Molecular epidemiology of carbapenem-resistance plasmids using publicly available sequences

Abstract

Carbapenem-resistant bacteria have quickly become a worldwide concern in nosocomial infections. Of the seven known carbapenemases, four have been shown to be particularly problematic: KPC, NDM, IMP, and VIM. To date, many local and species- or carbapenemase-specific epidemiological studies have been performed, which often focus on the organism itself. This report attempts to perform an inclusive (encompass both species and carbapenemase) epidemiologic study using publicly available plasmid sequences from NCBI. In this report, the gene content of these various plasmids has been characterized, replicon types of the plasmids identified, and the global spread and species promiscuity of the plasmids analyzed. Additionally, support to several groups targeting plasmid maintenance and transfer mechanisms to slow the spread of resistance plasmids is given.

Keywords: Enterobacteriaceae; antibiotic resistance; carbapenemase; carbapénémase; distribution mondiale; global distribution; plasmid; plasmide; résistance aux antimicrobiens.

Fig. 1.

Relative abundance of incompatibility groups among plasmids. Predominant incompatibility groups from each carbapenemase family: KPC, IncFIB (15.8%), IncN (15.8%), and multi-replicon (17.3%); NDM, IncA/C2 (15.1%), IncFII (25.3%), IncX3 (28.3%), and multi-replicon (11.4%); IMP, IncA/C2 (22.4%), IncN (32.7%), and NA (8/49 16.3%); VIM, IncA/C2 (16.1%), IncN (13.8%), IncR (10.3%), and NA (37.9%).

Fig. 2.

Relative abundance of incompatibility groups among bacterial species. Enterobacter cloacae, Serratia marcescens, and Enterobacter aerogenes prefer FII plasmids (30.3%, 50%, and 42.9%, respectively); Escherichia coli prefer X3 plasmids (26.8%); and FIB and multi-replicon plasmids predominate in Klebsiella pneumoniae (15.3% and 17.9%, respectively). Most plasmids from Pseudomonas aeruginosa could not be typed from the PlasmidFinder database (50%).

Fig. 3.

Indiscrete plasmid groups. Cladogram showing the nucleotide relationships between plasmids that have >98% query coverage and identity. The geographic distribution of these plasmids in the three largest groups has been identified by colored dots. Blue text, KPC-carrying plasmid; green, NDM; red, IMP; black, VIM.