Epidemiology and Infectious DiseasesEpidemiology and Infectious DiseasesЭпидемиология и инфекционные болезни3034-20073034-2015Eco-Vector63686910.17816/EID636869Original study articlesОригинальные исследованияResearch ArticleAnalysis of the genetic features of the structural organization of integrative conjugative elements of Vibrio cholerae strains of various originsАнализ генетических особенностей структурной организации интегративных конъюгативных элементов штаммов Vibrio cholerae различного происхожденияhttps://orcid.org/0000-0002-9056-32317319-3037VodopyanovAlexey S.ВодопьяновАлексей Сергеевич
Russian Federation

MD, Cand. Sci. (Medicine)

канд. мед. наук

vodopyanov_as@antiplague.ruhttps://orcid.org/0000-0002-7178-80214270-3091PisanovRuslan V.ПисановРуслан Вячеславович
Russian Federation

Cand. Sci. (Biology)

канд. биол. наук

plague@aaanet.ruhttps://orcid.org/0000-0003-4336-04394672-9310VodopyanovSergey O.ВодопьяновСергей Олегович
Russian Federation

MD, Dr. Sci. (Medicine)

д-р мед. наук

serge100v@gmail.comhttps://orcid.org/0000-0003-0550-22215378-3729NoskovAleksey K.НосковАлексей Кимович
Russian Federation

MD, Cand. Sci. (Medicine)

канд. мед. наук

noskov-epid@mail.ruRostov-on-Don Plague Control Researsh InstituteРостовский-на-Дону ордена Трудового Красного Знамени научно-исследовательский противочумный институт17122024280220252953653740910202415112024Copyright ©; 2024, Eco-vectorCopyright ©; 2024, Эко-вектор2024Eco-vectorЭко-векторhttps://rjeid.com/1560-9529/article/view/636869

Background: Integrative conjugative elements (ICEs) play a significant role in the dissemination of antibiotic resistance genes among Vibrio cholerae strains. However, there are currently no standardized methods for ICE typing that allow for the analysis of large genomic datasets.

Aim: To conduct a comparative analysis of ICE sequences in Vibrio cholerae strains of various origins and to develop an algorithm for their typing.

Materials and methods: The study utilized whole-genome sequencing data from 120 toxigenic (ctxAB+tcpA+) V. cholerae O1 El Tor strains obtained using the MiSeq platform (Illumina, USA) and MinION platform (Oxford Nanopore, UK), as well as data from NCBI databases (1,886 genomes) and the European Nucleotide Archive (441 strains). The software for ICE detection and typing was developed in Java (version 11.0.13) and is available at: http://antiplague.ru/ice-genotyper/.

Results: A comparative analysis of ICE elements in toxigenic V. cholerae strains was performed. An ICE typing algorithm based on gene composition was proposed. Analysis of the V. cholerae genome collection revealed three previously undescribed ICE elements, designated ICEVchRus1, ICEVchHai3, and ICEVchLaos.

Conclusions: The study identified three previously undescribed ICE elements and mapped their distribution across Russia and other regions of the world. It was established that during the cholera outbreak in Dagestan in 1994, strains containing ICEVchBan11 and ICEVchBan9 were circulating simultaneously.

Обоснование. Интегративные конъюгативные элементы (integrative conjugating element, ICE) вносят существенный вклад в распространение бактериальных генов антибиотикорезистентности среди штаммов возбудителя холеры. Однако на данный момент отсутствуют унифицированные методы типирования ICE-элементов, позволяющие проводить анализ большого количества геномов.

Цель исследования — провести сравнительный анализ последовательностей ICE-элементов штаммов Vibrio cholerae различного происхождения и разработать алгоритм их типирования.

Материалы и методы. В работе использованы данные полногеномного секвенирования 120 штаммов токсигенных (ctxAB+tcpA+) V. cholerae О1 El Tor, полученных на платформах MiSeq (Illumina, США) и MinIon (Oxford Nanopore, Великобритания), а также из баз данных NCBI (1886 геномов) и European Nucleotide Archive (441 штамм). Программное обеспечение для выявления и типирования ICE-элемента разработано на языке программирования Java (версии 11.0.13) и расположено по адресу http://antiplague.ru/ice-genotyper/.

Результаты. Проведён сравнительный анализ ICE-элементов у токсигенных штаммов холерных вибрионов. Предложен алгоритм типирования ICE-элементов на основе их генного состава. Анализ коллекции геномов штаммов V. cholerae позволил выявить три ранее не описанных ICE-элемента, обозначенных как ICEVchRus1, ICEVchHai3 и ICEVchLaos.

Заключение. В результате проведённого анализа обнаружены три не описанных ранее ICE-элемента и показано их распространение в России и мире. Установлено, что во время вспышки холеры в Дагестане в 1994 году зарегистрирована одновременная циркуляция как штаммов, содержащих ICEVchBan11, так и штаммов с ICEVchBan9.

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