch urine samples from Ca-UTI patients between 2019 and 2020. The urine sample was inoculated onto blood sheep and MacConkey agar and incubated overnight. A colony was selected for phenotypic and antimicrobial sensitivity testing using Vitex2. All isolates identified as E.coli were validated by the 16S specific gene of E.coli using Taqman real-time PCR. Furthermore, virulence genes fimH, sfaS, pap C, cnf-1, and hlyA were identified using real-time PCR, followed by a phylogeny group, according to Clermont. All those data were analyzed descriptively. Results: This study involved the collection of 188 urine samples from patients with Ca-UTI, and 54 isolates were confirmed to be true E.coli, and the B2 phylogeny group was observed to be the most dominant in cystitis (42%) and pyelonephritis (73%). However, groups A and B1 didn't appear in pyelonephritis patients. Both sfaS and hly-A were virulence genes detected in the B2 and D groups. Gene fimH that encoded adherence factor was seen in all phylogeny groups. Conclusions: Based on the result, it can be concluded that B2 is the dominant phylogeny group in Ca-UTI, sfaS and hlyA is a virulence gene responsible for pyelonephritis, and fimH is the adherence factor in all isolates.