microbeПроблемы особо опасных инфекцийProblems of Particularly Dangerous Infections0370-10692658-719XRussian Research Anti-Plague Institute “Microbe”10.21055/0370-1069-2023-4-68-76microbe-1899Research ArticleОРИГИНАЛЬНЫЕ СТАТЬИORIGINAL ARTICLESMLVA25- и CRISPR-генотипы штаммов Yersinia pestis из Прикаспийского песчаного очага чумыMLVA25 and CRISPR Genotypes of Yersinia pestis Strains from the Caspian Sandy Plague Focushttps://orcid.org/0000-0001-6522-2606ГорюноваП. А.GoryunovaP. A.

46, Universitetskaya St., Saratov, 410005

46, Universitetskaya St., Saratov, 410005

rusrapi@microbe.ruhttps://orcid.org/0000-0001-5403-989XЕрошенкоГ. А.EroshenkoG. A.

46, Universitetskaya St., Saratov, 410005

46, Universitetskaya St., Saratov, 410005

https://orcid.org/0000-0003-3766-7979БалыковаА. Н.BalykovaA. N.

46, Universitetskaya St., Saratov, 410005

46, Universitetskaya St., Saratov, 410005

https://orcid.org/0000-0002-7752-6321КоврижниковА. В.KovrizhnikovA. V.

46, Universitetskaya St., Saratov, 410005

46, Universitetskaya St., Saratov, 410005

https://orcid.org/0000-0002-3170-9827ШевченкоК. С.ShevchenkoK. S.

46, Universitetskaya St., Saratov, 410005

46, Universitetskaya St., Saratov, 410005

https://orcid.org/0000-0003-2438-8364КуклеваЛ. М.KuklevaL. M.

46, Universitetskaya St., Saratov, 410005

46, Universitetskaya St., Saratov, 410005

https://orcid.org/0000-0002-9190-099XНарышкинаЕ. А.NaryshkinaE. A.

46, Universitetskaya St., Saratov, 410005

46, Universitetskaya St., Saratov, 410005

https://orcid.org/0000-0003-3133-3820ЧервяковаН. С.ChervyakovaN. S.

46, Universitetskaya St., Saratov, 410005

46, Universitetskaya St., Saratov, 410005

https://orcid.org/0000-0003-3788-3452КутыревВ. В.KutyrevV. V.

46, Universitetskaya St., Saratov, 410005

46, Universitetskaya St., Saratov, 410005

ФКУН «Российский научно-исследовательский противочумный институт «Микроб»РоссияRussian Research Anti-Plague Institute “Microbe”Russian Federation202309012024046876Copyright © Горюнова П.А., Ерошенко Г.А., Балыкова А.Н., Коврижников А.В., Шевченко К.С., Куклева Л.М., Нарышкина Е.А., Червякова Н.С., Кутырев В.В., 20242024Горюнова П.А., Ерошенко Г.А., Балыкова А.Н., Коврижников А.В., Шевченко К.С., Куклева Л.М., Нарышкина Е.А., Червякова Н.С., Кутырев В.В.Goryunova P.A., Eroshenko G.A., Balykova A.N., Kovrizhnikov A.V., Shevchenko K.S., Kukleva L.M., Naryshkina E.A., Chervyakova N.S., Kutyrev V.V.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://journal.microbe.ru/jour/article/view/1899

Цель работы – изучение генетического разнообразия и пространственно-временной структуры Yersinia pestis в Прикаспийском песчаном очаге чумы с использованием методов MLVA25- и CRISPR-типирования.

Материалы и методы

Материалы и методы. В работе использовано 98 штаммов Y. pestis, выделенных на территории Прикаспийского песчаного очага чумы в 1925–2015 гг. Полногеномное секвенирование выполняли на платформах Ion GeneStudio S5 System (ThermoFisher Scientific) и MGI (DNBSEQ-G50RS). Фрагментное секвенирование проводили с помощью ABI PRISM 3500XL. Поиск VNTR- и CRISPR-локусов с последующим выравниванием нуклеотидных последовательностей осуществляли в программе MEGA X. Полученные последовательности вносили в созданную базу данных в программе Bionumerics v7.6 (Applied Maths). Построение филогенетического дерева осуществляли методом UPGMA.

Результаты и обсуждение

Результаты и обсуждение. По результатам проведенного MLVA25- и CRISPR-анализа 98 штаммов Y. pestis разделились на 60 генотипов (CS1 – CS60). Выявлена вариабельность по 23 VNTR-локусам. Описаны 7 новых CRISPR-спейсеров: 5 – в YPa и 2 – в YPb (размер – 31–33 п.н., GC-состав – 34–58 %). Описанные спейсеры получили названия а108, а109, а110, а111, a112, b53, b54. Выявлена взаимосвязь изменения копийности VNTRлокусов в зависимости от места и времени выделения штаммов. Полученные данные могут быть использованы для проведения молекулярно-генетической паспортизации территории Прикаспийского песчаного очага чумы и для изучения направлений и закономерностей эволюции и пространственно-временной циркуляции популяций Y. pestis в очагах чумы Прикаспия.

The aim of the work was to study the genetic diversity and spatial-temporal structure of Yersinia pestis in the Caspian sandy plague focus using MLVA25 and CRISPR typing methods.

Materials and methods

Materials and methods. 98 Y. pestis strains isolated in the territory of the Caspian sandy plague focus in 1925–2015 were used in the study. Whole genome sequencing was performed on Ion GeneStudio S5 System (ThermoFisher Scientific) and MGI (DNBSEQ-G50RS) platforms. Fragment sequencing was conducted using “ABI PRISM 3500XL”. The search for VNTR and CRISPR loci with subsequent alignment of nucleotide sequences was carried out in the MEGA X program. The obtained sequences were entered into the created database in the Bionumerics v7.6 (Applied Maths) software. The phylogenetic tree was constructed using the UPGMA method.

Results and discussion

Results and discussion. According to the results of MLVA25 and CRISPR analysis, 98 Y. pestis strains are divided into 60 genotypes (CS1 – CS60). Variability by 23 VNTR loci has been discovered. 7 new CRISPR spacers are described: 5 in YPa and 2 in YPb (size 31–33 bp, GC composition 34–58 %). The described spacers are designated as a108, a109, a110, a111, a112, b53, b54. The interrelation of changes in the copy number of VNTR loci depending on the place and time of isolation of strains has been revealed. The data obtained can be used to carry out molecular-genetic certification of the territory of the Caspian sandy plague focus and to study the routes and patterns of evolution and spatiotemporal circulation of Y. pestis populations in the Caspian plague foci.

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The authors declare that there are no conflicts of interest present.