title: Diversification of broad host range plasmids correlates with the presence of antibiotic resistance genes.
abstract: The IncP-1ε subgroup is a recently identified phylogenetic clade within IncP-1 plasmids, which plays an important role in the spread of antibiotic resistance and degradation of xenobiotic pollutants. Here, four IncP-1ε plasmids were exogenously captured from a petroleum-contaminated habitat in China and compared phylogenetically and genomically with previously reported IncP-1ε and other IncP-1 plasmids. The IncP-1ε plasmids can be clearly subdivided into two subclades, designated as ε-I and ε-II, based on phylogenetic analysis of backbone proteins TraI and TrfA. This was further supported by comparison of concatenated backbone genes. Moreover, the two subclades differed in the transposon types, phenotypes and insertion locations of the accessory elements. The accessory genes on ε-I plasmids were inserted between parA and traC, and harbored ISPa17 and Tn402-like transposon modules, typically carrying antibiotic resistance genes. In contrast, the accessory elements on ε-II plasmids were typically located between trfA and oriV, and contained IS1071, which was commonly inserted within the Tn501-like transposon, typically harboring a cluster of genes encoding mercury resistance and/or catabolic pathways. Our study is one of the first to compare IncP-1 plasmid genomes from China, expands the available collection of IncP-1ε plasmids and enhances our understanding of their diversity, biogeography and evolutionary history.
authors.affiliation: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Xiaobin
authors.initials: X
authors.lastname: Li
authors.affiliation: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China.
authors.forename: Yafei
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA.
authors.forename: Celeste J
authors.initials: CJ
authors.lastname: Brown
authors.affiliation: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Yao
authors.affiliation: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA.
authors.forename: Eva M
authors.initials: EM
authors.lastname: Top
authors.affiliation: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China huili@iae.ac.cn.
authors.forename: Hui
authors.initials: H
authors.lastname: Li
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001483:Base Sequence; D002681:China; D004265:DNA Helicases / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D004787:Environmental Pollution; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods*; D058507:Host Specificity; D010578:Petroleum / Q000378:metabolism; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics* / Q000302:isolation & purification; D020560:Proteobacteria / Q000187:drug effects / Q000235:genetics / Q000821:virology; D017422:Sequence Analysis, DNA; D012989:Soil Pollutants / Q000378:metabolism; D062065:Wastewater / Q000382:microbiology
chemical_list: D000900:Anti-Bacterial Agents; D004265:DNA Helicases; D010578:Petroleum; D012989:Soil Pollutants; D062065:Wastewater
keywords: IncP-1ε plasmid; antibiotic resistance; comparative genome analysis; horizontal gene transfer; petroleum polluted soil; wastewater