VNTR loci as indicators of proline-dependent plague microbe strains (Yersinia pestis) in the central caucasian mountain natural plague focus

Y. pestis MLVA typing is used both to seek for similarities and differences between individual isolates upon conducting epidemiological investigations as well as for clonal clustering of intraspecies phylogenetic groups while analyzing microevolution and taxonomy issues. It cannot be ruled out that...

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Autores principales:	V. M. Dubyanskiy, A. S. Volynkina, A. P. Anisimov
Formato:	article
Lenguaje:	RU
Publicado:	Sankt-Peterburg : NIIÈM imeni Pastera 2020
Materias:	plague natural focus strain vntr loci mlva prediction Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/f564a444dbc74c6995726ee7f9ed6586
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spelling	oai:doaj.org-article:f564a444dbc74c6995726ee7f9ed65862021-11-22T07:09:55ZVNTR loci as indicators of proline-dependent plague microbe strains (Yersinia pestis) in the central caucasian mountain natural plague focus2220-76192313-739810.15789/2220-7619-VLA-770https://doaj.org/article/f564a444dbc74c6995726ee7f9ed65862020-11-01T00:00:00Zhttps://www.iimmun.ru/iimm/article/view/770https://doaj.org/toc/2220-7619https://doaj.org/toc/2313-7398Y. pestis MLVA typing is used both to seek for similarities and differences between individual isolates upon conducting epidemiological investigations as well as for clonal clustering of intraspecies phylogenetic groups while analyzing microevolution and taxonomy issues. It cannot be ruled out that the most variable loci may be indicators allowing to approximate the unique strain-related properties circulating in certain natural plague foci. The Central Caucasian Highland Natural Plague Focus distinguished by heterogeneity of the circulating strains therein, including proline pro- and auxo-trophy, may represent a convenient model for testing this hypothesis. The purpose of our work was to assess the frequencies of the VNTR alleles associated with proline dependence among the Y. pestis strain VNTR loci, determined during previous MLVA-25 typing in the Central Caucasian Highland Natural Plague Focus. The main task was to identify the most informative sets of VNTR loci suitable for predicting proline pro— and auxotrophy (pro+, pro—). It was found that the loci ms45, ms56, ms46, ms07, ms69, ms62 displayed peak variability by allele frequencies and/or exhibited significant differences of mean allele frequencies in the pro— and pro+ strains. In particular, it was showed that the alleles of the ms45 locus contained 6 tandem repeats suggesting probability for pro+ reaching 0.944, whereas the alleles of the ms45 locus contained 7 tandem repeats with expected probability for pro— reaching 0.783. Moreover, the ms56 and ms46 contained 9 and more than 18 tandem repeats, respectively, thereby pointing at probability for pro+ equal to 0.933 and 0.818, respectively. Diagnostics for pro+/pro— phenotype by using specific statistical methods demonstrated statistical error 13.33% and 26.67% for the pro— and pro+ strains, respectively. All pro+ strains bearing a 6 tandem repeat complex from the ms45 locus, 9 tandem repeats derived from the ms56 locus and ms46 locus-derived 29—30 tandem repeats were accurately diagnosed solely based on these 3 loci. Thus, it is possible to predict some properties of Y. pestis strains based on determining the allele frequencies. While the number of MLVA typed plaque strains isolated in such natural focus has been progressively increased, it may be expected that opportunities for prognosing their properties based on determining locus tandem repeat composition having diagnostic value would be elevated.V. M. DubyanskiyA. S. VolynkinaA. P. AnisimovSankt-Peterburg : NIIÈM imeni Pasteraarticleplaguenatural focusstrainvntr locimlvapredictionInfectious and parasitic diseasesRC109-216RUInfekciâ i Immunitet, Vol 10, Iss 4, Pp 735-740 (2020)
institution	DOAJ
collection	DOAJ
language	RU
topic	plague natural focus strain vntr loci mlva prediction Infectious and parasitic diseases RC109-216
spellingShingle	plague natural focus strain vntr loci mlva prediction Infectious and parasitic diseases RC109-216 V. M. Dubyanskiy A. S. Volynkina A. P. Anisimov VNTR loci as indicators of proline-dependent plague microbe strains (Yersinia pestis) in the central caucasian mountain natural plague focus
description	Y. pestis MLVA typing is used both to seek for similarities and differences between individual isolates upon conducting epidemiological investigations as well as for clonal clustering of intraspecies phylogenetic groups while analyzing microevolution and taxonomy issues. It cannot be ruled out that the most variable loci may be indicators allowing to approximate the unique strain-related properties circulating in certain natural plague foci. The Central Caucasian Highland Natural Plague Focus distinguished by heterogeneity of the circulating strains therein, including proline pro- and auxo-trophy, may represent a convenient model for testing this hypothesis. The purpose of our work was to assess the frequencies of the VNTR alleles associated with proline dependence among the Y. pestis strain VNTR loci, determined during previous MLVA-25 typing in the Central Caucasian Highland Natural Plague Focus. The main task was to identify the most informative sets of VNTR loci suitable for predicting proline pro— and auxotrophy (pro+, pro—). It was found that the loci ms45, ms56, ms46, ms07, ms69, ms62 displayed peak variability by allele frequencies and/or exhibited significant differences of mean allele frequencies in the pro— and pro+ strains. In particular, it was showed that the alleles of the ms45 locus contained 6 tandem repeats suggesting probability for pro+ reaching 0.944, whereas the alleles of the ms45 locus contained 7 tandem repeats with expected probability for pro— reaching 0.783. Moreover, the ms56 and ms46 contained 9 and more than 18 tandem repeats, respectively, thereby pointing at probability for pro+ equal to 0.933 and 0.818, respectively. Diagnostics for pro+/pro— phenotype by using specific statistical methods demonstrated statistical error 13.33% and 26.67% for the pro— and pro+ strains, respectively. All pro+ strains bearing a 6 tandem repeat complex from the ms45 locus, 9 tandem repeats derived from the ms56 locus and ms46 locus-derived 29—30 tandem repeats were accurately diagnosed solely based on these 3 loci. Thus, it is possible to predict some properties of Y. pestis strains based on determining the allele frequencies. While the number of MLVA typed plaque strains isolated in such natural focus has been progressively increased, it may be expected that opportunities for prognosing their properties based on determining locus tandem repeat composition having diagnostic value would be elevated.
format	article
author	V. M. Dubyanskiy A. S. Volynkina A. P. Anisimov
author_facet	V. M. Dubyanskiy A. S. Volynkina A. P. Anisimov
author_sort	V. M. Dubyanskiy
title	VNTR loci as indicators of proline-dependent plague microbe strains (Yersinia pestis) in the central caucasian mountain natural plague focus
title_short	VNTR loci as indicators of proline-dependent plague microbe strains (Yersinia pestis) in the central caucasian mountain natural plague focus
title_full	VNTR loci as indicators of proline-dependent plague microbe strains (Yersinia pestis) in the central caucasian mountain natural plague focus
title_fullStr	VNTR loci as indicators of proline-dependent plague microbe strains (Yersinia pestis) in the central caucasian mountain natural plague focus
title_full_unstemmed	VNTR loci as indicators of proline-dependent plague microbe strains (Yersinia pestis) in the central caucasian mountain natural plague focus
title_sort	vntr loci as indicators of proline-dependent plague microbe strains (yersinia pestis) in the central caucasian mountain natural plague focus
publisher	Sankt-Peterburg : NIIÈM imeni Pastera
publishDate	2020
url	https://doaj.org/article/f564a444dbc74c6995726ee7f9ed6586
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VNTR loci as indicators of proline-dependent plague microbe strains (Yersinia pestis) in the central caucasian mountain natural plague focus

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