Abstract
Carbapenemase-mediated carbapenem resistance is a major public health concerns worldwide. In the present study, prevalence of circulating carbapenemases was estimated among carbapenem-resistant clinical isolates using PCR and sequencing. Diameters of zone of inhibition (ZDs) were compared for imipenem, meropenem and ertapenem among single carbapenemase producing isolates. Structure-based functional fitness of those carbapenemases was predicted through several in silico analyses. Approximately, 63.76% isolates demonstrated carbapenem resistance, of which 39.13% harboured carbapenemases like blaNDM-1 (33.23%), blaNDM-1-like (0.31%), blaVIM-2 (4.35%), blaKPC-2 (4.04%), blaOXA-181 (6.85%), blaOXA-23 (16.50%), blaOXA-69 (3.88%), blaOXA-66 (2.91%) and blaOXA-104 (1.94%). Omega values indicated selection pressure over blaOXA-69, blaOXA-66 and blaOXA-104. Protein structural dynamics predicted NDM-1 and KPC-2 to have the highest and least flexibility, indicating differences in β-lactam binding and catalytic efficiency. Increased requirement of free folding energy, improved solvent accessibility and decreased melting temperatures among NDM-1-like, OXA-181, OXA-66, OXA-69 and OXA-104 predicted functional improvement over their ancestral variants. NDM-1-like carbapenemases demonstrated improvement in binding stability, affinity and catalysis of meropenem than that of NDM-1. Catalytic activity of imipenem was predicted to improve among OXA-181, which could be correlated with more than 1.5 folds smaller ZDs around imipenem disc, than that of meropenem/ertapenem, among OXA-181 producing isolates. However, OXA-66 indicated greater binding stability and affinity for imipenem and meropenem. This study indicated structural/functional convergence as well as divergence among several carbapenemase variants and provided useful insights into carbapenemase-mediated carbapenem resistance that might help in identifying appropriate treatment regimen for bacterial infections.
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Acknowledgements
Authors are extremely grateful to Director, Calcutta School of Tropical Medicine, India for support, constant inspiration and providing necessary facilities for the study.
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Authors gratefully acknowledge Indian Council of Medical Research for providing financial support to the first author [no. 3/1/3/WL/JRF-2011/HRD-129 (41937)].
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AP and AT conceived and designed research. They analyzed data. IB provided clinical isolates. AP conducted experiments and wrote the manuscript. AT proof read the manuscript. All authors read and approved the manuscript.
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All the isolates used in this study were collected following guidelines of Institutional Clinical Research Ethics Committee (Ref. No. CREC-STM/260 dated 9/1/2013).
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Pal, A., Bhattacharyya, I. & Tripathi, A. Structure-based functional fitness analyses of carbapenemase variants identified among pathogenic carbapenem-resistant Gram-negative bacteria. World J Microbiol Biotechnol 36, 129 (2020). https://doi.org/10.1007/s11274-020-02905-3
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DOI: https://doi.org/10.1007/s11274-020-02905-3