Molecular Genetic Analysis of Vibrio cholerae O1 El Tor Strains Identified in 2023 in Russia

Abstract

A comparative analysis of the genome of nontoxigenic and toxigenic V. cholerae O1 El Tor strains identified in Russia in 2023 and their phylogenetic analysis were performed. We used V. cholerae O1 El Tor strains isolated from patients and from an aquatic environment in 2023 in Russia. Analysis of their sequenced genomes was performed with the UGENE v.45.1 and Bandage v.0.8.1 software. To carry out SNP analysis, nucleotide sequences of the complete genomes of 63 V. cholerae El Tor strains obtained by us (41 strains) and from the NCBI GenBank database (22 strains) were used. Conventional methods were used to assess the phenotypic characteristics of strains (susceptibility to antibiotics, hemolysin and protease production, and motility). Analysis of the sequenced complete genomes of V. cholerae El Tor strains isolated from patients and from an aquatic environment in 2023 in Russia showed their genetic diversity. Toxigenic strains belonged to different types of genovariants with different mutations in the genome of transposable elements, as well as in core genes associated with pathogenicity, the ability to spread epidemically, and drug resistance. The clinical strain M3208 had a full set of altered virulence genes (ctxB7, tcpA^CIRS101, and rtxA4) and epidemicity (VSP-II^Δ) characteristic of new variants with high pathogenic potential that were widespread during the third wave of the pandemic. In addition, the resulting mutations led to the emergence of resistance to nalidixic acid (Nal^r) and the loss of resistance to polymyxin B (Pol^s). The second toxigenic strain M3210, isolated from river water, differed from the strain M3208 in the composition of mutant genes, since it had only one altered gene (ctxB). The genotype of this strain (ctxB1tcpA^EltorrtxA1VSP-II) was identical to that of previously appearing genovariants with a lower level of virulence from the second wave of the pandemic, which persisted only in several endemic regions. By contrast, the nontoxigenic isolate M3209 from a patient with acute enteric disease was devoid of not only the CTXφ prophage but also other transposable elements carrying key pathogenicity and epidemic genes. Only the deleted VPI-2 pandemic island was present in its genome. This strain was shown to produce additional pathogenicity factors (hemolysin, soluble hemagglutinin/protease, and motility), which could lead to the development of gastroenteritis in infected individuals. The genomic diversity of V. cholerae El Tor strains introduced into Russia in 2023 was revealed. Toxigenic strains were shown to be different genovariants with altered epidemically important properties. Among them, the clinical toxigenic strain M3208 was classified as a new genovariant with high pathogenic potential based on its mutant genes.