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.
- 1Department of Bioinformatics, Pondicherry University, Puducherry, India.
- 2Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), León, Mexico.
- 3Biotechnology Department, Dayananda Sagar College of Engineering, Dr. C.D Sagar Centre for Life Sciences, Dayananda Sagar Institutions, Bengaluru, India.
Abstract
Urinary tract infections are a major global health concern, with Klebsiella pneumoniae emerging as a prominent multidrug-resistant uropathogen. The increasing prevalence of extended-spectrum β-lactamase-producing strains has reduced the effectiveness of β-lactam antibiotics. In this study, 87 clinical K. pneumoniae isolates from India were analysed using whole-genome sequencing, 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⁻¹ for blaSHV and -1.849 kcal mol⁻¹ 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.
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BibTeX
@article{nk2026genomic,
title = {{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.}},
author = {Liyana Nk and Tusar Mondal and Tobika R and Kumar Km and Yalpi Karthik and Ramakrishna D and Manoj-Kumar Arthikala},
journal = {Access microbiology},
year = {2026},
month = oct,
doi = {10.1099/acmi.0.001200.v3},
url = {https://europepmc.org/article/MED/42903812},
note = {CC BY},
}
RIS
TY - JOUR
TI - 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.
AU - Liyana Nk
AU - Tusar Mondal
AU - Tobika R
AU - Kumar Km
AU - Yalpi Karthik
AU - Ramakrishna D
AU - Manoj-Kumar Arthikala
PY - 2026
DA - 2026/10/20
JO - Access microbiology
DO - 10.1099/acmi.0.001200.v3
UR - https://europepmc.org/article/MED/42903812
AB - Urinary tract infections are a major global health concern, with Klebsiella pneumoniae emerging as a prominent multidrug-resistant uropathogen. The increasing prevalence of extended-spectrum β-lactamase-producing strains has reduced the effectiveness of β-lactam antibiotics. In this study, 87 clinical K. pneumoniae isolates from India were analysed using whole-genome sequencing, 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⁻¹ for blaSHV and -1.849 kcal mol⁻¹ 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.
SN - 2516-8290
ER -