Partition locus-based classification of selected plasmids in Klebsiella pneumoniae, Escherichia coli and Salmonella enterica spp.: An additional tool

Abstract

International audienceThe dissemination of antimicrobial resistance genes in Enterobacteriaceae has been largely attributed to plasmids, circular DNA molecules capable of autonomous replication. Whereas high-copy-number plasmids primarily rely on passive diffusion for plasmid maintenance, low-copy-number plasmids utilize so-called partition (par) systems. Plasmid partition relies on three structures, i.e. a centromere like DNA site, a centromere-binding protein and an ATPase or a GTPase motor protein for plasmid positioning. Identification and classification of plasmids is essential for tracing plasmids conferring drug resistance. PCR-based replicon typing is currently the standard method for plasmid identification but there are new classification schemes, especially the relaxase gene typing (PRaseT). Here we developed a multiplex PCR set targeting par loci found on the plasmids most frequently encountered in Enterobacteriaceae. This method, called “plasmid partition gene typing” (PAR-T), was validated with 136 transconjugants or transformants harboring various replicon types. The method was tested with 30 multidrug-resistant clinical isolates including Escherichia coli, Klebsiella pneumoniae and Salmonella enterica subsp. enterica carrying 1-4 replicons; all replicons were tested in parallel with PRaseT for comparison. Six multiplex PCRs and one simplex PCR including 18 pairs of primers recognized plasmids of groups IncA/C, FIA, FIB, FIC, FIIk, FII, HI1, HI2, I1, L/M, N, X. Our set of multiplex PCRs showed high specificity for the classification of resistance plasmids except for IncX replicons

Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner

“…Given the pleitropic role of these activators, this mode of regulation directly pairs the expression of DNA segregation functions to expression of conjugative transfer functions. However, although IncA/C plasmids retain a type II parMRC -like partitioning system (actin-type ATPase), they also carry a type I parABC -like partitioning system (Walker-type ATPase) ( vcrx031 / vcrx032 in pVCR94), which does not seem to be regulated by AcaCD [ 48 , 82 , 84 , 85 ]. The exact function and eventual redundancy of each par locus remains to be investigated for IncA/C plasmids.…”

Mobile Genetic Elements Associated with Antimicrobial Resistance

“…PlasmidFinder uses a database of amplicon sequences from PBRT and additional variants (170) and is a useful starting point for identifying plasmid types in whole-genome sequences. PCR methods for detecting different partitioning systems (179) or TA systems (180) are also available.…”

Characterization and Bio-Typing of Multidrug Resistance Plasmids From Uropathogenic Escherichia coli Isolated From Clinical Setting

“…However, due to insufficient data on the various incompatibility types from E. coli, the in silico analysis was extended to some plasmids of other Enterobactereace family. For the seven Inc groups of plasmids incident in this study pili and pili associated genes involved in conjugation event was used as template for nucleotide-Search 2 to identify candidate genes which were specific for individual incompatibility types (Bousquet et al, 2015). The target genes were further validated by blastN (see footnote 2) and ClustalW2 software 3 .…”