Integrative Phenotypic and Structural Characterization of Ciprofloxacin Resistance in Clinical Klebsiella pneumoniae: GyrA QRDR Mutations and Predicted Drug–Target Interactions

Original Article

Abstract

Background: Ciprofloxacin resistance in Klebsiella pneumoniae compromises an important therapeutic option for Gram-negative bacterial infections and may arise through alterations in quinolone targets, efflux mechanisms, and plasmid-mediated resistance determinants. This study investigated the phenotypic profile and potential molecular basis of ciprofloxacin resistance in clinical K. Pneumonia isolates using complementary microbiological and computational approaches.

Methods: Five clinical K. pneumoniae isolates recovered from sputum, urine, and wound specimens were subjected to antimicrobial susceptibility testing. Ciprofloxacin-resistant and susceptible isolates were comparatively evaluated for mutations within the quinolone resistance-determining region (QRDR) of GyrA and parC. Detected GyrA substitutions were assessed computationally using I-Mutant for predicted effects on protein stability. Molecular docking with AutoDock Vina was subsequently performed to characterize the interaction of ciprofloxacin with the K. pneumoniae GyrA target.

Results: Three of five isolates (60%) were resistant to ciprofloxacin, with resistance occurring alongside substantial resistance to other antimicrobial classes. QRDR analysis identified GyrA substitutions at positions 83 (Y83I) and 87 (G87N) exclusively among ciprofloxacin-resistant isolates, whereas no corresponding QRDR mutations were detected in susceptible isolates. Both substitutions were predicted to decrease GyrA stability. Ciprofloxacin exhibited a best predicted binding affinity of −6.0 kcal/mol, with docking interactions involving residues within the GyrA binding region.

Conclusion: Ciprofloxacin resistance in these clinical K. pneumoniae isolates was associated with QRDR alterations in GyrA and predicted structural effects on the drug target. These findings support continued phenotypic surveillance and molecular investigation of fluoroquinolone resistance, while larger studies incorporating MIC determination, whole-genome sequencing, and functional validation are warranted