Comparative genomics of IncP-1ε plasmids from water environments reveals diverse and unique accessory genetic elements

The goal of this study was to determine and compare the complete genome sequences of three new broad-host-range conjugative plasmids. Plasmids pMLUA1, pMLUA3 and pMLUA4 were previously recovered from estuarine water by exogenous plasmid isolation and ranged in size from similar to 55 to 59 kb. Comparative genomics showed that their backbone region was identical to the prototype pKJK5 and other IncP1-epsilon plasmids captured from soils. The accessory region was inserted between the tra region and parA, and presented the typical IncP-1 epsilon ISPa17 and Tn402-like transposon modules. Nevertheless, new class 1 integrons were identified (In794, carrying aadA5 and In795, carrying qacF5-aadA5), as well as a composite transposon IS26-msr(E)-mph(E)-IS26 carrying genes that confer resistance to macrolides. A new insertion sequence, termed ISUnCu17, was also identified on pMLUA3. The architecture of the accessory regions implies the occurrence of multiple insertions and deletions. These data support the notion that IncP-1 plasmids from the e subgroup are proficient in the capture of diverse genetic elements, including antibiotic resistance genes, and thus may contribute to the co-selection of several resistance determinants. This study constitutes the first report of completely sequenced IncP-1 epsilon plasmids from water environments, and enhances our understanding of the geographic distribution and genetic diversity of these replicons. (C) 2013 Elsevier Inc. All rights reserved.