{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T14:26:36Z","timestamp":1791815196292,"version":"4.3.4"},"reference-count":63,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T00:00:00Z","timestamp":1769990400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T00:00:00Z","timestamp":1769990400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100005003","name":"Baskent \u00dcniversitesi","doi-asserted-by":"publisher","award":["DA24\/22"],"award-info":[{"award-number":["DA24\/22"]}],"id":[{"id":"10.13039\/501100005003","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Arch Microbiol"],"published-print":{"date-parts":[[2026,4]]},"DOI":"10.1007\/s00203-026-04736-6","type":"journal-article","created":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T08:12:35Z","timestamp":1770019955000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Genomic insights into the genetic diversity, resistance determinants, and plasmid content of carbapenem-resistant Acinetobacter baumannii clinical isolates"],"prefix":"10.1007","volume":"208","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7490-7981","authenticated-orcid":false,"given":"Sezin","family":"Unlu Celebi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1434-2717","authenticated-orcid":false,"given":"Suleyman","family":"Yalcin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3171-8926","authenticated-orcid":false,"given":"Ozlem","family":"Kurt Azap","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1872-028X","authenticated-orcid":false,"given":"Aylin","family":"Uskudar Guclu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,2,2]]},"reference":[{"issue":"D1","key":"4736_CR1","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","volume":"51","author":"BP Alcock","year":"2022","unstructured":"Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR et al (2022) CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database. Nucleic Acids Res 51(D1):D690\u2013D699. https:\/\/doi.org\/10.1093\/nar\/gkac920","journal-title":"Nucleic Acids Res"},{"key":"4736_CR2","unstructured":"Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/"},{"issue":"W1","key":"4736_CR3","doi-asserted-by":"publisher","first-page":"W573","DOI":"10.1093\/nar\/gks485","volume":"40","author":"A Boc","year":"2012","unstructured":"Boc A, Diallo AB, Makarenkov V (2012) T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res 40(W1):W573\u2013W579. https:\/\/doi.org\/10.1093\/nar\/gks485","journal-title":"Nucleic Acids Res"},{"key":"4736_CR4","doi-asserted-by":"publisher","unstructured":"Bostanghadiri N, Narimisa N, Mirshekar M, Dadgar-Zankbar L, Taki E et al (2024) Prevalence of colistin resistance in clinical isolates of Acinetobacter baumannii: a systematic review and meta-analysis. Antimicrob Resist Infect Control 28;13(1):24. https:\/\/doi.org\/10.1186\/s13756-024-01376-7","DOI":"10.1186\/s13756-024-01376-7"},{"key":"4736_CR5","doi-asserted-by":"publisher","unstructured":"\u00c7a\u011flan E, Nigiz \u015e, Sancak B, G\u00fcr D (2020) Resistance and heteroresistance to colistin among clinical isolates of Acinetobacter baumannii. Acta Microbiol Immunol Hung 67(2):107\u2013111. https:\/\/doi.org\/10.1556\/030.66.2019.021","DOI":"10.1556\/030.66.2019.021"},{"key":"4736_CR6","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000878","volume":"8","author":"SM Cahill","year":"2022","unstructured":"Cahill SM, Hall RM, Kenyon JJ (2022) An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus. Microb Genom 8:mgen000878. https:\/\/doi.org\/10.1099\/mgen.0.000878","journal-title":"Microb Genom"},{"key":"4736_CR7","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.1016\/j.meegid.2011.04.024","volume":"11","author":"E Carretto","year":"2011","unstructured":"Carretto E, Barbarini D, Dijkshoorn L, van der Reijden TJ, Brisse S et al (2011) APSI acinetobacter study group: widespread carbapenem resistant Acinetobacter baumannii clones in Italian hospitals revealed by a multicenter study. Infect Genet Evol 11:1319\u20131326. https:\/\/doi.org\/10.1016\/j.meegid.2011.04.024","journal-title":"Infect Genet Evol"},{"key":"4736_CR8","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1016\/j.csbj.2021.12.038","volume":"20","author":"A Chukamnerd","year":"2022","unstructured":"Chukamnerd A, Singkhamanan K, Chongsuvivatwong V et al (2022) Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand. Comput Struct Biotechnol J 20:545\u2013558. https:\/\/doi.org\/10.1016\/j.csbj.2021.12.038","journal-title":"Comput Struct Biotechnol J"},{"issue":"5","key":"4736_CR9","first-page":"447","volume":"44","author":"\u0130H \u00c7ift\u00e7i","year":"2022","unstructured":"\u00c7ift\u00e7i \u0130H, Kilba\u015f \u0130, Kahraman K\u0131lba\u015f EP (2022) The War Against the Resistance of Acinetobacter Baumannii: A Meta-analysis of Findings in T\u00fcrkiye. J Clin Pract Res 44(5):447\u2013454","journal-title":"J Clin Pract Res"},{"issue":"1","key":"4736_CR10","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1186\/s12859-018-2336-6","volume":"19","author":"PTLC Clausen","year":"2018","unstructured":"Clausen PTLC, Aarestrup FM, Lund O (2018) Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 19(1):307","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"4736_CR11","doi-asserted-by":"publisher","first-page":"1843","DOI":"10.1128\/JCM.41.5.1843-1849.2003","volume":"41","author":"MA Davis","year":"2003","unstructured":"Davis MA, Hancock DD, Besser TE, Call DR (2003) Evaluation of pulsed-field gel electrophoresis as a tool for determining the degree of genetic relatedness between strains of Escherichia coli O157:H7. J Clin Microbiol 41(5):1843\u20139. https:\/\/doi.org\/10.1128\/JCM.41.5.1843-1849.2003","journal-title":"J Clin Microbiol"},{"key":"4736_CR12","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1111\/j.1469-0691.2010.03254.x","volume":"17","author":"A Di Popolo","year":"2011","unstructured":"Di Popolo A, Giannouli M, Triassi M, Brisse S, Zarrilli R (2011) Molecular epidemiology of multidrug-resistant Acinetobacter baumannii strains in four Mediterranean countries using a multilocus sequence typing scheme. Clin Microbiol Infect 17:197\u2013201. https:\/\/doi.org\/10.1111\/j.1469-0691.2010.03254.x","journal-title":"Clin Microbiol Infect"},{"issue":"2","key":"4736_CR13","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001345","volume":"11","author":"NS Din","year":"2025","unstructured":"Din NS, Mohd Rani F, Alattraqchi AG, Ismail S, A Rahman NI et al (2025) Whole-genome sequencing of Acinetobacter baumannii clinical isolates from a tertiary hospital in Terengganu, Malaysia (2011\u20132020), revealed the predominance of the Global Clone 2 lineage. Microb Genom 11(2):001345. https:\/\/doi.org\/10.1099\/mgen.0.001345","journal-title":"Microb Genom"},{"key":"4736_CR14","unstructured":"European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters. Version 13.0 (2023) http:\/\/www.eucast.org"},{"key":"4736_CR15","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1016\/j.jgar.2022.08.024","volume":"31","author":"EC Eze","year":"2022","unstructured":"Eze EC, Falgenhauer L, El Zowalaty ME (2022) Draft genome sequences of extensively drug resistant and pandrug resistant Acinetobacter baumannii strains isolated from hospital wastewater in South Africa. J Glob Antimicrob Resist 31:286\u2013291. https:\/\/doi.org\/10.1016\/j.jgar.2022.08.024","journal-title":"J Glob Antimicrob Resist"},{"key":"4736_CR16","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00930","volume":"10","author":"S Gaiarsa","year":"2019","unstructured":"Gaiarsa S, Batisti Biffignandi G, Esposito EP, Castelli M et al (2019) Comparative analysis of the two Acinetobacter baumannii multilocus sequence typing (MLST) schemes. Front Microbiol 10:930. https:\/\/doi.org\/10.3389\/fmicb.2019.00930","journal-title":"Front Microbiol"},{"issue":"4","key":"4736_CR17","doi-asserted-by":"publisher","first-page":"1223","DOI":"10.1128\/JCM.02263-09","volume":"48","author":"M Giannouli","year":"2010","unstructured":"Giannouli M, Cuccurullo S, Crivaro V, Di Popolo A, Bernardo M et al (2010) Molecular epidemiology of multidrug-resistant Acinetobacter baumannii in a tertiary care hospital in Naples, Italy, shows the emergence of a novel epidemic clone. J Clin Microbiol 48(4):1223\u201330. https:\/\/doi.org\/10.1128\/JCM.02263-09","journal-title":"J Clin Microbiol"},{"issue":"6","key":"4736_CR18","doi-asserted-by":"publisher","first-page":"1588","DOI":"10.1128\/jcm.30.6.1588-1591.1992","volume":"30","author":"A Gouby","year":"1992","unstructured":"Gouby A, Carles-Nurit MJ, Bouziges N, Bourg G, Mesnard R, Bouvet PJ (1992) Use of pulsed-field gel electrophoresis for investigation of hospital outbreaks of Acinetobacter baumannii. J Clin Microbiol 30(6):1588\u20131591. https:\/\/doi.org\/10.1128\/jcm.30.6.1588-1591.1992","journal-title":"J Clin Microbiol"},{"issue":"3","key":"4736_CR19","doi-asserted-by":"publisher","first-page":"200","DOI":"10.7883\/yoken.JJID.2020.478","volume":"24","author":"A Gozalan","year":"2021","unstructured":"Gozalan A, Unald\u0131 O, Guldemir D, Aydogan S, Kuzucu C et al (2021) Molecular characterization of carbapenem-resistant Acinetobacter baumannii blood culture isolates from three hospitals in Turkey. Jpn J Infect Dis 24(3):200\u2013208. https:\/\/doi.org\/10.7883\/yoken.JJID.2020.478","journal-title":"Jpn J Infect Dis"},{"key":"4736_CR20","doi-asserted-by":"publisher","unstructured":"Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35(Web Server issue):W52-7. https:\/\/doi.org\/10.1093\/nar\/gkm360","DOI":"10.1093\/nar\/gkm360"},{"key":"4736_CR21","doi-asserted-by":"publisher","unstructured":"Guclu AU, Gozen AG (2020) Genetic Diversity of OXA-like Genes in Multidrug-Resistant Acinetobacter baumannii Strains from ICUs. Clin Lab 1;66(10). https:\/\/doi.org\/10.7754\/Clin.Lab.2020.200135","DOI":"10.7754\/Clin.Lab.2020.200135"},{"key":"4736_CR22","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1101\/119545","volume":"34","author":"J Hadfield","year":"2017","unstructured":"Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM et al (2017) Phandango: an interactive viewer for bacterial population genomics. Bioinformatics 34:292\u2013293. https:\/\/doi.org\/10.1101\/119545","journal-title":"Bioinformatics"},{"issue":"9","key":"4736_CR23","doi-asserted-by":"publisher","first-page":"1271","DOI":"10.1089\/mdr.2017.0397","volume":"24","author":"M Haeili","year":"2018","unstructured":"Haeili M, Kafshdouz M, Feizabadi MM (2018) Molecular mechanisms of colistin resistance among Pandrug-Resistant isolates of acinetobacter baumannii with high Case-Fatality rate in intensive care unit patients. Microb Drug Resist 24(9):1271\u20131276. https:\/\/doi.org\/10.1089\/mdr.2017.0397","journal-title":"Microb Drug Resist"},{"issue":"3","key":"4736_CR24","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0264335","volume":"4","author":"C Hahm","year":"2022","unstructured":"Hahm C, Chung HS, Lee M (2022) Whole-genome sequencing for the characterization of resistance mechanisms and epidemiology of colistin-resistant Acinetobacter baumannii. PLoS One 4(3):e0264335. https:\/\/doi.org\/10.1371\/journal.pone.0264335","journal-title":"PLoS One"},{"issue":"10","key":"4736_CR25","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000306","volume":"5","author":"M Hamidian","year":"2019","unstructured":"Hamidian M, Nigro SJ (2019) Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii. Microb Genom 5(10):e000306. https:\/\/doi.org\/10.1099\/mgen.0.000306","journal-title":"Microb Genom"},{"issue":"1","key":"4736_CR26","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1128\/JCM.02452-13","volume":"52","author":"H Hasman","year":"2014","unstructured":"Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA et al (2014) Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol 52(1):139\u2013146","journal-title":"J Clin Microbiol"},{"key":"4736_CR27","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1089\/mdr.2011.0089","volume":"17","author":"N Karah","year":"2011","unstructured":"Karah N, Giske CG, Sundsfjord A, Samuelsen O (2011) A diversity of OXA-carbapenemases and class 1 integrons among carbapenem-resistant Acinetobacter baumannii clinical isolates from Sweden belonging to different international clonal lineages. Microb Drug Resist 17:545\u2013549. https:\/\/doi.org\/10.1089\/mdr.2011.0089","journal-title":"Microb Drug Resist"},{"key":"4736_CR28","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1093\/molbev\/msy096","volume":"35","author":"S Kumar","year":"2018","unstructured":"Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547. https:\/\/doi.org\/10.1093\/molbev\/msy096","journal-title":"Mol Biol Evol"},{"key":"4736_CR29","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02478-22","volume":"11","author":"MMC Lam","year":"2023","unstructured":"Lam MMC, Koong J, Holt KE, Hall RM, Hamidian M (2023) Detection and typing of plasmids in Acinetobacter baumannii using rep genes encoding replication initiation proteins. Microbiol Spectr 11:e0247822. https:\/\/doi.org\/10.1128\/spectrum.02478-22","journal-title":"Microbiol Spectr"},{"issue":"4","key":"4736_CR30","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/JCM.06094-11","volume":"50","author":"MV Larsen","year":"2012","unstructured":"Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H et al (2012) Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50(4):1355\u201361. https:\/\/doi.org\/10.1128\/JCM.06094-11","journal-title":"J Clin Microbiol"},{"key":"4736_CR31","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2017.00055","volume":"7","author":"CR Lee","year":"2017","unstructured":"Lee CR, Lee JH, Park M, Park KS, Bae IK et al (2017) Biology of Acinetobacter baumannii: Pathogenesis, Antibiotic Resistance Mechanisms, and Prospective Treatment Options. Front Cell Infect Microbiol 7:55. https:\/\/doi.org\/10.3389\/fcimb.2017.00055","journal-title":"Front Cell Infect Microbiol"},{"issue":"W1","key":"4736_CR32","doi-asserted-by":"publisher","first-page":"W256","DOI":"10.1093\/nar\/gkz239","volume":"47","author":"I Letunic","year":"2019","unstructured":"Letunic I, Bork P (2019) Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47(W1):W256-9. https:\/\/doi.org\/10.1093\/nar\/gkz239","journal-title":"Nucleic Acids Res"},{"key":"4736_CR33","doi-asserted-by":"publisher","unstructured":"Levy-Blitchtein S, Roca I, Plasencia-Rebata S, Vicente-Taboada W, Vel\u00e1squez-Pomar J et al (2018) Emergence and spread of carbapenem-resistant Acinetobacter baumannii international clones II and III in Lima, Peru. Emerg Microbes Infect 4;7(1):119. https:\/\/doi.org\/10.1038\/s41426-018-0127-9","DOI":"10.1038\/s41426-018-0127-9"},{"key":"4736_CR34","doi-asserted-by":"publisher","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","volume":"50","author":"B Liu","year":"2022","unstructured":"Liu B, Zheng D, Zhou S, Chen L, Yang J (2022) VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res 50:D912\u2013D917. https:\/\/doi.org\/10.1093\/nar\/gkab1107","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"4736_CR35","doi-asserted-by":"publisher","first-page":"1617","DOI":"10.1128\/JCM.00001-14","volume":"52","author":"D Marchaim","year":"2014","unstructured":"Marchaim D, Pogue JM, Tzuman O, Hayakawa K, Lephart PR et al (2014) Major variation in MICs of tigecycline in Gram-negative bacilli as a function of testing method. J Clin Microbiol 52(5):1617\u201321. https:\/\/doi.org\/10.1128\/JCM.00001-14","journal-title":"J Clin Microbiol"},{"issue":"D1","key":"4736_CR36","doi-asserted-by":"publisher","first-page":"D801","DOI":"10.1093\/nar\/gkab902","volume":"50","author":"JP Meier-Kolthoff","year":"2022","unstructured":"Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, G\u00f6ker M (2022) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 50(D1):D801\u2013D807. https:\/\/doi.org\/10.1093\/nar\/gkab902","journal-title":"Nucleic Acids Res"},{"key":"4736_CR37","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae1095","author":"LA Molano","year":"2024","unstructured":"Molano LA, Hirsch P, Hannig M, M\u00fcller R, Keller A (2024) The PLSDB 2025 update: enhanced annotations and improved functionality for comprehensive plasmid research. Nucleic Acids Res. https:\/\/doi.org\/10.1093\/nar\/gkae1095","journal-title":"Nucleic Acids Res"},{"key":"4736_CR38","doi-asserted-by":"publisher","first-page":"2952","DOI":"10.1093\/jac\/dky290","volume":"73","author":"MM Mustapha","year":"2018","unstructured":"Mustapha MM, Li B, Pacey MP, Mettus RT, McElheny CL, Marshall CW et al (2018) Phylogenomics of colistin-susceptible and resistant XDR Acinetobacter baumannii. J Antimicrob Chemother 73:2952\u20132959. https:\/\/doi.org\/10.1093\/jac\/dky290","journal-title":"J Antimicrob Chemother"},{"issue":"4","key":"4736_CR39","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000977","volume":"9","author":"NH Muzahid","year":"2023","unstructured":"Muzahid NH, Hussain MH, Hu\u00ebt MAL, Dwiyanto J, Su TT et al (2023) Molecular characterization and comparative genomic analysis of Acinetobacter baumannii isolated from the community and the hospital: an epidemiological study in Segamat, Malaysia. Microb Genom 9(4):mgen000977. https:\/\/doi.org\/10.1099\/mgen.0.000977","journal-title":"Microb Genom"},{"issue":"4","key":"4736_CR40","doi-asserted-by":"publisher","first-page":"700","DOI":"10.3390\/microorganisms10040700","volume":"10","author":"B N\u00e9ron","year":"2022","unstructured":"N\u00e9ron B, Courtois V, Jeannot K, Branger C, Perrin A (2022) IntegronFinder 2.0: identification and analysis of integrons across bacteria, with a focus on antibiotic resistance in Klebsiella. Microorganisms 10(4):700. https:\/\/doi.org\/10.3390\/microorganisms10040700","journal-title":"Microorganisms"},{"issue":"15","key":"4736_CR41","doi-asserted-by":"publisher","first-page":"2379","DOI":"10.1093\/bioinformatics\/btx157","volume":"33","author":"Y Nishimura","year":"2017","unstructured":"Nishimura Y, Yoshida T, Kuronishi M et al (2017) ViPTree: the viral proteomic tree server. Bioinformatics 33(15):2379\u20132380. https:\/\/doi.org\/10.1093\/bioinformatics\/btx157","journal-title":"Bioinformatics"},{"issue":"22","key":"4736_CR42","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31(22):3691\u20133. https:\/\/doi.org\/10.1093\/bioinformatics\/btv421","journal-title":"Bioinformatics"},{"issue":"1","key":"4736_CR43","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.diagmicrobio.2010.12.002","volume":"70","author":"L Poirel","year":"2011","unstructured":"Poirel L, Walsh TR, Cuvillier V et al (2011) Multiplex PCR for detection of Acquired Carbapenemase genes. Diagn Microbiol Infect Dis 70(1):119\u2013123. https:\/\/doi.org\/10.1016\/j.diagmicrobio.2010.12.002","journal-title":"Diagn Microbiol Infect Dis"},{"issue":"8","key":"4736_CR44","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000206","volume":"4","author":"J Robertson","year":"2018","unstructured":"Robertson J, Nash JHE (2018) MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom 4(8):e000206. https:\/\/doi.org\/10.1099\/mgen.0.000206","journal-title":"Microb Genom"},{"key":"4736_CR45","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1016\/j.ijantimicag.2019.08.010","volume":"54","author":"CH Rodriguez","year":"2019","unstructured":"Rodriguez CH, Traglia G, Bastias N, Pandolfo C, Bruni G, Nastro M et al (2019) Discrepancies in susceptibility testing to colistin in Acinetobacter baumannii: The influence of slow growth and heteroresistance. Int J Antimicrob Agents 54:587\u2013591. https:\/\/doi.org\/10.1016\/j.ijantimicag.2019.08.010","journal-title":"Int J Antimicrob Agents"},{"key":"4736_CR46","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-5243-3","volume":"19","author":"J Rumore","year":"2018","unstructured":"Rumore J, Tschetter L, Kearney A et al (2018) Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective. BMC Genomics 19:870. https:\/\/doi.org\/10.1186\/s12864-018-5243-3","journal-title":"BMC Genomics"},{"issue":"3","key":"4736_CR47","doi-asserted-by":"publisher","first-page":"275","DOI":"10.5578\/flora.2025031344","volume":"30","author":"NM Said","year":"2025","unstructured":"Said NM, \u00dcsk\u00fcdar G\u00fc\u00e7l\u00fc A (2025) Biofilm formation ability of carbapenem-resistant Acinetobacter baumannii isolates from intensive care unit patients and genetic factors contributing to biofilm formation. Flora 30(3):275\u2013288. https:\/\/doi.org\/10.5578\/flora.2025031344","journal-title":"Flora"},{"issue":"4","key":"4736_CR48","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1093\/oxfordjournals.molbev.a040454","volume":"4","author":"N Saitou","year":"1987","unstructured":"Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406\u2013425. https:\/\/doi.org\/10.1093\/oxfordjournals.molbev.a040454","journal-title":"Mol Biol Evol"},{"key":"4736_CR49","unstructured":"Seemann T (2015) snippy: fast bacterial variant calling from NGS reads. https:\/\/github.com\/tseemann\/snippy"},{"key":"4736_CR50","doi-asserted-by":"publisher","unstructured":"Shahriar S, Mohammad AD, Amir R, Abbas B, Vajihe K, Zahra KJ (2017) Molecular evaluation of colistin-resistant gene expression changes in Acinetobacter baumannii with real-time polymerase chain reaction. Infect Drug Resist. 2017 10: 455\u2013462. https:\/\/doi.org\/10.2147\/IDR.S141196","DOI":"10.2147\/IDR.S141196"},{"issue":"9","key":"4736_CR51","doi-asserted-by":"publisher","first-page":"2233","DOI":"10.1128\/jcm.33.9.2233-2239.1995","volume":"33","author":"FC Tenover","year":"1995","unstructured":"Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE et al (1995) Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 33(9):2233\u20139. https:\/\/doi.org\/10.1128\/jcm.33.9.2233-2239.1995","journal-title":"J Clin Microbiol"},{"key":"4736_CR52","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10020205","volume":"10","author":"M Tyumentseva","year":"2021","unstructured":"Tyumentseva M, Mikhaylova Y, Prelovskaya A, Tyumentsev A, Petrova L et al (2021) Genomic and phenotypic analysis of multidrug-resistant Acinetobacter baumannii clinical isolates carrying different types of CRISPR\/Cas systems. Pathogens 10:205. https:\/\/doi.org\/10.3390\/pathogens10020205","journal-title":"Pathogens"},{"issue":"5","key":"4736_CR53","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1080\/17460794.2024.2357918","volume":"19","author":"S Unlu","year":"2024","unstructured":"Unlu S, Uskudar-Guclu A, Yalcin S, Kurt-Azap O, Basustaoglu A (2024) Characterization of four virulent bacteriophages as potential therapeutics for clinical multidrug-resistant & extensively drug-resistant acinetobacter baumannii. Future Virol 19(5):199\u2013213. https:\/\/doi.org\/10.1080\/17460794.2024.2357918","journal-title":"Future Virol"},{"issue":"6","key":"4736_CR54","doi-asserted-by":"publisher","first-page":"1171","DOI":"10.1007\/s10096-024-04831-w","volume":"43","author":"A Uskudar-Guclu","year":"2024","unstructured":"Uskudar-Guclu A, Danyildiz S, Mirza HC, Akcil Ok M, Basustaoglu (2024) In vitro activity of Cefiderocol against carbapenem-resistant acinetobacter baumannii carrying various \u03b2-lactamase encoding genes. Eur J Clin Microbiol Infect Di 43(6):1171\u20131179. https:\/\/doi.org\/10.1007\/s10096-024-04831-w","journal-title":"Eur J Clin Microbiol Infect Di"},{"key":"4736_CR55","unstructured":"WHO (2017) Global priority list of Antibiotic-resistant bacteria to guide Research, Discovery, and development of new antibiotics. World Health Organisation (WHO), pp 1\u20137"},{"key":"4736_CR56","unstructured":"Wick RR (2025) Porechop. GitHub repository. Published 2017. Accessed July 28. https:\/\/github.com\/rrwick\/Porechop"},{"key":"4736_CR57","doi-asserted-by":"publisher","unstructured":"Wishart DS, Han S, Saha S, Oler E, Peters H et al (2023) PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res 5;51(W1):W443-W450. https:\/\/doi.org\/10.1093\/nar\/gkad382","DOI":"10.1093\/nar\/gkad382"},{"issue":"4","key":"4736_CR58","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/j.ijantimicag.2006.01.004","volume":"27","author":"N Woodford","year":"2006","unstructured":"Woodford N, Ellington MJ, Coelho JM (2006) Multiplex PCR for genes encoding prevalent OXA carbapenemases in Acinetobacter spp. Int J Antimicrob Agents 27(4):351\u2013353. https:\/\/doi.org\/10.1016\/j.ijantimicag.2006.01.004","journal-title":"Int J Antimicrob Agents"},{"issue":"21","key":"4736_CR59","doi-asserted-by":"publisher","first-page":"3340","DOI":"10.1093\/bioinformatics\/btx433","volume":"33","author":"Z Xie","year":"2017","unstructured":"Xie Z, Tang H (2017) ISEScan: automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics 33(21):3340\u20133347. https:\/\/doi.org\/10.1093\/bioinformatics\/btx433","journal-title":"Bioinformatics"},{"issue":"10","key":"4736_CR60","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1007\/s10482-017-0844-4","volume":"110","author":"SH Yoon","year":"2017","unstructured":"Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110(10):1281\u20131286. https:\/\/doi.org\/10.1007\/s10482-017-0844-4","journal-title":"Antonie Van Leeuwenhoek"},{"issue":"1","key":"4736_CR61","doi-asserted-by":"publisher","DOI":"10.1186\/s13756-020-00876-6","volume":"10","author":"K Yu","year":"2021","unstructured":"Yu K, Zeng W, Xu Y, Liao W, Xu W, Zhou T, Cao J, Chen L (2021) Bloodstream infections caused by ST2 Acinetobacter baumannii: risk factors, antibiotic regimens, and virulence over 6 years period in China. Antimicrob Resist Infect Control 10(1):16. https:\/\/doi.org\/10.1186\/s13756-020-00876-6","journal-title":"Antimicrob Resist Infect Control"},{"key":"4736_CR62","doi-asserted-by":"publisher","unstructured":"Zack KM, Sorenson T, Joshi SG (2024) Types and Mechanisms of Efflux Pump Systems and the Potential of Efflux Pump Inhibitors in the Restoration of Antimicrobial Susceptibility, with a Special Reference to Acinetobacter baumannii. Pathogens 23;13(3):197. https:\/\/doi.org\/10.3390\/pathogens13030197","DOI":"10.3390\/pathogens13030197"},{"key":"4736_CR63","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.ijantimicag.2012.09.008","volume":"41","author":"R Zarrilli","year":"2013","unstructured":"Zarrilli R, Pournaras S, Giannouli M, Tsakris A (2013) Global evolution of multidrug-resistant Acinetobacter baumannii clonal lineages. Int J Antimicrob Agents 41:11\u201319. https:\/\/doi.org\/10.1016\/j.ijantimicag.2012.09.008","journal-title":"Int J Antimicrob Agents"}],"container-title":["Archives of Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00203-026-04736-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00203-026-04736-6","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00203-026-04736-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T12:00:20Z","timestamp":1774699220000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00203-026-04736-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,2]]},"references-count":63,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,4]]}},"alternative-id":["4736"],"URL":"https:\/\/doi.org\/10.1007\/s00203-026-04736-6","relation":{},"ISSN":["0302-8933","1432-072X"],"issn-type":[{"value":"0302-8933","type":"print"},{"value":"1432-072X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,2]]},"assertion":[{"value":"30 October 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 January 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 January 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 February 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors have no relevant financial or non-financial interests to disclose.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"Not applicable. This study was approved by Baskent University Institutional Review Board (Decision Date: 02.10.2024).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"<!--Emphasis Type='Bold' removed-->Ethical approval"}}],"article-number":"169"}}