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New Genetic Variants of the Cholera Agent and Their Distribution in Endemic Countries and Russia

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Abstract

In the course of the three waves of the seventh cholera pandemic, the genome of the pathogen has undergone significant changes, which resulted in the emergence of new genetic variants with a high pathogenic and epidemic in the last decade. The aim of this study is to investigate the genomic diversity of the cholera agent and the prevalence of new genetic variants both in cholera-endemic regions and Russia, as well as to identify their phylogenetic relations. To search for new variants of the pathogen, bioinformatic analyses of the whole genome nucleotide sequences of 124 V. cholerae El Tor strains have been carried out. These strains were previously obtained by us or taken from the NCBI Gen Bank and European Nucleotide Archive database. Phylogenetic relations have been established based on SNP analysis for 115 different strains isolated in Asia, Africa, Russia, and Ukraine during three waves of the pandemic. Genomic analyses have been performed for 91 strains isolated in seven endemic countries between 2007 and 2019. According to the sets of mutant virulence and epidemicity genes localized in mobile genetic elements (CTXφ prophage, pathogenicity island VPI-1, and pandemic island VSP-II) and the core region, 74.7% of the studied strains are classified as new genetic variants of the pathogen. The genomic analyses of toxigenic strains from Russia and Ukraine (1970–2014) have revealed five groups that differ in mutations in key genes associated with virulence, epidemic potential, and drug resistance. According to the spectrum of mutant genes, 80.0% of the strains imported from endemic regions in recent years (2010–2014) have been recognized as new variants. According to the analysis of phylogenetic relations based on SNP typing of 115 strains, the new variants from Russia and Ukraine are phylogenetically similar to those circulating in Africa and Asia over the past decade. The results obtained are of interest for understanding the molecular mechanisms and dynamics of changes in the most important genetic properties of this pathogen and can also be used to develop methods for gene diagnostics of new variants of the pathogen.

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Authors and Affiliations

  1. Russian Research Anti-Plague Institute “Microbe”, 410005, Saratov, Russia

    N. I. Smirnova, D. A. Rybal’chenko, N. A. Plekhanov, Yu. V. Lozovsky, A. V. Fedorov & V. V. Kutyrev

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  1. N. I. Smirnova
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  2. D. A. Rybal’chenko
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  3. N. A. Plekhanov
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  4. Yu. V. Lozovsky
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Correspondence to N. I. Smirnova.

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Translated by T. Kuznetsova

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Smirnova, N.I., Rybal’chenko, D.A., Plekhanov, N.A. et al. New Genetic Variants of the Cholera Agent and Their Distribution in Endemic Countries and Russia. Mol. Genet. Microbiol. Virol. 38, 8–15 (2023). https://doi.org/10.3103/S0891416823010093

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