Genotypic properties of collection plague microbes strains from the natural plague foci of Kazakhstan

Background. Epidemiological and epizootological monitoring of natural plague foci requires an integrated approach to solving problems, taking into account the phenotypic and genetic variability of Y. pestis and zoning of natural plague foci. The introduction of a new molecular genetic methodology aimed at studying the genomic polymorphism of the plague pathogen provides reliable results for the differentiation of not only groups, but also individual strains.
The aim. To determine the genotypes of the plague microbe from different autonomous foci of the Republic of Kazakhstan.
Materials and methods. 105 strains of Y. pestis isolated from various natural plague foci of Kazakhstan in 1951–2015 were studied. The phenotypic properties of the strains were studied using standard microbiological methods. A polymerase chain reaction (PCR) was used to detect fragments of the cafl, pst and YPO2088 genes. Multilocus variable number tandem repeat (VNTR) analysis (MLVA) was performed for 25 VNTR loci.
Results. The phenotypic properties of the strains were preliminarily studied and the strains of the plague microbe were tested for specificity using the Pest-Quest test system (Kazakhstan). The PCR study confirmed the species-specific affiliation of Y. pestis strains. A variety of strains with typical phenotypic characteristics was revealed. MLVA for 25 key loci (MLVA25) revealed that the studied strains of the plague microbe are phylogenetically closest to the Mediaevalis biovar representatives. A phylogenetic tree of the studied strains has been obtained. It was found that 9 genotypes circulate on the territory of Kazakhstan, and their distribution in certain natural plague foci was determined.
Conclusions. The resulting clustering indicates the relationship between the strain groups obtained on the dendrogram by the MLVA25 method and the territories of certain natural plague foci.

1. 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 U S A. 1999; 96(24): 14043-14048. doi: 10.1073/pnas.96.24.14043

2. Qiu J, Guo Z, Liu H, Zhou D, Han Y, Yang R. DNA microarraybased global transcriptional profiling of Yersinia pestis in multicellularity. J Microbiol. 2008; 46(5): 557-563. doi: 10.1007/s12275-008-0140-0

3. Knirel YA, Dentovskaya SV, Senchenkova SN, Shaikhutdinova RZ, Kocharova NA, Anisimov AP. Structural features and structural variability of the lipopolysaccharide of Yersinia pestis, the cause of plague. J Endotoxin Res. 2006; 12(1): 3-9. doi: 10.1179/096805105X67283

4. Ruiz M, Rodríguez JC, Sirvent E, Escribano I, Cebrián L, Royo G. Usefulness of different techniques in the study of the epidemiology of salmonellosis. APMIS. 2003; 111(9): 848-856. doi: 10.1034/j.1600-0463.2003.1110903.x

5. Eroshenko GA, Odinokov GN, Kukleva LM, Pavlova AI, Krasnov YaM, Shavina NYu, et al. Standard algorithm for molecular typing of Yersinia pestis strains. Journal of Microbiology, Epidemiology and Immunobiology. 2012; 3: 25-35. (In Russ.).

6. Kukleva LM, Shavina NYu, Odinokov GN, Oglodin EG, Nosov NYu, Vinogradova NA, et al. Analysis of diversity and identification of the genovariants of plague agent strains from Mongolian foci. Russian Journal of Genetics. 2015; 51(3): 298-305. (In Russ.). doi: 10.1134/S1022795415010068

7. Cui Y, Yu C, Yan Y, Li D, Li Y, Jombart T, et al. Historical variation in mutational rate in an epidemic pathogen Yersinia pestis. Proc Natl Acad Sci U S A. 2013; 110(2): 577-582. doi: 10.1073/pnas.1205750110

8. Eroshenko GA, Kutyrev VV. Biochemical and genetic peculiarities and the phylogenetic relationship of the non-main subspecies in the general scheme of the plague agent evolution. Adv Exp Med Biol. 2012; 954(1): 45-51. doi: 10.1007/978-1-4614-3561-7_6

9. Yan G, Evchenko YuM, Grizhebovsky GM, et al. Diagnosis, treatment and prevention of dangerous infectious diseases. Biotekhnologiya. Veterinariya. 1998: 408-409. (In Russ.).

10. Platonov ME, Evseeva VV, Dentovskaya SV, Anisimov AP. Molecular typing of Yersinia pestis. Molecular Genetics, Microbiology and Virology. 2013; (2): 3-11. (In Russ.). doi: 10.3103/S0891416813020067

11. Smirnova NI, Kutyrev VV. A comparative analysis of molecular-genetic peculiarities, of the genomes of cholera, plague

12. and anthrax agents and their evolutional transformations. Molecular Genetics, Microbiology and Virology. 2006; (2): 9-19. (In Russ.).

13. Le Flèche P, Hauck Yo, Onteniente L, Prieur A, Denoeud F, Ramisse V, et al. A tandem repeats database for bacterial genomes: Application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiology. 2001; 1(2): 2180-2193. doi: 10.1186/1471-2180-1-2

14. Pourcel C, André-Mazeaud F, Neubauer H, Ramisse F, Vergnaud G. Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis. BMC Microbiol. 2004; 4: 22. doi: 10.1186/1471-2180-4-22