Genetic Diversity and Phylogenetic Relatedness of R-Variant штаммов <i>Vibrio cholerae</i> Strains

Abstract

Cholera vibrios, isolated from surface water bodies during monitoring activities, can differ from typical ones in terms of agglutinability with diagnostic cholera sera, which makes it difficult to assign them to a specific serogroup. Therefore, the determination of the causes for these deviations through the study of the structure of genetic determinants responsible for the synthesis of O‑antigen (wb* clusters) is considered a relevant task. The aim of this work was to identify wb* clusters in the genomes of R-variant Vibrio cholerae, study their structure, and conduct phylogenetic analysis of the strains. Materials and methods. Full genome sequencing was performed using Illumina MiSeq and MinION platforms. The assembly was conducted de novo using the SPAdes assembler software (v.3.11.1). Manipulation of cluster sequences and data visualization were carried out using the BLAST program from the ncbi-blast-suite package version 2.13.0, Python scripts and packages such as pyGenomeViz and Biopython. The phylogenetic tree was constructed using the roary program (v.3.13.0). Full genome alignment was carried out using the nucmer and promer programs from the MUMmer 4 package version 4.0. Results and discussion. R-variant V. cholerae contains different types of wb* clusters in the genome, with most commonly occurring O23 and O59. A comparison has been made between translated amino acid sequences of wb* regions in R-variant strains and amino acid sequences of reference strains present in the NCBI database. Some of the analyzed clusters completely match with reference strains, while others show high variability. Phylogenetically, the strains primarily group together according to the wb* cluster type, regardless of the S/R phenotype. Classifying R-variant V. cholerae strains based on agglutinability is challenging. Molecular research methods, polymerase chain reaction, in particular, are necessary to determine the pathogenic potential of such strains.

Keywords

• vibrio cholerae
• r-variant
• wb* cluster
• serogroup
• wbe