Molecular Detection and Analysis of Carbapenemase Encoding Genes (NDM & OXA-48) in Clinical Strains of Klebsiella pneumoniae Isolated from Urine Samples

Abstract

Carbapenem resistance among uropathogens is a growing public health concern due to the spread of carbapenemase genes such as blaNDM and blaOXA-48, which reduce the effectiveness of last-line β-lactam antibiotics. This study investigated the presence of these genes in bacteria isolated from urine samples of patients with suspected urinary tract infections (UTIs), with initial attention to presumptive Klebsiella pneumoniae isolates. Thirty urine samples were examined using physical, chemical, microscopic, cultural, biochemical, and molecular methods. Culture on Blood agar, MacConkey agar, CLED agar, and CHROM agar revealed diverse uropathogens. Escherichia coli was the predominant organism (61.12%), followed by Citrobacter spp., while only a few isolates appeared to be Klebsiella pneumoniae on chromogenic media. Biochemical testing confirmed just one isolate as K. pneumoniae, which was fully sensitive to carbapenems (imipenem, meropenem, doripenem). Genomic DNA from selected isolates was analyzed by End-Point PCR and Real-Time PCR targeting blaNDM and blaOXA-48. The blaNDM gene was detected in two pediatric samples, and blaOXA-48 in one of these. Importantly, these gene-positive isolates were not confirmed as K. pneumoniae, indicating the presence of carbapenemase genes in non-Klebsiella uropathogens. The findings demonstrate silent circulation of carbapenemase genes in urinary bacteria without phenotypic carbapenem resistance. Such isolates may act as hidden reservoirs for resistance transfer under antibiotic pressure. This study underscores the need for molecular surveillance alongside routine susceptibility testing to identify early dissemination of antimicrobial resistance in clinical settings.