Rapid detection of carbapenem resistance in Klebsiella pneumoniae clinical isolates: Flow cytometry as an alternative to multiplex PCR.

BACKGROUND

Klebsiella pneumoniae is a leading cause of diverse infections, making rapid diagnosis and effective treatment critical to reducing adverse outcomes. Carbapenems, the most potent beta-lactam antibiotics, are widely used due to their broad-spectrum activity. However, the rise and spread of carbapenem-resistant strains pose a significant global health threat. We aimed to compare the sensitivity and specificity of flow cytometry versus multiplex PCR for detecting carbapenemase classes A, B, and D in clinical isolates of K. pneumoniae.

METHODS

A total of 671 clinical samples were collected from two hospitals in Shiraz, Iran, from which 100 K. pneumoniae were identified using biochemical and molecular methods. Carbapenemase production was phenotypically confirmed by the modified Carbapenem Inactivation Method (mCIM), while multiplex PCR assays determined the genotypic profile. Additionally, flow cytometry was used as a rapid diagnostic tool for detecting carbapenem-resistant strains.

RESULTS

Molecular analysis identified carbapenemase genes in the isolates as follows: blaIMI/IMP (91%), blaOXA-48 (19%), blaKPC (11%), and blaNDM (2%). Flow cytometry demonstrated high sensitivity for detecting blaKPC (91.67%), class B carbapenemases (100%), and class D carbapenemases (86.4%), with specificities of 97.8%, 86.7%, and 75%, respectively.

CONCLUSIONS

This study validates the role of flow cytometry in rapidly identifying carbapenemase-producing K. pneumoniae, with high sensitivity (86.7-100%) but class-specific specificity (75-97.8%). Given the high prevalence of blaIMI/IMP (91%), the need for rapid diagnostics, flow cytometry with perfect specificity (100%) and moderate sensitivity (53.4%), can serve as a first line practical screening tool alongside PCR, aiding in the containment of carbapenem resistance.