microbeПроблемы особо опасных инфекцийProblems of Particularly Dangerous Infections0370-10692658-719XRussian Research Anti-Plague Institute “Microbe”10.21055/0370-1069-2021-2-87-93microbe-1499Research ArticleОРИГИНАЛЬНЫЕ СТАТЬИORIGINAL ARTICLESХарактеристика и филогенетический анализ штаммов Yersinia pseudotuberculosis из Сарыджазского высокогорного очага в Тянь-ШанеCharacteristics and Philogenetic Analysis of Yersinia pseudotuberculosis Strains from the Sarydzhaz High-Mountain Focus in the Tien-ShanДжапароваА. К.DzhaparovaA. K.

Бишкек, ул. Скрябина, 92

92, Skryabina St., Bishkek

ai_moon74@mail.ruhttps://orcid.org/0000-0001-5403-989XЕрошенкоГ. А.EroshenkoG. A.

410005, Саратов, ул. Университетская, 46

46, Universitetskaya St., Saratov, 410005

https://orcid.org/0000-0002-4115-9486НикифоровК. А.NikiforovK. A.

410005, Саратов, ул. Университетская, 46

46, Universitetskaya St., Saratov, 410005

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

410005, Саратов, ул. Университетская, 46

46, Universitetskaya St., Saratov, 410005

https://orcid.org/0000-0001-7681-5773АльховаЖ. В.Al’khovaZh. V.

410005, Саратов, ул. Университетская, 46

46, Universitetskaya St., Saratov, 410005

БердиевС. К.BerdievS. K.

Бишкек, ул. Скрябина, 92

92, Skryabina St., Bishkek

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

410005, Саратов, ул. Университетская, 46

46, Universitetskaya St., Saratov, 410005

Республиканский центр карантинных и особо опасных инфекцийРоссияRepublican Center of Quarantine and Particularly Dangerous InfectionsRussian FederationФКУЗ «Российский научно-исследовательский противочумный институт «Микроб»РоссияRussian Research Anti-Plague Institute “Microbe”Russian Federation202121072021028793Copyright © Джапарова А.К., Ерошенко Г.А., Никифоров К.А., Куклева Л.М., Альхова Ж.В., Бердиев С.К., Кутырев В.В., 20212021Джапарова А.К., Ерошенко Г.А., Никифоров К.А., Куклева Л.М., Альхова Ж.В., Бердиев С.К., Кутырев В.В.Dzhaparova A.K., Eroshenko G.A., Nikiforov K.A., Kukleva L.M., Al’khova Z.V., Berdiev S.K., 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/1499

Цель исследования – характеристика и молекулярно-генетическая идентификация штаммов Yersinia pseudotuberculosis, выделенных в Сарыджазском высокогорном очаге Тянь-Шаня.

Материалы и методы

Материалы и методы. Дифференциацию культур Y. pestis и Y. pseudotuberculosis проводили по чувствительности к диагностическим бактериофагам, подвижности, ферментации мочевины, продукции пестицина. Полногеномное секвенирование выполняли с помощью Ion S5 XL System (Thermo Fischer Scientific). Для обработки данных и сборки последовательностей сырых ридов de novo использовали Ion Torrent Suite software package, 5.12 и Newbler gsAssembler 2.6. Дендрограмму строили методом Maximum Likelihood с применением программы PhyML 3.1.

Результаты и обсуждение

Результаты и обсуждение. Из смешанных с Y. pestis музейных культур, полученных от сурков в Сарыджазском высокогорном очаге, выделены штаммы Y. pseudotuberculosis. По данным полногеномного SNP-анализа они относятся к филогенетической группе O:3 серовара, широко распространенной по всему миру. Y. pseudotuberculosis часто присутствует в смешанных с Y. pestis культурах, выделяемых от грызунов, что следует учитывать при проведении лабораторной диагностики чумы в природных очагах. 

The aim of the study was to characterize and carry out molecular-genetic identification of Yersinia pseudotuberculosis strains isolated in the Sarydzhaz high-mountain focus of the Tien-Shan.

Materials and methods

Materials and methods. The Y. pestis and Y. pseudotuberculosis cultures were differentiated according to their sensitivity to diagnostic bacteriophages, motility, urea fermentation, and pesticin production. Whole genome sequencing was performed using the Ion S5 XL System (Thermo Fischer Scientific). Ion Torrent Suite software package, 5.12 and Newbler gsAssembler 2.6 were used for data processing and de novo assembly of raw read sequences. The dendrogram was constructed using the Maximum Likelihood method applying the PhyML 3.1 software.

Results and discussion

Results and discussion. Strains of Y. pseudotuberculosis were isolated from museum mixed with Y. pestis cultures obtained from marmots in the Sarydzhaz high-mountain focus. According to whole genome SNP analysis, they belong to the phylogenetic group O:3 serovar, which is widespread throughout the world. Y. pseudotuberculosis is often present in mixed with Y. pestis cultures, isolated from rodents, which should be taken into account when carrying out laboratory diagnostics of plague in natural foci. 

возбудители псевдотуберкулеза и чумыТянь-Шаньский высокогорный очагфилогенетический анализ штаммовпатогенностьcausative agents of pseudotuberculosis and plagueTien-Shan high-mountain focusphylogenetic analysis of strainspathogenicityReferencesParkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T., Prentice M.B., Sebaihia M., James K.D., Churcher C., Mungall K.L., Baker S., Basham D., Bentley S.D., Brooks K., CerdeñoTárraga A.M., Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T., Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S., Oyston P.C., Quail M., Rutherford K., Simmonds M., Skelton J., Stevens K., Whitehead S., Barrell B.G. Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 2001; 413(6855):523–7. DOI: 10.1038/35097083.Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T., Prentice M.B., Sebaihia M., James K.D., Churcher C., Mungall K.L., Baker S., Basham D., Bentley S.D., Brooks K., CerdeñoTárraga A.M., Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T., Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S., Oyston P.C., Quail M., Rutherford K., Simmonds M., Skelton J., Stevens K., Whitehead S., Barrell B.G. Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 2001; 413(6855):523–7. DOI: 10.1038/35097083.Skurnik M., Peippo A., Ervelä E. Characterization of the O-antigen gene clusters of Yersinia pseudotuberculosis and the cryptic O-antigen gene cluster of Yersinia pestis shows that the plague bacillus is most closely related to and has evolved from Y. pseudotuberculosis serotype O:1b. Mol. Microbiol. 2000; 37(2):316–30. DOI: 10.1046/j.1365-2958.2000.01993.x.Skurnik M., Peippo A., Ervelä E. Characterization of the O-antigen gene clusters of Yersinia pseudotuberculosis and the cryp- tic O-antigen gene cluster of Yersinia pestis shows that the plague bacillus is most closely related to and has evolved from Y. pseudotu- berculosis serotype O:1b. Mol. Microbiol. 2000; 37(2):316–30. DOI: 10.1046/j.1365-2958.2000.01993.x.Wren B.W. The Yersiniae – a model genus to study the rapid evolution of bacterial pathogens. Nat. Rev. Microbiol. 2003; 1(1):55– 64. DOI: 10.1038/nrmicro730.Wren B.W. The Yersiniae – a model genus to study the rapid evolution of bacterial pathogens. Nat. Rev. Microbiol. 2003; 1(1):55– 64. DOI: 10.1038/nrmicro730.Chain P.S., Carniel E., Larimer F.W., Lamerdin J., Stoutland P.O., Regala W.M., Georgescu A.M., Vergez L.M., Land M.L., Motin V.L., Brubaker R.R., Fowler J., Hinnebusch J., Marceau M., Medigue C., Simonet M., Chenal-Francisque V., Souza B., Dacheux D., Elliott J.M., Derbise A., Hauser L.J., Garcia E. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Natl Acad. Sci. USA. 2004; 101(38):13826–31. DOI: 10.1073/pnas.0404012101.Chain P.S., Carniel E., Larimer F.W., Lamerdin J., Stoutland P.O., Regala W.M., Georgescu A.M., Vergez L.M., Land M.L., Motin V.L., Brubaker R.R., Fowler J., Hinnebusch J., Marceau M., Medigue C., Simonet M., Chenal-Francisque V., Souza B., Dacheux D., Elliott J.M., Derbise A., Hauser L.J., Garcia E. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Natl Acad. Sci. USA. 2004; 101(38):13826–31. DOI: 10.1073/pnas.0404012101.Reuter S., Connor T.R., Barquist L., Walker D., Feltwell T., Harris S.R., Fookes M., Hall M.E., Petty N.K., Fuchs T.M., Corander J., Dufour M., Ringwood T., Savin C., Bouchier C., Martin L., Miettinen M., Shubin M., Riehm J.M., Laukkanen-Ninios R., Sihvonen L.M., Siitonen A., Skurnik M., Falcão J.P., Fukushima H., Scholz H.C., Prentice M.B., Wren B.W., Parkhill J., Carniel E., Achtman M., McNally A., Thomson N.R. Parallel independent evo- lution of pathogenicity within the genus Yersinia. Proc. Natl Acad. Sci. USA. 2014; 111(18):6768–73. DOI: 10.1073/pnas.1317161111.Reuter S., Connor T.R., Barquist L., Walker D., Feltwell T., Harris S.R., Fookes M., Hall M.E., Petty N.K., Fuchs T.M., Corander J., Dufour M., Ringwood T., Savin C., Bouchier C., Martin L., Miettinen M., Shubin M., Riehm J.M., Laukkanen-Ninios R., Sihvonen L.M., Siitonen A., Skurnik M., Falcão J.P., Fukushima H., Scholz H.C., Prentice M.B., Wren B.W., Parkhill J., Carniel E., Achtman M., McNally A., Thomson N.R. Parallel independent evo- lution of pathogenicity within the genus Yersinia. Proc. Natl Acad. Sci. USA. 2014; 111(18):6768–73. DOI: 10.1073/pnas.1317161111.McNally A., Thomson N.R., Reuter S., Wren B.W. Add, stir and reduce: Yersinia spp. as model bacteria for pathogen evo- lution. Nat. Rev. Microbiol. 2016; 14(3):177–90. DOI: 10.1038/nrmicro.2015.29.McNally A., Thomson N.R., Reuter S., Wren B.W. Add, stir and reduce: Yersinia spp. as model bacteria for pathogen evo- lution. Nat. Rev. Microbiol. 2016; 14(3):177–90. DOI: 10.1038/nrmicro.2015.29.Tsubokura M., Aleksić S. A simplified antigenic scheme for serotyping of Yersinia pseudotuberculosis: phenotypic character- ization of reference strains and preparation of O and H factor sera. Contrib. Microbiol. Immunol. 1995; (13):99–105.Tsubokura M., Aleksić S. A simplified antigenic scheme for serotyping of Yersinia pseudotuberculosis: phenotypic character- ization of reference strains and preparation of O and H factor sera. Contrib. Microbiol. Immunol. 1995; (13):99–105.Gemski O.P., Lazere J.R., Casey T., Wohlhieter J.A. Presence of a virulence-associated plasmid in Yersinia pseudotuberculosis. Infect. Immun. 1980; 28(3):1044–7. DOI: 10.1128/iai.28.3.1044-1047.1980.Gemski O.P., Lazere J.R., Casey T., Wohlhieter J.A. Presence of a virulence-associated plasmid in Yersinia pseudotuberculosis. Infect. Immun. 1980; 28(3):1044–7. DOI: 10.1128/iai.28.3.1044-1047.1980.Gemski P., Lazere J.R., Casey T. Plasmid associated with pathogenicity and calcium dependency of Yersinia enterocolitica. Infect. Immun. 1980; 27(2):682–5. DOI: 10.1128/iai.27.2.682-685.1980.Gemski P., Lazere J.R., Casey T. Plasmid associated with pathogenicity and calcium dependency of Yersinia enterocolitica. Infect. Immun. 1980; 27(2):682–5. DOI: 10.1128/iai.27.2.682-685.1980.Portnoy D.A., Martinez R.J. Role of a plasmid in the pathogenicity of Yersinia species. Curr. Top. Microbiol. Immunol. 1985; 118:29–51. DOI: 10.1007/978-3-642-70586-1_3.Portnoy D.A., Martinez R.J. Role of a plasmid in the patho- genicity of Yersinia species. Curr. Top. Microbiol. Immunol. 1985; 118:29–51. DOI: 10.1007/978-3-642-70586-1_3.Кутырев В.В., Попов Ю.А., Проценко О.А. Плазмиды патогенности Yersinia pestis. Молекулярная генетика, микробио- логия и вирусология. 1986; 6:3–11.Kutyrev V.V., Popov Yu.A., Protsenko O.A. [Plasmids of pathogenicity of Yersinia pestis]. Molekulyarnaya Genetika, Mikrobiologiya i Virusologiya [Molecular Genetics, Microbiology and Virology]. 1986; 6:3–11.Eroshenko G.A., Nosov N.Y., Krasnov Y.M., Oglodin Y.G., Kukleva L.M., Guseva N.P., Kuznetsov A.A., Abdikarimov S.T., Dzhaparova A.K., Kutyrev V.V. Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high-mountain plague foci of Kyrgyzstan. PLoS One. 2017; 12(10):e0187230. DOI: 10.1371/journal.pone.0187230.Eroshenko G.A., Nosov N.Y., Krasnov Y.M., Oglodin Y.G., Kukleva L.M., Guseva N.P., Kuznetsov A.A., Abdikarimov S.T., Dzhaparova A.K., Kutyrev V.V. Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high-mountain plague foci of Kyrgyzstan. PLoS One. 2017; 12(10):e0187230. DOI: 10.1371/journal.pone.0187230.Kutyrev V.V., Eroshenko G.A., Motin V.L., Nosov N.Y., Krasnov J.M., Kukleva L.M., Nikiforov K.A., Al’hova Zh.V., Oglodin E.G., Guseva N.P. Phylogeny and classification of Yersinia pestis through the lens of strains from the plague foci of Commonwealth of Independent States. Front. Microbiol. 2018; 9:1106. DOI: 10.3389/fmicb.2018.01106.Kutyrev V.V., Eroshenko G.A., Motin V.L., Nosov N.Y., Krasnov J.M., Kukleva L.M., Nikiforov K.A., Al’hova Zh.V., Oglodin E.G., Guseva N.P. Phylogeny and classification of Yersinia pestis through the lens of strains from the plague foci of Commonwealth of Independent States. Front. Microbiol. 2018; 9:1106. DOI: 10.3389/fmicb.2018.01106.Ерошенко Г.А., Джапарова А.К., Оглодин Е.Г., Альхова Ж.В., Куклева Л.М., Кузнецов А.А., Краснов Я.М., Абдикаримов С.Т., Кутырев В.В. Филогеография штаммов Yersinia pestis вет- ви 0.ANT, выделенных в Тянь-Шане и Памиро-Алае в XX–XXI веках. Проблемы особо опасных инфекций. 2020; 1:76–84. DOI: 10.21055/0370-1069-2020-1-76-84.Eroshenko G.A., Dzhaparova A.K., Oglodin E.G., Al’khova Zh.V., Kukleva L.M., Kuznetsov A.A., Krasnov Ya.M., Abdikarimov S.T., Kutyrev V.V. [Phylogeny of Yersinia pestis Strains Belonging to 0.ANT Branch, Isolated in Tien-Shan and Pamir-Alay in XX– XXI Centuries]. Problemy Osobo Opasnykh Infektsii [Problems of Particularly Dangerous Infections]. 2020; (1):76–84. DOI: 10.21055/0370-1069-2020-1-76-84.Онищенко Г.Г., Кутырев В.В., редакторы. Лабораторная диагностика особо опасных инфекционных болезней. Практическое руководство. М.: ЗАО «Шико»; 2013. 560 с.Onishchenko G.G., Kutyrev V.V., editors. [Laboratory Diagnostics of Particularly Dangerous Infectious Diseases. Practice Guidelines]. Moscow: “Shiko”; 2013. 560 p.Platonov M.E., Blouin Y., Evseeva V.V., Afanas'ev M.V., Pourcel C., Balakhonov S.V., Vergnaud G., Anisimov A.P. Draft genome sequences of five Yersinia pseudotuberculosis ST19 isolates and one isolate variant. Genome Announc. 2013; 1(2):e0012213. DOI: 10.1128/genomeA.00122-13.Platonov M.E., Blouin Y., Evseeva V.V., Afanas’ev M.V., Pourcel C., Balakhonov S.V., Vergnaud G., Anisimov A.P. Draft ge- nome sequences of five Yersinia pseudotuberculosis ST19 isolates and one isolate variant. Genome Announc. 2013; 1(2):e0012213. DOI: 10.1128/genomeA.00122-13.

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