Structure-based functional fitness analyses of carbapenemase variants identified among pathogenic carbapenem-resistant Gram-negative bacteria

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 bla_NDM-1 (33.23%), bla_NDM-1-like (0.31%), bla_VIM-2 (4.35%), bla_KPC-2 (4.04%), bla_OXA-181 (6.85%), bla_OXA-23 (16.50%), bla_OXA-69 (3.88%), bla_OXA-66 (2.91%) and bla_OXA-104 (1.94%). Omega values indicated selection pressure over bla_OXA-69, bla_OXA-66 and bla_OXA-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.