Distribution of carbapenemase-encoding genes (blaIMP, blaNDM, blaKPC, blaVIM, and blaOXA-48) in carbapenem-resistant Klebsiella pneumoniae from Yemen

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major threat to global public health and substantially limits therapeutic options. Surveillance of carbapenemase resistance determinants is important to guide infection control and antimicrobial stewardship. This study aimed to determine the prevalence and distribution of five carbapenemase-encoding genes ( blaKPC , blaNDM , blaIMP , blaVIM , and blaOXA-48 ) among clinical K. pneumoniae isolates from hospitals in Sana'a, Yemen. A cross-sectional study was conducted in Sana'a, Yemen, from October 2023 to December 2024. A total of 118 non-duplicate carbapenem-resistant K. pneumoniae isolates were recovered from wound, urine, sputum, blood, and pus specimens collected from two private hospitals and the National Center of Public Health Laboratories (NCPHL). Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method. Colistin minimum inhibitory concentrations (MICs) were determined by broth disk elution according to CLSI 2023 guidelines. Carbapenemase production was screened by reduced carbapenem susceptibility and phenotypically confirmed using the combined imipenem/EDTA disk test for metallo-β-lactamases. Genotypic detection of blaKPC , blaNDM , blaIMP , blaVIM , and blaOXA-48 was performed by real-time PCR following DNA extraction by boiling. Data were analyzed using SPSS version 26. Of the 118 isolates, 84 (71.2%) tested positive for at least one carbapenemase-encoding gene. The most prevalent gene was blaOXA-48 (59.3%, n = 70), followed by blaNDM (38.9%, n = 46), blaVIM (33.9%, n = 40), blaIMP (6.8%, n = 8), and blaKPC (1.7%, n = 2). Notably, private hospitals showed a significantly higher positivity rate (77.1%) compared to NCPHL (57.9%) (OR = 2.5, 95% CI: 1.09–5.9, P = 0.03). The highest positivity rates were observed in pus (85.7%) and wound (77.8%) samples. Co-occurrence of multiple genes was frequent: 22 isolates (18.6%) harbored two genes, 24 (20.4%) harbored three genes, and 4 (3.4%) harbored four genes. All isolates were 100% resistant to the β-lactams tested, including meropenem, imipenem, and ceftazidime. High resistance rates were also observed for ciprofloxacin (95.7%) and gentamicin (93.2%). Colistin remained the most active agent, with 97.5% susceptibility. Carbapenemase genes—particularly blaOXA-48 , blaNDM , and blaVIM —are widespread among carbapenem-resistant K. pneumoniae in Sana'a, Yemen, with significantly higher prevalence in private hospitals, and with frequent co-occurrence and extensive multidrug resistance. These findings highlight the need for strengthened antimicrobial stewardship, molecular surveillance in reference laboratories, and enhanced infection control measures.