{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T18:08:25Z","timestamp":1785434905473,"version":"3.56.0"},"reference-count":69,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T00:00:00Z","timestamp":1777852800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003196","name":"Italian Ministry of Health","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003196","id-type":"DOI","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/00789fa95","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background\/Objectives:\u00a0Acinetobacter baumannii is a critical opportunistic pathogen causing severe healthcare-associated infections, particularly in intensive care units. The global dissemination of carbapenem-resistant A. baumannii (CRAB) and its environmental persistence necessitate continuous genomic surveillance to monitor high-risk clones. Methods: We conducted whole-genome sequencing (WGS), core genome multi-locus sequence typing (cgMLST), and phylogenomic analyses on 26 CRAB isolates collected at the National Institute for Infectious Diseases (INMI) \u201cLazzaro Spallanzani\u201d IRCCS (September 2023\u2013September 2024). Antimicrobial resistance determinants, virulence-related genes, and capsular (KL) and lipooligosaccharide outer core (OCL) loci were characterized by interrogation of comprehensive bioinformatic pipelines. Results: All CRAB isolates displayed an extensively drug-resistant (XDR) phenotype, with a shared resistance pattern to carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and sulfonamides, while being susceptible only to colistin and cefiderocol. The carbapenemase gene blaOXA-23 was detected in all CRAB isolates, together with clone-specific blaOXA-51-like variants. For all isolates, the resistome profile fully matched the observed resistance phenotype. All isolates belonged to the International Clonal Lineage II (ICL II), Pasteur Sequence Type (ST) 2, and Oxford ST369, ST208, and ST455. Integration of cgMLST data with phylogenomic analyses and genome-based classification of KL and OCL loci revealed five distinct clusters, each one including nearly identical isolates, indicating both intra-hospital dissemination and possible inter-hospital transmission. Virulome profiling revealed heterogeneous repertoires of virulence-associated genes, resulting in cluster-specific patterns, while patristic analysis identified phylogenetic clusters linking the study isolates to other Italian and other European lineages. Conclusions: This study underscores the complex genomic landscape of CRAB in our setting, driven by the circulation of different ICL II clonal types, and reinforces the urgency of integrated genomic surveillance and robust antimicrobial stewardship to mitigate the spread of high-risk XDR A. baumannii clones.<\/jats:p>","DOI":"10.3390\/antibiotics15050464","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T07:57:29Z","timestamp":1777967849000},"page":"464","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["High-Resolution Genomic Surveillance of Carbapenem-Resistant Acinetobacter baumannii: IC-2 Clonal Diversity, Resistance Determinants, and Virulence Signatures"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2461-5221","authenticated-orcid":false,"given":"Arianna","family":"Basile","sequence":"first","affiliation":[{"name":"Department of Science, Roma Tre University, 00146 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-9796-7813","authenticated-orcid":false,"given":"Valentina","family":"Antonelli","sequence":"additional","affiliation":[{"name":"Microbiology and Biobank Unit, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-4214-2812","authenticated-orcid":false,"given":"Claudia","family":"Rotondo","sequence":"additional","affiliation":[{"name":"Microbiology and Biobank Unit, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1768-6017","authenticated-orcid":false,"given":"Michele","family":"Properzi","sequence":"additional","affiliation":[{"name":"Microbiology and Biobank Unit, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8076-7217","authenticated-orcid":false,"given":"Francesco","family":"Messina","sequence":"additional","affiliation":[{"name":"Microbiology and Biobank Unit, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7783-6194","authenticated-orcid":false,"given":"Silvia","family":"D\u2019Arezzo","sequence":"additional","affiliation":[{"name":"Microbiology and Biobank Unit, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4729-577X","authenticated-orcid":false,"given":"Valentina","family":"Dimartino","sequence":"additional","affiliation":[{"name":"Microbiology and Biobank Unit, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-6594-0064","authenticated-orcid":false,"given":"Ivano","family":"Petriccione","sequence":"additional","affiliation":[{"name":"Microbiology and Biobank Unit, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Loiacono","sequence":"additional","affiliation":[{"name":"Clinical and Research Infectious Disease Department, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6100-8442","authenticated-orcid":false,"given":"Maria Grazia","family":"Bocci","sequence":"additional","affiliation":[{"name":"Intensive Care Unit, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0304-6712","authenticated-orcid":false,"given":"Giulia","family":"Capecchi","sequence":"additional","affiliation":[{"name":"Intensive Care Unit, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessia","family":"Arcangeli","sequence":"additional","affiliation":[{"name":"Clinical Risk Management, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3120-1417","authenticated-orcid":false,"given":"Alessandra","family":"Marani","sequence":"additional","affiliation":[{"name":"Health Direction, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-0629-866X","authenticated-orcid":false,"given":"Filippo Pasquale","family":"Riggio","sequence":"additional","affiliation":[{"name":"Department of Science, Roma Tre University, 00146 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3238-9164","authenticated-orcid":false,"given":"Massimiliano","family":"Lucidi","sequence":"additional","affiliation":[{"name":"Department of Science, Roma Tre University, 00146 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5080-5665","authenticated-orcid":false,"given":"Francesco","family":"Imperi","sequence":"additional","affiliation":[{"name":"Department of Science, Roma Tre University, 00146 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6128-7039","authenticated-orcid":false,"given":"Paolo","family":"Visca","sequence":"additional","affiliation":[{"name":"Department of Science, Roma Tre University, 00146 Rome, Italy"},{"name":"National Biodiversity Future Center, 90133 Palermo, Italy"},{"name":"Santa Lucia Foundation IRCCS, 00179 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2198-1947","authenticated-orcid":false,"given":"Carla","family":"Fontana","sequence":"additional","affiliation":[{"name":"Microbiology and Biobank Unit, National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1099\/jmm.0.077503-0","article-title":"An outbreak of blaOXA-51-like- and blaOXA-66-positive Acinetobacter baumannii ST208 in the emergency intensive care unit","volume":"63","author":"Asai","year":"2014","journal-title":"J. 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