Genomic Analysis of Vibrio cholerae Strains Isolated in Siberia and the Far East during the Seventh Cholera Pandemic: Determining the Appurtenance to Global Phylogenetic Lines

Abstract

The aim was to determine the phylogenetic position and features of the genome organization of individual groups of Vibrio cholerae strains isolated in Siberia and the Far East under different epidemiological situations during the seventh cholera pandemic.Materials and methods. We examined 275 V. cholerae strains, isolated during epidemic complications and during the cholera-free period in Siberia and the Far East, with different profiles of the main genomic loci of pathogenicity. The genomes of 969 V. cholerae strains from GenBank were used for phylogenetic analysis. The phylogeny reconstruction was carried out through calculating the distances between strains based on the occurrence of k-mers. The search, analysis and visualization of the loci structure in mobile genetic elements in V. cholerae genomes were performed using the blastn and Prokka programs and the author’s R and Python scripts.Results and discussion. Strains of V. cholerae isolated in Siberia and the Far East have been included in three global phylogenetic lines – L2, L3, L4. The distribution of strains from Siberia and the Far East along phylogenetic lines corresponds to the epidemiological situation in which they were isolated. We have identified the differentiation of strains by groups consistent with the global waves of spread of the etiological agent of the seventh cholera pandemic. We also traced potential paths for the import of the cholera pathogen into the territory of the Russian Federation. It has been revealed that spontaneous mutants that lost cholera toxin genes during storage and cultivation on nutrient media belong to the L2 phylogenetic lineage as well as toxigenic El Tor vibrios. The structural analysis confirms the differences in their genome organization and strains that do not have a CTX prophage during primary PCR screening. We recommend a two-stage algorithm of phylogenetic analysis within the framework of genomic monitoring of cholera agent: the first stage is a simplified assessment based on the occurrence of k-mers for express epidemiological analysis; the second stage is an in-depth analysis of genomes using a complex of phylogenetic methods for the reconstruction of links in individual epidemic complications, to establish patterns of origin and time of divergence of the pathogen clones.