The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination

Abstract

Plasmids are important members of the bacterial mobile gene pool, and are among the most important contributors to horizontal gene transfer between bacteria. They typically harbour a wide spectrum of host beneficial traits, such as antibiotic resistance, inserted into their backbones. Although these inserted elements have drawn considerable interest, evolutionary information about the plasmid backbones, which encode plasmid related traits, is sparse. Here we analyse 25 complete backbone genomes from the broad-host-range IncP-1 plasmid family. Phylogenetic analysis reveals seven clades, in which two plasmids that we isolated from a marine biofilm represent a novel clade. We also found that homologous recombination is a prominent feature of the plasmid backbone evolution. Analysis of genomic signatures indicates that the plasmids have adapted to different host bacterial species. Globally circulating IncP-1 plasmids hence contain mosaic structures of segments derived from several parental plasmids that have evolved in, and adapted to, different, phylogenetically very distant host bacterial species.

The Challenge of Efflux-Mediated Antibiotic Resistance in Gram-Negative Bacteria

“…Li, unpublished data]) into two conjugative broadhost-range plasmids from a marine microbial biofilm (721). Initially isolated as mercury resistance plasmids from marine samples collected in 1993 (722) and maintained in Pseudomonas putida, these two plasmids from an unknown host are largely identical and evolved through homologous recombination, and each plasmid contains transposons and various gene clusters (trb for mating pair function, tra for conjugative gene transfer, mer for mercury resistance, and mexEF-oprN-like genes for the RND pump) (Table 4) (721,723). When tested for susceptibility to chloramphenicol, nalidixic acid, and trimethoprim, an E. coli isolate carrying one of these two plasmids did not show altered drug susceptibility.…”

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

“…This suggests that these plasmids are not maintained long enough outside of this phylum to be significantly affected by non-Proteobacterial genomes. Long-term evolutionary adaptation of the plasmid backbone to the new host, as known for IncP plasmids (Norberg et al, 2011), might therefore also not take place. Poor maintenance of these plasmids in non-proteobacterial hosts is the likely bottleneck explaining the difference between the very wide realized transfer range and the narrower evolutionary range.…”

The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICE clc Controls both a Putative Efflux System and Initiation of ICE Transfer

“…Many of the known efflux systems play a role in antibiotic resistance; therefore, their distribution and propagation in clinically relevant strains pose a major health concern (3). Although mostly located on the bacterial chromosome (1), genes for efflux systems can be transmitted via mobile genetic elements like plasmids or integrative and conjugative elements (ICE) (4)(5)(6). Recently, we described a class of widespread ICE among beta-and gammaproteobacteria, which, through a region permissive for gene insertions, can carry a wide range of auxiliary gene functions (7)(8)(9).…”