Molecular characterization of virulence and antibiotic resistance genes in Klebsiella pneumoniae isolated from sputum samples at a tertiary hospital in Ethiopia

Klebsiella pneumoniae, a Gram-negative, encapsulated rod and prominent member of the ESKAPE pathogen group, ranks among the leading causes of bacterial pneumonia worldwide. It has become increasingly problematic due to multidrug resistance (MDR) and the emergence of hypervirulent strains. In Ethiopia, there are growing reports of the increasing prevalence of MDR K. pneumoniae strains. However, molecular data on the resistance mechanisms and virulence determinants among clinical isolates remain limited. This study molecularly identified K. pneumoniae in sputum samples from patients clinically suspected of pneumonia at a tertiary hospital in Ethiopia, and evaluated their antibiotic resistance profiles, as well as molecularly characterized the isolates for key virulence and antimicrobial resistance (AMR) associated genes. A total of 182 sputum samples from pneumonia- suspected patients were collected and processed following standard microbiological procedures for bacterial isolation and antimicrobial sensitivity testing. K. pneumoniae isolates were confirmed by MALDI-TOF and PCR. Antibiotic susceptibility was assessed via the Kirby–Bauer disk diffusion method. Key virulence and AMR associated genes were detected via PCR. Among the 182 sputum samples, 32 K. pneumoniae isolates were identified, 94% of which were MDR. The predominant resistance genes detected included blaCTX-M (40.6%), blaNDM (34.4%), blaSHV (31.3%), and blaTEM (18.8%). Among the virulence genes, fimH was found in 56.3% of the isolates, mrkA in 28.1%, and rmpA in 9.4%. Additionally, the major outer membrane porin gene ompK35 and the mdtK efflux pump gene were detected in 62.6% and 28.1% of the isolates, respectively. This study reveals a high prevalence of MDR K. pneumoniae strains, and emergence of hypervirulent phenotypes posing a significant threat to therapeutic efficacy. The findings highlight complicated resistance mechanisms driven by molecular synergies, underscoring the urgent need for enhanced molecular surveillance, infection control, and antibiotic stewardship in healthcare settings.