{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:10:55Z","timestamp":1792789855801,"version":"4.5.0"},"reference-count":76,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T00:00:00Z","timestamp":1761177600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Project funded under the National Recovery and Resilience Plan","award":["PE00000007"],"award-info":[{"award-number":["PE00000007"]}]},{"name":"One Health Basic and Translational Research Actions addressing Unmet Needs on Emerging Infectious Diseases","award":["B83C22004750006"],"award-info":[{"award-number":["B83C22004750006"]}]},{"name":"dall\u2019Unione europea","award":["PE0000013-FAIR"],"award-info":[{"award-number":["PE0000013-FAIR"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen that poses critical challenges in hospital settings due to its environmental resilience and high resistance to antibiotics. Genomic surveillance has become essential for identifying transmission patterns, guiding antimicrobial stewardship, and informing infection control policies. We conducted whole-genome sequencing on 44 A. baumannii isolates collected between 2022 and 2023 from diverse wards in an Italian hospital. Illumina-based sequencing was followed by a comprehensive bioinformatics pipeline, including genome assembly, taxonomic validation, MLST, SNP-based phylogeny, pan-genome analysis, antimicrobial resistance (AMR) gene profiling, and virulence factor prediction. Most isolates were classified as ST2; SAMPLE-34 was ST1 and genetically distinct. Phylogenetic analysis revealed four clonal clusters with cluster-specific AMR and accessory gene content. The pan-genome included 5050 genes, with notable variation linked to hospital ward origin. ICU and internal medicine strains carried higher loads of AMR genes, especially against aminoglycosides, \u03b2-lactams, and quinolones. Virulence profiling highlighted widespread immune evasion mechanisms; \u201cAcenovactin\u201d was predominant, while some isolates lacked key adhesion or toxin factors. Our findings underscore the clinical relevance of integrating genomic epidemiology into routine hospital surveillance. Identifying clonal clusters and resistance signatures supports real-time outbreak detection, risk stratification, and targeted infection prevention strategies.<\/jats:p>","DOI":"10.3390\/microorganisms13112429","type":"journal-article","created":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T00:47:36Z","timestamp":1761266856000},"page":"2429","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Genomic Surveillance and Resistance Profiling of Multidrug-Resistant Acinetobacter baumannii Clinical Isolates: Clonal Diversity and Virulence Insights"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0886-1126","authenticated-orcid":false,"given":"Maria Vittoria","family":"Ristori","sequence":"first","affiliation":[{"name":"Research Unit of Clinical Laboratory Science, Department of Medicine and Surgery, Universit\u00e0 Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy"},{"name":"Operative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Al-varo del Portillo, 200, 00128 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-0929-1452","authenticated-orcid":false,"given":"Ilaria","family":"Pirona","sequence":"additional","affiliation":[{"name":"GenomeUp SRL, 00144 Rome, Italy"},{"name":"Istituto Di Patologia Speciale Medica, Catholic University of the Sacred Heart, 00168 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"De Florio","sequence":"additional","affiliation":[{"name":"Research Unit of Clinical Laboratory Science, Department of Medicine and Surgery, Universit\u00e0 Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-9280-3293","authenticated-orcid":false,"given":"Sara Elsa","family":"Aita","sequence":"additional","affiliation":[{"name":"Operative Research Unit of General Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriele","family":"Macari","sequence":"additional","affiliation":[{"name":"GenomeUp SRL, 00144 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8799-4997","authenticated-orcid":false,"given":"Silvia","family":"Spoto","sequence":"additional","affiliation":[{"name":"Diagnostic and Therapeutic Medicine Department, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raffaele","family":"Antonelli Incalzi","sequence":"additional","affiliation":[{"name":"Operative Research Unit of Internal Medicine, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy"},{"name":"Research Unit of Internal Medicine, Department of Medicine and Surgery, Universit\u00e0 Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Angeletti","sequence":"additional","affiliation":[{"name":"Research Unit of Clinical Laboratory Science, Department of Medicine and Surgery, Universit\u00e0 Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy"},{"name":"Operative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Al-varo del Portillo, 200, 00128 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.2147\/IDR.S166750","article-title":"Insight into Acinetobacter baumannii: Pathogenesis, Global Resistance, Mechanisms of Resistance, Treatment Options, and Alternative Modalities","volume":"11","author":"Asif","year":"2018","journal-title":"Infect. 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