microbeПроблемы особо опасных инфекцийProblems of Particularly Dangerous Infections0370-10692658-719XRussian Research Anti-Plague Institute “Microbe”10.21055/0370-1069-2026-3-131-138microbe-2401Research ArticleОРИГИНАЛЬНЫЕ СТАТЬИORIGINAL ARTICLESОсобенности структуры генома токсигенного штамма Vibrio cholerae nonО1/nonO139, выделенного в 2024 г. из поверхностного водоема в Ростовской областиPeculiarities of Genome Structure of Toxigenic Vibrio cholerae nonO1/nonO139 Strain Isolated in 2024 from a Surface Water Body in the Rostov Regionhttps://orcid.org/0000-0002-9996-4189ПодойницынаО. А.PodoynitsynaO. A.

Подойницына Оксана Андреевна.

344002, Ростов-на-Дону, ул. М. Горького, 117/40

Oksana A. Podoynitsyna.

117/40, M. Gorkogo St., Rostov-on-Don, 344002

podoynitcina_oa@antiplague.ruhttps://orcid.org/0000-0002-9216-7777МонаховаЕ. В.MonakhovaE. V.

344002, Ростов-на-Дону, ул. М. Горького, 117/40

117/40, M. Gorkogo St., Rostov-on-Don, 344002

plague@aaanet.ruhttps://orcid.org/0000-0002-6540-2778КругликовВ. Д.KruglikovV. D.

344002, Ростов-на-Дону, ул. М. Горького, 117/40

117/40, M. Gorkogo St., Rostov-on-Don, 344002

plague@aaanet.ruhttps://orcid.org/0000-0001-8481-6442МироноваЛ. В.MironovaL. V.

664047, Иркутск, ул. Трилиссера, 78

78, Trilissera St., Irkutsk, 664047

adm@chumin.irkutsk.ruhttps://orcid.org/0000-0002-6003-4283МеньшиковаЕ. А.Men’shikovaE. A.

344002, Ростов-на-Дону, ул. М. Горького, 117/40

117/40, M. Gorkogo St., Rostov-on-Don, 344002

plague@aaanet.ruhttps://orcid.org/0000-0001-6350-065XЕгиазарянЛ. А.EgiazaryanL. A.

344002, Ростов-на-Дону, ул. М. Горького, 117/40

117/40, M. Gorkogo St., Rostov-on-Don, 344002

plague@aaanet.ruhttps://orcid.org/0000-0003-4336-0439ВодопьяновС. О.Vodop’yanovS. O.

344002, Ростов-на-Дону, ул. М. Горького, 117/40

117/40, M. Gorkogo St., Rostov-on-Don, 344002

plague@aaanet.ruhttps://orcid.org/0000-0001-5522-9097ЕвдокимоваВ. В.EvdokimovaV. V.

344002, Ростов-на-Дону, ул. М. Горького, 117/40

117/40, M. Gorkogo St., Rostov-on-Don, 344002

plague@aaanet.ruhttps://orcid.org/0000-0002-0762-3628ГаевскаяН. Е.GaevskayaN. E.

344002, Ростов-на-Дону, ул. М. Горького, 117/40

117/40, M. Gorkogo St., Rostov-on-Don, 344002

plague@aaanet.ruРостовский-на-Дону научно-исследовательский противочумный институтРоссияRostov-on-Don Research Anti-Plague InstituteRussian FederationИркутский научно-исследовательский противочумный институт Сибири и Дальнего ВостокаРоссияIrkutsk Research Anti-Plague Institute of Siberia and the Far EastRussian Federation20260810202603131138Copyright © Подойницына О.А., Монахова Е.В., Кругликов В.Д., Миронова Л.В., Меньшикова Е.А., Егиазарян Л.А., Водопьянов С.О., Евдокимова В.В., Гаевская Н.Е., 20262026Подойницына О.А., Монахова Е.В., Кругликов В.Д., Миронова Л.В., Меньшикова Е.А., Егиазарян Л.А., Водопьянов С.О., Евдокимова В.В., Гаевская Н.Е.Podoynitsyna O.A., Monakhova E.V., Kruglikov V.D., Mironova L.V., Men’shikova E.A., Egiazaryan L.A., Vodop’yanov S.O., Evdokimova V.V., Gaevskaya N.E.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/2401

Цель исследования – комплексная молекулярно-генетическая характеристика токсигенного штамма Vibrio cholerae nonО1/nonO139, выделенного из р. Дон в 2024 г. в Ростовской области. Материалы и методы. Полногеномное секвенирование проведено на платформах MiSeq Illumina и MinIon Oxford Nanopore. Первичная сборка выполнялась de novo программой Canu на основе длинных ридов, последующая полировка проведена с использованием коротких ридов с помощью программы Pilon. В биоинформационном анализе геномов использовали пакет Vector NTI, программы BLASTN, BLASTP, BioEdit, Ugene, abricate (база данных CARD), SnapGene Viewer. Поиск границ wb* кластеров и сопоставление их генов проводились с помощью авторской программы O-cluster. Филогенетическое дерево построено с использованием программ roary и FastTree. Результаты и обсуждение. В России впервые выявлен токсигенный штамм НАГ-вибриона. Посредством гибридной сборки генома определены последовательности обеих хромосом штамма. По результатам анализа региона, кодирующего биосинтез О-антигена, штамм отнесен к серогруппе О105, он обладает высокой степенью родства с клиническими штаммами этой серогруппы, выделенными ранее в Китае. Биоинформационный анализ показал присутствие на большой хромосоме тандемов из двух идентичных копий профагов CTX и RS1, заметно отличных от прототипов. Ген ctxB представлен аллелем ctxB12, а все гены RS1, кроме rstC, не имеют сходства с каноническими последовательностями. Выявлены остров VPI-1 с альтернативным аллелем tcpA, кластер T3SS в составе острова VPI-3, ген cholix-токсина, что является редким сочетанием в геноме одного штамма. Набор интактных детерминант других факторов патогенности достаточен для реализации патогенетического потенциала. Присутствие в геноме ряда детерминант антибиотикорезистентности не всегда совпадало с фенотипическим проявлением устойчивости/чувствительности к антимикробным агентам in vitro. Структура генома штамма и близкое родство с клиническими изолятами указывают на потенциальную способность вызвать острые кишечные инфекции. Поскольку существует вероятность новых заносов таких штаммов в РФ, их обнаружение в водоемах требует проведения комплекса противоэпидемических мероприятий.

The aim of the study was to perform a detailed molecular-genetic characterization of the toxigenic Vibrio cholerae nonO1/nonO139 strain isolated from the Don River in the Rostov Region in 2024. Materials and methods. Whole-genome sequencing was carried out on the MiSeq Illumina and Oxford Nanopore platforms. Primary assembly was performed de novo through the Canu software based on long reads, and subsequent alignment was carried out using short reads with the Pilon program. Vector NTI package, BLASTN, BLASTP, BioEdit, Ugene, abricate (CARD database) and SnapGene Viewer were used in the bioinformatics analysis of genomes. The search for the limits of wb* clusters and comparison of their genes were conducted by means of the author’s program “O-cluster”. The phylogenetic tree was constructed using the roary and FastTree software. Results and discussion. A toxigenic strain of NAG-vibrio has been identified for the first time in Russia. The sequences of both chromosomes of the studied strain have been determined via hybrid genome assembly. Based on the analysis of the O-antigen biosynthesis region, the strain has been classified into serogroup O105 and it shows a high degree of closeness to clinical strains of this serogroup previously isolated in China. Bioinformatic analysis has revealed the presence of tandems of two identical copies of CTX and RS1 prophages on the large chromosome, which are notably distinct from their prototypes. The ctxB gene is represented by the ctxB12 allele, and all RS1 genes, except for rstC, show no similarity to canonical sequences. A VPI-1 island with an alternative tcpA allele, a T3SS cluster within the VPI-3 island, and the cholix toxin gene have been identified, which constitutes a rare combination within a single strain’s genome. The set of intact determinants of other pathogenicity factors is sufficient for the realization of pathogenic potential. The presence of a number of antibiotic resistance determinants in the genome did not always correlate with the phenotypic manifestation of resistance/susceptibility to antimicrobial agents in vitro. The genome structure of the strain and its close relationship to clinical isolates indicate a potential capacity to cause acute intestinal infections. Since there is a possibility of new introductions of such strains into the Russian Federation, their detection in water bodies necessitates the implementation of a set of anti-epidemic measures.

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