Phylotyping and genotyping of Escherichia coli isolates obtained from patients with colorectal cancer

Abstract

© 2020, Advanced Scientific Research. All rights reserved. Objective of the research was to phylotype the E. coli isolates from the malignant and adjacent normal epithelium of the rectal mucosa of patients diagnosed with colorectal cancer, identifying and discriminating phylogroups by a set of genes, and also genotyping them by the fimH-gene locus by identifying fimH types. Samples of bacterial cultures isolated from paired biopsy specimens of patients diagnosed with colorectal cancer were subjected to molecular genetic research for species identification, as well as E. coli phylo- and genotyping. By sequencing the 16S rRNA locus, bacterial cultures are identified both as isolates of monocultures of E. coli and as mixed cultures of E. coli and K. pneumonia. The procedure for the phylotyping of E. coli isolates by identifying and discriminating phylogroups by a set of genes established the affiliation of samples of bacterial cultures with phylogroups A and B2. The genotyping procedure for E. coli isolates at the fimH gene locus by identifying the fimH types characterized the studied samples by signs of the third (f-3), fourth (f-4), and seventh (f-7) types, respectively. The strategy for identifying fimH-types during genotyping of E. coli at the fimH-gene locus has been improved, based on the analysis of SNP sequenced DNA sequences, and includes 52 fimH-types, three of which are justified in this paper.