Molecular Detection and Characterization of Carbapenemases Among Carbapenem-Resistant Escherichia Coli And Klebsiella Pneumoniae Isolated from Urine

Hussaini I.M.^1*, Suleiman A.B.¹, Olonitola O.S.¹, Oyi R.A.²

Molecular detection of blaOXA and blaNDM carbapenemases in E. coli and K. pneumoniae underscores urgent monitoring of transferable carbapenem resistance, critical for public health.

Abstract

Objective: Carbapenem resistance mediated by carbapenemases poses a significant public health threat due to its transferable nature, unlike other carbapenem resistance mechanisms. This study aimed to molecularly detect and characterize carbapenemases among carbapenem-resistant Escherichia coli and Klebsiella pneumoniae isolated from urine samples. Methods: A total of 123 non-duplicate isolates (70 E. coli and 53 K. pneumoniae) were screened for carbapenem resistance using Clinical Laboratory Standard Institute guidelines. Carbapenem-resistant isolates were further tested for the presence of carbapenemase genes (blaKPC, blaOXA, blaNDM) using PCR. Positive PCR products were sequenced, and sequence similarity was analyzed using nucleotide BLAST. Multiple sequence alignment was performed using ClustalW and BioEdit. Results: Among the 123 isolates screened, 6 (4.88%) were carbapenem-resistant, including 2 (2.86%) E. coli and 4 (7.55%) K. pneumoniae isolates. Carbapenemase genes were detected in five out of the six carbapenem-resistant isolates. The most frequently detected carbapenemase gene was blaOXA (57.14%), followed by blaNDM (42.86%). No blaKPC gene was detected. Co-harboring of blaNDM and blaOXA genes was observed in two isolates. Sequence similarity analysis showed 98–100% identity with carbapenemase genes from GenBank. Nucleotide substitutions were absent in blaNDM gene sequences, while nucleotide substitutions leading to corresponding amino acid changes were observed in blaOXA gene sequences at various positions. Conclusion: Carbapenem resistance in the studied isolates was predominantly mediated by OXA and NDM carbapenemases. These findings underscore the importance of monitoring carbapenemase spread among Gram-negative bacteria to mitigate the emergence and dissemination of carbapenem-resistant strains, which jeopardize the efficacy of carbapenems as last-resort antibiotics.

Keywords: Carbapenem resistance, carbapenemases, Escherichia coli, Klebsiella pneumoniae, PCR detection

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