Journal of microbiology, epidemiology and immunobiologyJournal of microbiology, epidemiology and immunobiologyЖурнал микробиологии, эпидемиологии и иммунобиологии0372-93112686-7613Central Research Institute for Epidemiology1909410.36233/0372-9311-844WSCUJMSCIENCE AND PRACTICEНАУКА И ПРАКТИКАUnknownInternational high-risk clones of Acinetobacter baumannii in Genbank: analysis of 47 738 whole-genome sequencesМеждународные эпидемические клоны Acinetobacter baumannii в Genbank: анализ 47 738 полногеномных последовательностейhttps://orcid.org/0000-0002-7409-077X23098248300ShelenkovAndrey AleksandrovichШеленковАндрей Александрович
Russian Federation

PhD in Physical and Mathematical Sciences,Senior Researcher of Laboratory of Molecular Mechanisms of Antibiotic Resistance of the Central Research Institute of Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing

кандидат физико-математических наук, старший научный сотрудник лаборатории молекулярных механизмов антибиотикорезистентности

fallandar@gmail.comhttps://orcid.org/0000-0001-7025-304423010863200SlavokhotovaAnna AleksandrovnaСлавохотоваАнна Александровна
Russian Federation

PhD in Biological Sciences, Senior Researcherof the Laboratory of Molecular Mechanisms of Antibiotic Resistance

кандидат биологических наук, старший научный сотрудник лаборатории молекулярных механизмов антибиотикорезистентности

slavokhotova@cmd.suhttps://orcid.org/0000-0002-5646-538X58861421400MikhaylovaYulia VladimirovnaМихайловаЮлия Владимировна
Russian Federation

PhD in Biological Sciences, Head of the Laboratoryof Molecular Mechanisms of Antibiotic Resistance

кандидат биологических наук, заведующий лабораторией Молекулярных механизмов антибиотикорезистентности

mihailova@cmd.suhttps://orcid.org/0000-0003-4228-9044AkimkinVasiliy GennadievichАкимкинВасилий Геннадьевич
Russian Federation

MD, PhD, DSc, Professor, Academician of the RussianAcademy of Sciences, Director of the Central Research Instituteof Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing

доктор медицинских наук, профессор,академик Российской академии наук, директор Центрального НИИ эпидемиологии Роспотребнадзора

vgakimkin@yandex.ruCentral research institute of epidemiologyФБУН Центральный научно-исследовательский институт эпидемиологии РоспотребнадзораCentral Research Institute of Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human WellbeingФБУН Центральный научно-исследовательский институт эпидемиологии РоспотребнадзораCentral Research Institute of Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human WellbeingФБУН Центральный научно-исследовательский институт эпидемиологии РоспотребнадзораCentral Research Institute of Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human WellbeingФБУН Центральный научно-исследовательский институт эпидемиологии Роспотребнадзора200820260304202620082026Copyright ©; , Shelenkov A.A., Slavokhotova A.A., Mikhaylova Y.V., Akimkin V.G.Copyright ©; , Шеленков А.А., Славохотова А.А., Михайлова Ю.В., Акимкин В.Г.Shelenkov A.A., Slavokhotova A.A., Mikhaylova Y.V., Akimkin V.G.Шеленков А.А., Славохотова А.А., Михайлова Ю.В., Акимкин В.Г.https://creativecommons.org/licenses/by/4.0https://microbiol.crie.ru/jour/article/view/19094

Introduction. Acinetobacter baumannii is a major cause of hospital-acquired infections and is frequently associated with multidrug resistance, particularly among international clones of high risk (ICs), whose identification within the hospital is important for risk assessment. Since our previous analysis of the Genbank database, the number of genomes has increased threefold, while the number of recognized ICs has expanded to 12, making an updated analysis necessary.

Objective. To analyze A. baumannii genomes deposited in Genbank in order to identify ICs and to characterize antimicrobial resistance determinants, virulence factors, and plasmid replicons.

Materials and methods. A total of 47,738 A. baumannii whole-genome sequences available in Genbank as of March 10, 2026, were included in the study. Isolates were typed using the Pasteur MLST scheme, cgMLST profiles, and OXA-51-like carbapenemase variants using ResFinder, Kaptive, and MentaList. Statistical analysis was conducted using nonparametric methods with Holm correction.

Results. Overall, 76.3% of isolates were assigned to IC1-IC12. IC2 was the predominant clone, accounting for 66.0% of all genomes and 86.5% of IC isolates. In total, 1,067 sequence types, 156 OXA-51-like variants, 236 KL types, and 22 OCL types were identified. IC isolates carried significantly more resistance genes than non-IC isolates; for IC2, IC5, IC7, and IC1, the excess was approximately 1.7- to 1.8-fold. Distinct clone-specific associations with carbapenemases were observed: NDM in IC11, IC9, and IC1, and GES in IC12 and IC9.

Conclusions. This large-scale genomic analysis confirmed the predominance of ICs within the Genbank A. baumannii population and their key role in the accumulation of antimicrobial resistance determinants. The resulting database may support molecular surveillance, comparative genomic studies, and detection of emerging epidemic clones. The database is available at: https://doi.org/10.5281/zenodo.10143377.

Введение. Acinetobacter baumannii является одним из ведущих возбудителей внутрибольничных инфекций и часто характеризуется множественной лекарственной устойчивостью, особенно среди международных эпидемических клонов (international clones of high risk, IC), выявление которых в стационаре является важным для оценки рисков. С момента нашего предыдущего анализа базы Genbank число геномов увеличилось в 3 раза, а перечень признанных IC был расширен до 12, что потребовало проведения повторного анализа.

Целью исследования является анализ геномов A. baumannii, представленных в Genbank, для идентификации IC, а также для изучения полного профиля детерминант резистентности, факторов вирулентности и плазмидных репликонов.

Материалы и методы. В исследование включили 47738 полногеномных последовательностей A. baumannii из Genbank по состоянию на 10 марта 2026 г. Для типирования использовали схему Pasteur MLST, профили cgMLST, варианты OXA-51-подобных карбапенемаз, а также инструменты ResFinder, Kaptive и MentaList; статистический анализ выполняли непараметрическими методами с поправкой Холма. ​

Результаты. К IC1–IC12 были отнесены 76,3% изолятов; доминировал IC2, составивший 66,0% всех геномов и 86,5% IC-изолятов. Всего выявлено 1067 ST, 156 вариантов OXA-51-подобных ферментов, 236 KL-типов и 22 OCL-типа. Изоляты IC содержали значимо больше генов резистентности, чем другие изоляты, а для IC2, IC5, IC7 и IC1 это превышение составляло примерно 1,7–1,8 раза. Для отдельных клонов IC показана выраженная ассоциация с карбапенемазами: NDM — для IC11, IC9 и IC1, GES — для IC12 и IC9.

Выводы. Анализ большого массива геномов подтвердил доминирование IC в структуре A. baumannii из Genbank и их ведущую роль в накоплении детерминант антибиотикорезистентности. Сформированная база данных может использоваться для молекулярно-генетического мониторинга, сравнительного анализа и выявления новых эпидемических клонов. База данных доступна по адресу: https://doi.org/10.5281/zenodo.10143377.

Acinetobacter baumanniiinternational clones of high riskwhole-genome analysisantimicrobial resistancecgMLST analysisAcinetobacter baumanniiмеждународные эпидемические клоныполногеномный анализантибиотикорезистентностьанализ cgMLSTSati H, Carrara E, Savoldi A, Hansen P, Garlasco J, Campagnaro E, et al. The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance. Lancet Infect Dis. 2025;25:1033–43. DOI: https://doi.org/10.1016/S1473-3099(25)00118-5Boutzoukas A, Doi Y. The global epidemiology of carbapenem-resistant Acinetobacter baumannii. JAC-Antimicrob Resist. 2025;7:dlaf134. DOI: https://doi.org/10.1093/jacamr/dlaf134Shek EA, Sukhorukova MV, Edelstein MV, Skleenova EYu, Ivanchik NV, Shajdullina ER, et al. Antimicrobial resistance, carbapenemase production, and genotypes of nosocomial Acinetobacter spp. isolates in Russia: results of multicenter epidemiological study ”MARATHON 2015–2016”. Clin Microbiol Antimicrob Chemother. 2019;21:171–80. DOI: https://doi.org/10.36488/cmac.2019.2.171-180Lemos EV, De La Hoz FP, Einarson TR, McGhan WF, Quevedo E, Castañeda C, et al. Carbapenem resistance and mortality in patients with Acinetobacter baumannii infection: systematic review and meta-analysis. Clin Microbiol Infect. 2014;20:416–23. DOI: https://doi.org/10.1111/1469-0691.12363Yoon E-J, Kim D, Lee H, Lee HS, Shin JH, Uh Y, et al. Counter Clinical Prognoses of Patients With Bloodstream Infections Between Causative Acinetobacter baumannii Clones ST191 and ST451 Belonging to the International Clonal Lineage II. Front Public Health. 2019;7:233. DOI: https://doi.org/10.3389/fpubh.2019.00233Shelenkov A, Mikhaylova Y, Akimkin V. Genomic Epidemiology Dataset for the Important Nosocomial Pathogenic Bacterium Acinetobacter baumannii. Data. 2024;9:22. DOI: https://doi.org/10.3390/data9020022Shelenkov A, Akimkin V, Mikhaylova Y. International Clones of High Risk of Acinetobacter Baumannii—Definitions, History, Properties and Perspectives. Microorganisms. 2023;11:2115. DOI: https://doi.org/10.3390/microorganisms11082115Karah N, Faille N, Allard N, Grenier F, Abou-Fayad A, Higgins PG, et al. Global emergence of Acinetobacter baumannii International Clone 12 predominantly found in the Middle East. Microb Genomics. 2025;11. DOI: https://doi.org/10.1099/mgen.0.001572Diancourt L, Passet V, Nemec A, Dijkshoorn L, Brisse S. The Population Structure of Acinetobacter baumannii: Expanding Multiresistant Clones from an Ancestral Susceptible Genetic Pool. PLoS ONE. 2010;5:e10034. DOI: https://doi.org/10.1371/journal.pone.0010034Stanton TD, Hetland MAK, Löhr IH, Holt KE, Wyres KL. Fast and accurate in silico antigen typing with Kaptive 3. Microb Genomics. 2025;11. DOI: https://doi.org/10.1099/mgen.0.001428Higgins PG, Prior K, Harmsen D, Seifert H. Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii. PLOS ONE. 2017;12:e0179228. DOI: https://doi.org/10.1371/journal.pone.0179228Mikhaylova Y, Shelenkov A, Chernyshkov A, Tyumentseva M, Saenko S, Egorova A, et al. Whole-Genome Analysis of Staphylococcus aureus Isolates from Ready-to-Eat Food in Russia. Foods. 2022;11:2574. DOI: https://doi.org/10.3390/foods11172574Cain AK, Hamidian M. Portrait of a killer: Uncovering resistance mechanisms and global spread of Acinetobacter baumannii. PLOS Pathog. 2023;19:e1011520. DOI: https://doi.org/10.1371/journal.ppat.1011520Pournaras S, Gogou V, Giannouli M, Dimitroulia E, Dafopoulou K, Tsakris A, et al. Single-Locus-Sequence-Based Typing of blaOXA-51-like Genes for Rapid Assignment of Acinetobacter baumannii Clinical Isolates to International Clonal Lineages. J Clin Microbiol. 2014;52:1653–7. DOI: https://doi.org/10.1128/JCM.03565-13Yang J-L, Yang C-J, Chuang Y-C, Sheng W-H, Chen Y-C, Chang S-C. Association of capsular polysaccharide locus 2 with prognosis of Acinetobacter baumannii bacteraemia. Emerg Microbes Infect. 2022;11:83–90. DOI: https://doi.org/10.1080/22221751.2021.2011624Sorbello BM, Cahill SM, Kenyon JJ. Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive. Microb Genomics. 2023;9. DOI: https://doi.org/10.1099/mgen.0.001042Khuntayaporn P, Kanathum P, Houngsaitong J, Montakantikul P, Thirapanmethee K, Chomnawang MT. Predominance of international clone 2 multidrug-resistant Acinetobacter baumannii clinical isolates in Thailand: a nationwide study. Ann Clin Microbiol Antimicrob. 2021;20:19. DOI: https://doi.org/10.1186/s12941-021-00424-zKyriakidis I, Vasileiou E, Pana ZD, Tragiannidis A. Acinetobacter baumannii Antibiotic Resistance Mechanisms. Pathogens. 2021;10:373. DOI: https://doi.org/10.3390/pathogens10030373Lam MMC, Hamidian M. Examining the role of Acinetobacter baumannii plasmid types in disseminating antimicrobial resistance. Npj Antimicrob Resist. 2024;2:1. DOI: https://doi.org/10.1038/s44259-023-00019-yLam MMC, Koong J, Holt KE, Hall RM, Hamidian M. Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins. Microbiol Spectr. 2023;11:e02478-22. DOI: https://doi.org/10.1128/spectrum.02478-22Müller C, Reuter S, Wille J, Xanthopoulou K, Stefanik D, Grundmann H, et al. A global view on carbapenem-resistant Acinetobacter baumannii. mBio. 2023;14:e02260-23. DOI: https://doi.org/10.1128/mbio.02260-23Shelenkov A, Slavokhotova A, Mikhaylova Y, Akimkin V. Genomic typing, antimicrobial resistance gene, virulence factor and plasmid replicon database for the important pathogenic bacteria Klebsiella pneumoniae. BMC Microbiol. 2025;25:3. DOI: https://doi.org/10.1186/s12866-024-03720-8Iovleva A, Mustapha MM, Griffith MP, Komarow L, Luterbach C, Evans DR, et al. Carbapenem-Resistant Acinetobacter baumannii in U.S. Hospitals: Diversification of Circulating Lineages and Antimicrobial Resistance. mBio. 2022;13:e02759-21. DOI: https://doi.org/10.1128/mbio.02759-21Baleivanualala SC, Matanitobua S, Samisoni Y, Soqo V, Smita S, Mailulu J, et al. Environmental contamination with carbapenem resistant Acinetobacter baumannii in healthcare settings in Fiji: a potential source of infection. Front Cell Infect Microbiol. 2024;14:1429443. DOI: https://doi.org/10.3389/fcimb.2024.1429443Castanheira M, Mendes RE, Gales AC. Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex. Clin Infect Dis. 2023;76:S166–78. DOI: https://doi.org/10.1093/cid/ciad10926. Naderi G, Asadian M, Seifi A, Ghourchian S, Talebi M, Rahbar M, et al. Dissemination of the Acinetobacter baumannii isolates belonging to global clone 2 containing AbGRI resistance islands in a referral hospital. Microbiol Spectr. 2023;11:e05373-22. DOI: https://doi.org/10.1128/spectrum.05373-22Sánchez-Urtaza S, Alfonso-Alarcón L, Arazo Del Pino R, Burgwinkel T, Ocampo-Sosa A, Gonzalez R, et al. Genomic characterization of multidrug-resistant clinical Acinetobacter baumannii isolates from a hospital in Paraguay. Front Cell Infect Microbiol. 2025;15:1620479. DOI: https://doi.org/10.3389/fcimb.2025.1620479Gonçalves RS, Musen MA. The variable quality of metadata about biological samples used in biomedical experiments. Sci Data. 2019;6:190021. DOI: https://doi.org/10.1038/sdata.2019.21Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124. DOI: https://doi.org/10.12688/wellcomeopenres.14826.1Liu H, Moran RA, Doughty EL, Hua X, Snaith AE, Zhang L, et al. Longitudinal genomics reveals carbapenem-resistant Acinetobacter baumannii population changes with emergence of highly resistant ST164 clone. Nat Commun. 2024;15:9483. DOI: https://doi.org/10.1038/s41467-024-53817-xNaing SY, Hordijk J, Duim B, Broens EM, Van Der Graaf-van Bloois L, Rossen JW, et al. Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands. Pathogens. 2022;11:123. DOI: https://doi.org/10.3390/pathogens11020123Fernández-Cuenca F, Rodríguez-Pallares S, López-Cerero L, Gutiérrez-Fernández J, Bautista MF, Sánchez Gómez JA, et al. Regional distribution of carbapenemase-producing Acinetobacter baumannii isolates in southern Spain (Andalusia). Eur J Clin Microbiol Infect Dis. 2025;44:1069–76. DOI: https://doi.org/10.1007/s10096-025-05047-2