Genomic Features of Non-Toxigenic Vibrio cholerae O1 El Tor Strains: Variability and Prevalence of Pathogenicity, Drug Resistance, and Persistence Genes

The aim of the study was to analyze comparatively the structure and prevalence of pathogenicity, drug resistance, and persistence genes among non-toxigenic Vibrio cholerae O1 biovar El Tor strains of different phylogenetic lineages. Materials and Methods. Nucleotide sequences of complete genomes of 233 toxigenic and 58 non-toxigenic strains of cholera vibrios were analyzed. For multilocus sequence typing of the strains, the MLST 2.0 (Multilocus Sequence Typing) online service on CGE (Center Genomic Epidemiology) platform was used, analyzing the sequences of seven “housekeeping” genes: adk, gyrB, mdhI, metE, pntA, purM, and pyrC. Phylogenetic analysis was performed using the MrBayes v.3.2.7a program based on SNP matrix obtained using the Snippy program. Results. New genomic features of non-toxigenic V. cholerae El Tor strains with the ctxAB−tcpA+ and ctxAB−tcpA− genotypes, belonging to the L3 and L4 phylogenetic lineages, were identified. A significant variability in various pathogenicity and persistence genes of non-toxigenic ctxA−tcpA− (L4) strains was found. The persistence genes localized in the composition of VPI-2 pathogenicity island genome, as well as the genes involved in biofilm formation, were the most variable. Significant genetic differences between ctxAB−tcpA+ strains of the L3 lineage were revealed. It was established that a number of non-toxigenic strains have a significant genetic similarity with toxigenic ones by the ST type, the presence of ICE and VSP-II mobile elements, allelic profile of pathogenicity genes (tcpA, rtxA), and drug resistance genes (gyrA and parC), as well as the presence of the VC2346 gene, and are apparently derivatives of typical or genetically modified cholera strains. Phylogenetic analysis confirmed a pronounced genetic proximity of these isolates to toxigenic ones and demonstrated their belonging to the phylogenetic lineage of epidemically dangerous L2 strains. Conclusions. A high level of persistence gene polymorphism underlies the extensive genetic diversity of non-toxigenic ctxA−tcpA− strains and can determine a high population adaptability to changing environmental conditions. The strains with genetic markers of the cholera pathogen were detected among non-toxigenic vibrios ctxAB−tcpA+, which indicates their origin from toxigenic strains and the need to develop diagnostic tools for differentiating non-toxigenic strains with different pathogenic potential.