Epidemiological and Genetic Features of Plasmids Carrying blaNDM Genes: An In Silico Analysis with Emphasis on Replicon Types, and Resistome

Background: New Delhi metallo-β-lactamase (NDM) is a metallo-β-lactamase that has been disseminated worldwide. Plasmids harboring the blaNDM gene belonged to many incompatibility groups, of which IncX3, IncF, and IncA/C were the most represented. This in silico study aimed at analyzing a set of 649 plasmids carrying NDM-type carbapenemase (pNDMs) previously assigned in GenBank. Materials and Methods: The selected plasmids were analyzed by ResFinder (antibiotic resistome identification), BacMet (metal/biocides resistome identification), PlasmidFinder/PLSDB (replicon typing), TAfinder (toxin-antitoxin system [TAS] identification), and OriTfinder (prediction of the transferability). Results: We found that Escherichia coli and Klebsiella pneumoniae amounted to about 68.6% of all reported species. The distribution of these plasmids by samples showed a diversity of origins. Many plasmids carried different genes encoding resistance to antibiotics, heavy metals, and biocides with different frequencies. The TAfinder allowed the identification of a TAS in 292 plasmids (45%). Twenty-four different incompatibility groups were predicted, of which IncX3 (34.2%; n = 222), IncC (10.9%, n = 71), and IncFII (9.9%, n = 64) were the most often described. Besides, 23.6% (n = 151) of pNDMs were recognized as multireplicon plasmids. Conclusion: This study has shown the importance of plasmids in the dissemination of the NDM carbapenemase and raises the importance of monitoring these elements to better understand the evolution of the antibiotic resistance threat.