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Variability of the Genome of El Tor Cholera Vibrios Isolated before the Onset and in Different Periods of the Current Pandemic

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Abstract

The genomic instability of the cholera agent leads to the emergence of its new variants with altered epidemically significant features. This makes investigation of the dynamics in pathogenicity gene structure and cholera vibro persistence changes over extended periods of time important. Bioinformatic analysis of whole genome nucleotide sequences was carried out in 44 toxigenic and nontoxigenic Vibrio cholerae O1 strains, biovar El Tor, isolated before the onset and in different periods of the current pandemic, with 29 of them being found in Russia. SNP-typing was performed using Bayesian evolutionary analysis with BEAST v2.5.1. Based on SNP-analysis, it was demonstrated that the importation of epidemically hazardous strains into the territory of Russia (1970–2014) overlapped with three different waves of the global spread of cholera. Comparison of the nucleotide sequences of genomic regions determining their virulence and ability to spread epidemically confirmed that there were multilayered rapid changes in cholera vibrios during evolution. For the first time ever, it has been established that the genomes of pathogenicity islands, VPI-1 and VPI-2, of prepandemic strains contained different mutations, which distinguish them from the genome of pandemic strains. At the same time, we have revealed conservation of nucleotide sequences of all the studied persistence genes from VPI-2 and EPI of pandemic isolates. On the contrary, the modern nontoxigenic strains ctxA–tcpA– show considerable variability of persistence genes that are parts of the structure of these mobile elements. New data on the structure of regions of the V. cholerae genome associated with persistence can be used to differentiate V. cholerae of different epidemic significance.

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Authors and Affiliations

  1. Federal Public Health Institution, Russian Research Anti-Plague Institute “Microbe”, 410005, Saratov, Russia

    N. I. Smirnova, D. V. Badanin, D. A. Rybal’chenko, Ya. M. Krasnov, A. A. Kritsky, Yu. V. Lozovsky, A. V. Fedorov & V. V. Kutyrev

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  1. N. I. Smirnova
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  2. D. V. Badanin
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Correspondence to N. I. Smirnova.

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The authors declare that they have no conflicts of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.

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Translated by E. V. Makeeva

ADDITIONAL INFORMATION

Smirnova N.I.: https://orcid.org/0000-0002-7115-6286; e-mail: rusrapi@microbe.ru

Badanin D.V.: https://orcid.org/0000-0002-9662-8438; e-mail: rusrapi@microbe.ru

Rybal’chenko D.A.: https://orcid.org/0000-0002-3117-8229; e-mail: rusrapi@microbe.ru

Krasnov Ya.M.: https://orcid.org/0000-0002-4909-2394; e-mail: rusrapi@microbe.ru

Kritsky A.A.: https://orcid.org/0000-0002-5506-4285; e-mail: rusrapi@microbe.ru

Lozovsky Yu.V.: https://orcid.org/0000-0003-4382-7254; e-mail: rusrapi@microbe.ru

Fedorov A.V.: https://orcid.org/0000-0001-7190-4427; e-mail: rusrapi@microbe.ru

Kutyrev V.V.: https://orcid.org/0000-0003-3788-3452; e-mail: rusrapi@microbe.ru

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Smirnova, N.I., Badanin, D.V., Rybal’chenko, D.A. et al. Variability of the Genome of El Tor Cholera Vibrios Isolated before the Onset and in Different Periods of the Current Pandemic. Mol. Genet. Microbiol. Virol. 36, 79–91 (2021). https://doi.org/10.3103/S0891416821020087

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