Investigation of the Lipopolysaccharide Cluster Structure in the Genomes of <i>Vibrio cholerae</i> Rough Variants

Abstract

Determination of Vibrio cholerae affiliation to one or another serogroup may meet some difficulties in cases of atypical agglutination with diagnostic cholera sera. The study of genetic determinants that allows for identifying a serogroup is a relevant task in monitoring of surface water body contamination with cholera vibrios. The aim of the work was to compare the structural organization (quantitative and qualitative gene composition) of LPS clusters in V. cholerae rough variants. Materials and methods. We used Illumina MiSeq for the whole genome sequencing; SPAdes software (version 3.11.1) for de novo assembly; and blastn (v. 2.5.0) for gene searching. GeneMarkS software was deployed for annotation of the genes incorporated in the clusters; nucmer – for searching homologous sites. Visualization of O-LPS clusters was carried out by means of SnapGene Viewer. Results and discussion. Strains of V. cholerae rough variants had diverse gene clusters responsible for O-antigen biosynthesis. We have identified three types of O-LPS clusters with different size and number of genes. Unique DNA sites, common to the whole group of V. cholerae rough variants, have not been detected. Two genes present in all rough strains have been defined, but they are not unique for this group of strains and can be found in representatives of other serogroups. For two types of clusters, a region containing the IS‑element, common with V. cholerae O1, has been revealed.