{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T05:22:08Z","timestamp":1788326528921,"version":"build-2803163510"},"reference-count":80,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Higher Education, Research and Innovation","award":["RCGRG-MEDMICR\/21\/01"],"award-info":[{"award-number":["RCGRG-MEDMICR\/21\/01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) increasingly combines high-risk clonal expansion, mobile resistance platforms and limited treatment options. We investigated the genomic epidemiology, resistance and virulence architecture, plasmid backbones, and therapeutic vulnerabilities of CRKP circulating in Oman. Methods: Between 2021 and 2024, 135 non-duplicate CRKP isolates were recovered from diverse clinical specimens. New antimicrobial agents were evaluated phenotypically, while 38 representative extensively drug-resistant (XDR)\/pan-drug resistant (PDR) isolates underwent whole-genome sequencing (WGS) for multilocus sequence typing (MLST), capsular typing, resistome, virulome, plasmid and mobile genetic elements (MGEs) analysis. In vitro synergy of ceftazidime\u2013avibactam\/aztreonam, meropenem\/fosfomycin and amikacin\/fosfomycin was assessed using gradient diffusion-based FICI. Results: WGS revealed a striking shift towards OXA-232-producing ST-2096, which dominated the sequenced collection and carried KL64 with a conserved multidrug-resistant backbone. NDM-5\/ST147 and NDM-1 + KPC-2\/ST11 formed distinct high-risk lineages with broader extended-spectrum \u03b2-lactamase (ESBL) repertoires, greater plasmid heterogeneity and, in co-producers, the highest MGE burden. Across isolates, resistance was reinforced by widespread blaCTX-M variants, armA, aac(6\u2032)-Ib-cr, fosA, porin alterations and fluoroquinolone-resistance mutations, while core virulence and fitness loci including fimH, mrkA, iutA, fyuA and irp2 were widely retained. Cefiderocol showed the most consistent in vitro activity across carbapenemase groups, and eravacycline remained active, whereas plazomicin and fosfomycin activity was compromised by methyltransferase and fos genes. Ceftazidime\u2013avibactam\/aztreonam demonstrated universal synergy, while meropenem\/fosfomycin and amikacin\/fosfomycin showed limited, carbapenemase-dependent activity. Conclusions: CRKP in Oman is characterised by convergent clonal expansion, plasmid-mediated resistance, retained virulence potential and narrowing therapeutic options. Integrated genomic surveillance with carbapenemase-directed susceptibility and synergy testing is essential to guide precision antimicrobial stewardship in high-risk healthcare settings and inform early infection prevention responses to emerging regional CRKP lineages.<\/jats:p>","DOI":"10.3390\/antibiotics15090844","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T10:32:18Z","timestamp":1788258738000},"page":"844","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Evolving Clonal, Plasmid-Mediated Resistome, Virulome and Therapeutic Landscape of Carbapenem-Resistant Klebsiella pneumoniae in Oman"],"prefix":"10.3390","volume":"15","author":[{"given":"Arwa","family":"Al Rujaibi","sequence":"first","affiliation":[{"name":"Fisheries Water Resources, Central Laboratory of Animal Health, Ministry of Agriculture, Saal, P.O. Box 467, Muscat 100, Oman"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0000-3781","authenticated-orcid":false,"given":"Zaaima Al","family":"Jabri","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6275-5866","authenticated-orcid":false,"given":"Azza Mohammed","family":"Al Mamari","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6813-7896","authenticated-orcid":false,"given":"Amira","family":"ElBaradei","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8776-2327","authenticated-orcid":false,"given":"Hafidha","family":"Al-Hattali","sequence":"additional","affiliation":[{"name":"Department of Biomedical Science, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9887-4125","authenticated-orcid":false,"given":"Faiza","family":"Syed","sequence":"additional","affiliation":[{"name":"DASH to Protect Antibiotics, Muscat 111, Oman"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6373-3354","authenticated-orcid":false,"given":"Zakariya","family":"Al Muharrmi","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Sultan Qaboos University Hospital and University Medical City, Muscat 112, Oman"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6314-6849","authenticated-orcid":false,"given":"Amina","family":"Al-Jardani","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratories, Center for Disease Control and Prevention, Ministry of Health, Muscat 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8769-947X","authenticated-orcid":false,"given":"Meher","family":"Rizvi","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (2024). 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