New genetic variants of cholera agent and their distribution in epidemic countries and Russia

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THE PURPOSE OF THIS STUDY

Is to investigate the genomic diversity of the cholera agent and the prevalence of new genetic variants in cholera-endemic regions and Russia, and to identify their phylogenetic relations.

MATERIALS AND METHODS

To search for new variants of the pathogen, bioinformatic analysis of the whole genome nucleotide sequences of 124 V. cholerae El Tor strains obtained by us earlier and taken from the NCBI Gen Bank and European Nucleotide Archive database was carried out. Phylogenetic relations have been established for 115 different strains isolated in Asia, Africa, Russia and Ukraine during three waves of the pandemic, based on SNP analysis.

RESULTS AND DISCUSSION

Analysis of the genomes of 91 strains isolated in seven endemic countries between 2007 and 2019 showed that, by the set of mutant virulence and epidemicity genes localized in mobile genetic elements (CTXφ prophage, pathogenicity island VPI-1 and pandemicity island VSP-II) and the core region, 74.7% of them are classified as new genetic variants of the pathogen. When analyzing the genomes of toxigenic strains from Russia and Ukraine (1970—2014), five groups were identified that differ in mutations in key genes associated with virulence, epidemic potential, and drug resistance. Among them, imported from endemic regions in recent years (2010—2014), 80.0% are classified as new variants by the spectrum of mutant genes.

CONCLUSION

Analysis of phylogenetic relations based on SNP typing of 115 strains showed the phylogenetic similarity of new variants from Russia and Ukraine with 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.

Keywords:

Vibrio cholerae

new genetic variants

virulence

epidemic potential

mutations

phylogeny

Authors:

Smirnova N.I.

FGHI Russian Research Anti-Plague Institute «Microbe»

Rybal’chenko D.A.

FGHI Russian Research Anti-Plague Institute «Microbe»

Plekhanov N.A.

Irkutsk State Medical University

ORCID: 0000-0001-8945-775X

Lozovsky Yu.V.

FGHI Russian Research Anti-Plague Institute «Microbe»

Fedorov A.V.

Vishnevsky National Medical Research Center for Surgery;
Russian Society of Surgeons

ORCID: 0000-0002-8456-8685

Kutyrev V.V.

FGHI Russian Research Anti-Plague Institute «Microbe»

Received:

02.02.2022

Accepted:

15.04.2022

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