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.

中文翻译：

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在致病性碳青霉烯耐药革兰氏阴性菌中鉴定的碳青霉烯酶变异体的基于结构的功能适合度分析

碳青霉烯酶介导的碳青霉烯耐药性是全球主要的公共卫生问题。在本研究中，使用 PCR 和测序估算了耐碳青霉烯临床分离株中循环碳青霉烯酶的流行率。比较了产生单一碳青霉烯酶的分离株中亚胺培南、美罗培南和厄他培南的抑菌圈 (ZD) 直径。这些碳青霉烯酶的基于结构的功能适应性是通过几项计算机分析预测的。大约 63.76% 的分离株表现出碳青霉烯类耐药性，其中 39.13% 含有碳青霉烯酶，如 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%) 和 blaOXA-104 (1.94%)。Omega 值表明对 blaOXA-69、blaOXA-66 和 blaOXA-104 的选择压力。蛋白质结构动力学预测 NDM-1 和 KPC-2 具有最高和最低的灵活性，表明 β-内酰胺结合和催化效率存在差异。NDM-1 样、OXA-181、OXA-66、OXA-69 和 OXA-104 对自由折叠能的需求增加、溶剂可及性的提高和熔化温度的降低预示着其祖先变体的功能改进。NDM-1 样碳青霉烯酶证明美罗培南的结合稳定性、亲和力和催化作用比 NDM-1 有所改善。预测亚胺培南的催化活性在 OXA-181 中提高，这可能与亚胺培南圆盘周围比美罗培南/厄他培南小 1.5 倍以上的 ZD 相关，在产生 OXA-181 的分离株中。然而，OXA-66 对亚胺培南和美罗培南具有更高的结合稳定性和亲和力。