Genomic Analysis and Antimicrobial Resistance Profiling of Klebsiella pneumoniae Clinical Isolates from Urinary Tract Infections in India: Prevalence of Class A β-lactamase with Molecular Docking and Simulation Insights

Urinary tract infections (UTIs) are a major global health concern, with Klebsiella pneumoniae emerging as a prominent multidrug-resistant uropathogen. The increasing prevalence of extended-spectrum β-lactamase (ESBL)–producing strains has reduced the effectiveness of β-lactam antibiotics. In this study, 87 clinical K. pneumoniae isolates from India were analyzed using whole-genome sequencing, multilocus sequence typing (MLST), and antimicrobial resistance profiling. β-lactam resistance was the dominant phenotype, with blaSHV and blaCTX-M identified as the most prevalent class A β-lactamase genes. Molecular docking and 100-ns molecular dynamics simulations were conducted to examine enzyme–antibiotic interactions. Meropenem exhibited the lowest binding affinity with both proteins (−2.695 kcal/mol for blaSHV and −1.849 kcal/mol for blaCTX-M), forming unstable complexes, particularly with blaCTX-M. These findings highlight the growing challenge of β-lactam resistance and emphasize the need for genomic surveillance and alternative therapeutic strategies against multidrug-resistant K. pneumoniae.