Background: The alarming increase in carbapenemase-producing Enterobacterales is a matter of grave public health concern. The most ubiquitous carbapenemases, Klebsiella pneumoniae carbapenemase (KPC)-, New Delhi metallo-β-lactamase (NDM)-, and oxacillinase (OXA-48)-like enzymes, belong to the Ambler molecular classes A, B, and D, respectively. KPC- and OXA-48-like enzymes have a serine-based hydrolytic mechanism, while NDMs are metallo-β-lactamases that contain zinc in the active site. For the judicious use of reserve drugs and promoting antimicrobial stewardship, timely detection of carbapenemases is essential. While molecular tools are the gold standard for the detection of these enzymes, many laboratories have limited access to them. This study focused on evaluating in-house tools and commercial phenotypic tests for the detection of OXA-48-, KPC-, and NDM-like enzymes in K. pneumoniae, the predominant extremely drug-resistant pathogen in Oman. Methods: In total, 80 GeneXpert/PCR-confirmed (40 OXA-48 and 20 KPC and NDM each) and 37 whole-genome-sequenced (25 OXA-232 and 6 KPC-2, plus NDM-1 and NDM-5) K. pneumoniae were subjected to screening by temocillin (30 μg disk) (MAST Diagnostica, Germany) and D71C (MASTDISCS^®). Isolates resistant to temocillin (<11 mm) and D71C were subjected to four tests: an in-house tool (OXA-48 disk test) and three commercial phenotypic tests: (i) the MASTDISCS^® Combi (D72C) (MAST Group Ltd., Bootle, UK); (ii) the MASTDISCS^® Combi (D73C) (MAST Group Ltd., UK); and (iii) an immunochromatographic assay (ICT), which is the KPC/IMP/NDM/VIM/OXA-48 Combo test kit (Medomics, China), for the detection of OXA-48-, KPC-, and NDM-like carbapenemases. Results: Temocillin exhibited good sensitivity and specificity (100% and 97.50%) compared to D71C (70% and 100%). Among the confirmatory tests, the in-house OXA-48 disk test had 92.50% sensitivity and 100% specificity, while the commercial MAST DISC tests D72C, D73C, and ICT had 97.50%, 95.00%, and 100% sensitivity and 100%, 91.67%, and 95% specificity, respectively. Conclusions: The temocillin disk test is a good screening tool. With high sensitivity and specificity, ease of performance, short turnaround time, and low cost, we recommend the ICT format for routine diagnostic use. In resource-constrained centers, the OXA-48 disk test is an excellent alternative with high sensitivity and specificity.

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 XDR/PDR isolates underwent WGS for MLST, capsular typing, resistome, virulome, plasmid and MGE analysis. In-vitro synergy of ceftazidime-avibactam/aztreonam, meropenem/fosfomycin and amikacin/fosfomycin was assessed using E-test-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 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')-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-avibactam/aztreonam demonstrated universal synergy, while meropenem/fosfomycin and amikacin/fosfomycin showed limited, carbapenemase-dependent activity. Conclusion: CRKP in Oman is characterized 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.

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–avibactam/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 β-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′)-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–avibactam/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.