Novel IncX5 Plasmid in Environmental Enterobacter asburiae

Sunday, February 14, 2016
Amara Thind, University of California, Irvine, Chino Hills, CA
High horizontal gene flow allows bacteria to have a relatively conserved species-specific core genome and a large fluid pan-genome. Plasmids are key vectors responsible for horizontal gene transfer and the dissemination of antibiotic resistance and virulence genes. Thus, understanding plasmid mobility and classification is principal in understanding the origin and evolution of these bacterial traits, which can cause human illnesses. The objective of our study was to elucidate the genetic composition of plasmids from environmental bacteria and compare them with those that carry antibiotic resistant genes from clinical settings. We hypothesized that bacteria from aquatic environments would carry plasmids similar to those found in clinical settings but lacking antibiotic resistance genes. An Enterobacter asburiae isolate (SW0867R) was collected from a lake in Southern California. A plasmid was isolated with a Qiagen kit and sequenced using the Illumina platform. De novo assembly was done in Geneious, annotated with RAST, similar plasmids were retrieved with BLAST from NCBI GenBank, and comparative genome alignment was done using Mauve. The size of the plasmid was 32,917 bp. We discovered that the plasmid belongs to a new incompatibility group IncX5, harboring 45 predicted ORF. This plasmid is strikingly similar to the structure of blaKPC-5 -harboring plasmid pBK31567 from Klebsiella pneumoniae obtained from a hospital in New Jersey provided by NCBI. These IncX5 plasmids have a set of core genes in the following order: pir-bis (replication initiation)-par (partitioning)–hns (transcription regulation)-topB (DNA replication)-virB (DNA transfer)-actX (transcription regulation)-taxCA (DNA transfer and replication). Both plasmids contain 99% similar relaxase (the protein used to classify plasmid incompatibility type) genes and encode type IV secretion system (T4SS) enabling their own conjugative transfer. 31 genes show >91% sequence similarity in shared genes with pBK31567. Both plasmids harbor taxA, taxB, taxC, actX, virB1-11, topB, hha, hns, parA, ddp3, replication initiation protein encoding gene, and DNAJ molecular chaperone encoding gene. Our plasmid, however, possesses zinc metalloproteinase and no antibiotic resistance genes while the clinical plasmid contains a large acquired region containing blaKPC-5 - harboring Tn4401 element and a class I integron. Phylogenetic analysis based on the relaxase gene of the plasmids suggests that the two plasmids may have originated from a common ancestor. Possession of T4SS makes the IncX5 plasmid highly conjugative ensuring the ability to spread from one bacterium to another. Selective pressure in clinical settings may account for the acquisition of antibiotic resistant genes located outside of the core gene region on the plasmid.