Phylogenetic Analysis of Yersinia pestis Strains of Medieval Biovar from Natural Plague Foci of the Russian Federation and Bordering Countries
https://doi.org/10.21055/0370-1069-2016-2-75-78
Abstract
Objective of the study is to conduct phylogenetic investigation of Yersinia pestis strains (medieval biovar) from plague foci of Russia and bordering countries, using SNP-analysis of the genome-wide sequences of these strains. Materials and methods. Carried out has been sequencing of 14 Y. pestis strains, medieval biovar, from 13 natural plague foci of Russia and neighboring states, as well as their comparison to 9 strains of the same biovar, contained in the NCBI GenBank database. Using software products - Wombac 2.0 and Bionumerics 7.1, revealed is the presence of 1875 core SNPs, on the basis of which a dendrogram of phylogenetic relations between medieval strains is constructed. Results and conclusions. In consequence of genome-wide SNP-analysis, it is established that Y. pestis strains, medieval biovar, from plague foci of Russia and bordering states are assigned to 2.MED1 phylogenetic line and fall under two major evolutionary branches, the first one of which includes strains from the Caucasus and Caspian-Sea regions, and the second one - from Central Asia and China. The data obtained can be used for the development of molecular-genetic methods for differentiation of Y. pestis strains, medieval biovar.
About the Authors
N. Yu. Nosov
Russian Research Anti-Plague Institute “Microbe”
Russian Federation
Russian Federation
E. G. Oglodin
Russian Research Anti-Plague Institute “Microbe”
Russian Federation
Russian Federation
Ya. M. Krasnov
Russian Research Anti-Plague Institute “Microbe”
Russian Federation
Russian Federation
L. M. Kukleva
Russian Research Anti-Plague Institute “Microbe”
Russian Federation
Russian Federation
N. Yu. Shavina
Russian Research Anti-Plague Institute “Microbe”
Russian Federation
Russian Federation
G. A. Eroshenko
Russian Research Anti-Plague Institute “Microbe”
Russian Federation
Russian Federation
V. V. Kutyrev
Russian Research Anti-Plague Institute “Microbe”
Russian Federation
Russian Federation
References
1. Bobrov A.G., Filippov A.A. [Occurrence of IS285 and IS100 in genomes of Yersinia pestis and Yersinia pseudotuberculosis]. Mol. Genet. Mikrobiol. Virusol. 1997; 2:36–40.
2. Domaradsky I.V. [Plague]. M.: Meditsina; 1998. 176 p.
3. Eroshenko G.A., Pavlova A.I., Kukleva L.M., Shavina N.Yu., Kutyrev V.V. [Genotyping of Yersinia pestis strains based on rRNA biosynthesis gene variability]. Zh. Mikrobiol. Epidemiol. Immunobiol. 2007; 3:6–10.
4. Pavlova A.I., Eroshenko G.A., Odinokov G.N., Koukleva L.M., Shavina N.Yu., Krasnov Ya.M., Kutyrev V.V. [Analysis of genetic variability of Yersinia pestis strains (medieval biovar) isolated in natural plague foci of the Russian Federation and Mongolia]. Probl. Osobo Opasn. Infek. 2012; 4(114):49–53.
5. Popov Yu.A., Savostina E.P. Kashtanova T.N., Yashechkin Yu.I. [Analysis of genomic polymorphism in typical and atypical strains of plague agent, using polymerase chain reaction with universal primers]. Mol. Genet. Mikrobiol. Virusol. 2004; 1:22–6.
6. Odinokov G.N., Eroshenko G.A., Krasnov Ya.M., Kukleva L.M., Cherkasov A.V., Shavina N.Yu., Kutyrev V.V. [Analysis of the genome wide sequence of Yersinia pestis strains based on the consecutive 680-SNP algorithm]. Probl. Osobo Opasn. Infek. 2013; 3:49–54
7. Supotnitsky M.V., Supotnitskaya N.S. [An Outline of Plague History]. M.: “Vuzovskaya Kniga”; 2006. 468 p.
8. Suchkov I.Yu., Vodop’yanov A.S., Vodop’yanov S.O., Shishnyanu M.V., Mishan’kin B.N. [Multi-locus VNTR-Analysis in Studies of Population Structure of Yersinia pestis in Natural Foci]. Mol. Genet. Mikrobiol. Virusol. 2004; 4:19–23.
9. Achtman M., Zurth K., Morelli G., Torrea G., Guiyoule A., Carniel E. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci USA. 1999; 96:14043–48.
10. Cui Y., Yu C., Yan Y., Li D., Li Y., Jombart T., Weinert L.A., Wang Z., Guo Z., Xu L., Zhang Y., Zheng H., Qin N., Xiao X., Wu M., Wang X., Zhou D., Qi Z., Du Z., Wu H., Yang X., Cao H., Wang H., Wang J., Yao S., Rakin A., Li Y., Falush D., Balloux F., Achtman M., Song Y., Wang J., Yang R. Historical variation in mutational rate in an epidemic pathogen Yersinia pestis. Proc. Natl. Acad. Sci. USA. 2013; 110(2):577–82. DOI: 10.1073/pnas.1205750110.
11. Kotetishvili M., Kreger A., Wauters G.J., Morris J.G., Sulakvelidze A., Stine O.C. Multilocus sequence typing for studying genetic relationships among Yersinia species. J. Clin. Microbiol. 2005; 43:2674–24. DOI: 10.1128/JCM.43.6.2674-2684.2005.
12. Li Y., Cui Y., Hauck Y., Platonov M.E, Dai E., Song Y., Guo Z., Pourcel C., Dentovskaya S., Anisimov A.P., Yang R., Vergnaud G. Genotyping and phylogenetic analysis of Yersinia pestis by MLVA: insights into the worldwide expansion of Central Asia plague foci. PLoS ONE. 2009; 4(6):e6000. DOI: 10.1371/journal.pone.0006000.
13. Morelli G., Song Y., Mazzoni C.J., Eppinger M., Roumagnac P., Wagner D.M., Feldkamp M., Kusecek B., Vogler A.J., Li Y., Cui Y., Thomson N.R., Jombart T., Leblois R., Lichtner P., Rahalison L., Petersen J.M., Balloux F., Keim P., Wirth T., Ravel J., Yang R., Carniel E., Achtman M. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat. Genet. 2010; 42(12):1140–3. DOI: 10.1038/ng.705.
Review
For citations:
Nosov N.Yu., Oglodin E.G., Krasnov Ya.M., Kukleva L.M., Shavina N.Yu., Eroshenko G.A., Kutyrev V.V. Phylogenetic Analysis of Yersinia pestis Strains of Medieval Biovar from Natural Plague Foci of the Russian Federation and Bordering Countries. Problems of Particularly Dangerous Infections. 2016;(2):75-78. (In Russ.) https://doi.org/10.21055/0370-1069-2016-2-75-78
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