Peculiarities of Genome Structure of Toxigenic Vibrio cholerae nonO1/nonO139 Strain Isolated in 2024 from a Surface Water Body in the Rostov Region

The aim of the study was to perform a detailed molecular-genetic characterization of the toxigenic Vibrio cholerae nonO1/nonO139 strain isolated from the Don River in the Rostov Region in 2024. Materials and methods. Whole-genome sequencing was carried out on the MiSeq Illumina and Oxford Nanopore platforms. Primary assembly was performed de novo through the Canu software based on long reads, and subsequent alignment was carried out using short reads with the Pilon program. Vector NTI package, BLASTN, BLASTP, BioEdit, Ugene, abricate (CARD database) and SnapGene Viewer were used in the bioinformatics analysis of genomes. The search for the limits of wb* clusters and comparison of their genes were conducted by means of the author’s program “O-cluster”. The phylogenetic tree was constructed using the roary and FastTree software. Results and discussion. A toxigenic strain of NAG-vibrio has been identified for the first time in Russia. The sequences of both chromosomes of the studied strain have been determined via hybrid genome assembly. Based on the analysis of the O-antigen biosynthesis region, the strain has been classified into serogroup O105 and it shows a high degree of closeness to clinical strains of this serogroup previously isolated in China. Bioinformatic analysis has revealed the presence of tandems of two identical copies of CTX and RS1 prophages on the large chromosome, which are notably distinct from their prototypes. The ctxB gene is represented by the ctxB12 allele, and all RS1 genes, except for rstC, show no similarity to canonical sequences. A VPI-1 island with an alternative tcpA allele, a T3SS cluster within the VPI-3 island, and the cholix toxin gene have been identified, which constitutes a rare combination within a single strain’s genome. The set of intact determinants of other pathogenicity factors is sufficient for the realization of pathogenic potential. The presence of a number of antibiotic resistance determinants in the genome did not always correlate with the phenotypic manifestation of resistance/susceptibility to antimicrobial agents in vitro. The genome structure of the strain and its close relationship to clinical isolates indicate a potential capacity to cause acute intestinal infections. Since there is a possibility of new introductions of such strains into the Russian Federation, their detection in water bodies necessitates the implementation of a set of anti-epidemic measures.

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