Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats

Abstract

Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection. Comparative genomic analysis showed that many of them had conserved backbones. Plasmid coding sequences corresponding to plasmid specific functions were bioinformatically and functionally analyzed. Replication initiation protein analysis revealed the predominance of the Rep_3 superfamily. The phylogenetic tree constructed from all Acinetobacter Rep_3 superfamily plasmids showed 16 intermingled clades originating from nosocomial and environmental habitats. Phylogenetic analysis of relaxase proteins revealed the presence of a new sub-clade named MOBQAci, composed exclusively of Acinetobacter relaxases. Functional analysis of proteins belonging to this group showed that they behaved differently when mobilized using helper plasmids belonging to different incompatibility groups.

The plasmid diversity ofAcinetobacter bereziniaeHPC229 provides clues on the ability of the species to thrive on both clinical and environmental habitats

“…It shows an oriV-repB replication region, with an encoded RepB replication initiator protein of the Rep_3 superfamily (pfam01051 conserved domain) displaying complete amino acid identity with their homologs encoded in A. ursingii UMB1319 and in A. nosocomialis 2010S01-197 (WP_043972782.1; S2 Table). pAbe229-114 was assigned to the Acinetobacter AR3G4 plasmid group, following the classification of Acinetobacter plasmids based on Rep_3 proteins recently proposed [30] (S3 Table). The oriV region, which is located 549 bp upstream of the repB start codon, contains six imperfect direct repeats of 22 bp each (Table 1, Fig 1) likely corresponding to iteron sequences playing roles during the initiation of replication and plasmid copy number control [47].…”

“…A. bereziniae plasmids bearing rep replication initiator protein (Rep) genes were classified following the scheme recently proposed by Salto et al [30] for Acinetobacter plasmids. First, a search for known plasmid Rep domains as judged by the NCBI conserved domain database [44] was conducted among the A. bereziniae plasmid sequences reported in this work and those retrieved from A. bereziniae genomes available in the GenBank public database.…”

“…First, a search for known plasmid Rep domains as judged by the NCBI conserved domain database [44] was conducted among the A. bereziniae plasmid sequences reported in this work and those retrieved from A. bereziniae genomes available in the GenBank public database. Putative Rep candidates were then used as queries for a BlastP search against a local protein database that included all the Rep sequences reported by Salto et al [30], and subsequently assigned to the corresponding Acinetobacter AR3G groups following the criterium described by these authors.…”

“…A. bereziniae plasmids bearing relaxase genes were classified following the scheme of MOB classification in families and subfamilies essentially following described procedures [30]. First, a local database that included all the MOB proteins used for the classification of Acinetobacter relaxases into MOB groups and subgroups was constructed [30]. Then, a search for proteins encoded in A. bereziniae genomic sequences available in the GenBank database with conjugation and/or mobilization functions was performed.…”

“…Contrary to the acquired resistance plasmids mentioned above, the available information on the natural plasmids circulating among the population of this species and which may also contribute to the adaptation to different habitats is rather limited. This general lack of information on the A. bereziniae intrinsic plasmid repertoire reflects the case of most other species of the genus except for A. baumannii [29,30].…”