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Shintani M, Vestergaard G, Milaković M, Kublik S, Smalla K, Schloter M, Udiković-Kolić N. Integrons, transposons and IS elements promote diversification of multidrug resistance plasmids and adaptation of their hosts to antibiotic pollutants from pharmaceutical companies. Environ Microbiol 2023; 25:3035-3051. [PMID: 37655671 DOI: 10.1111/1462-2920.16481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/01/2023] [Indexed: 09/02/2023]
Abstract
Plasmids are important vehicles for the dissemination of antibiotic resistance genes (ARGs) among bacteria by conjugation. Here, we determined the complete nucleotide sequences of nine different plasmids previously obtained by exogenous plasmid isolation from river and creek sediments and wastewater from a pharmaceutical company. We identified six IncP/P-1ε plasmids and single members of IncL, IncN and IncFII-like plasmids. Genetic structures of the accessory regions of the IncP/P-1ε plasmids obtained implied that multiple insertions and deletions had occurred, mediated by different transposons and Class 1 integrons with various ARGs. Our study provides compelling evidence that Class 1 integrons, Tn402-like transposons, Tn3-like transposons and/or IS26 played important roles in the acquisition of ARGs across all investigated plasmids. Our plasmid sequencing data provide new insights into how these mobile genetic elements could mediate the acquisition and spread of ARGs in environmental bacteria.
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Affiliation(s)
- Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
| | | | - Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Croatia
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Zagreb, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Zagreb, Germany
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2
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Hitherto-Unnoticed Self-Transmissible Plasmids Widely Distributed among Different Environments in Japan. Appl Environ Microbiol 2022; 88:e0111422. [PMID: 36069618 PMCID: PMC9499019 DOI: 10.1128/aem.01114-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Various conjugative plasmids were obtained by exogenous plasmid capture, biparental mating, and/or triparental mating methods from different environmental samples in Japan. Based on phylogenetic analyses of their whole-nucleotide sequences, new IncP/P-1 plasmids that could be classified into novel subgroups were obtained. Mini-replicons of the plasmids were constructed, and each of them was incompatible with at least one of the IncP/P-1 plasmids, although they showed diverse iteron sequences in their oriV regions. There were two large clades of IncP/P-1 plasmids, clade I and II. Plasmids in clade I and II included antibiotic resistance genes. Notably, nucleotide compositions of newly found plasmids exhibited different tendencies compared with those of the previously well-studied IncP/P-1 plasmids. Indeed, the host range of plasmids of clade II was different from that of clade I. Although few PromA plasmids have been reported, the number of plasmids belonging to PromAβ, and -γ subgroups detected in this study was close to that of IncP/P-1 plasmids. The host ranges of PromAγ and PromAδ plasmids were broad and transferred to different and distinct classes of Proteobacteria. Interestingly, PromA plasmids and many IncP/P-1 plasmids do not carry any accessory genes. These findings indicate the presence of "hitherto-unnoticed" conjugative plasmids, including IncP/P-1 or PromA derivative ones in nature. These plasmids would have important roles in the exchange of various genes, including antibiotic resistance genes, among different bacteria in nature. IMPORTANCE Plasmids are known to spread among different bacteria. However, which plasmids spread among environmental samples and in which environments they are present is still poorly understood. This study showed that unidentified conjugative plasmids were present in various environments. Different novel IncP/P-1 plasmids were found, whose host ranges were different from those of known plasmids, showing wide diversity of IncP/P-1 plasmids. PromA plasmids, exhibiting a broad host range, were diversified into several subgroups and widely distributed in varied environments. These findings are important for understanding how bacteria naturally exchange their genes, including antibiotic resistance genes, a growing threat to human health worldwide.
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3
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Law A, Solano O, Brown CJ, Hunter SS, Fagnan M, Top EM, Stalder T. Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria. Front Microbiol 2021; 12:606409. [PMID: 33967971 PMCID: PMC8098119 DOI: 10.3389/fmicb.2021.606409] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/09/2021] [Indexed: 12/05/2022] Open
Abstract
Antibiotic resistance (AR) is a threat to modern medicine, and plasmids are driving the global spread of AR by horizontal gene transfer across microbiomes and environments. Determining the mobile resistome responsible for this spread of AR among environments is essential in our efforts to attenuate the current crisis. Biosolids are a wastewater treatment plant (WWTP) byproduct used globally as fertilizer in agriculture. Here, we investigated the mobile resistome of biosolids that are used as fertilizer. This was done by capturing resistance plasmids that can transfer to human pathogens and commensal bacteria. We used a higher-throughput version of the exogenous plasmid isolation approach by mixing several ESKAPE pathogens and a commensal Escherichia coli with biosolids and screening for newly acquired resistance to about 10 antibiotics in these strains. Six unique resistance plasmids transferred to Salmonella typhimurium, Klebsiella aerogenes, and E. coli. All the plasmids were self-transferable and carried 3-6 antibiotic resistance genes (ARG) conferring resistance to 2-4 antibiotic classes. These plasmids-borne resistance genes were further embedded in genetic elements promoting intracellular recombination (i.e., transposons or class 1 integrons). The plasmids belonged to the broad-host-range plasmid (BHR) groups IncP-1 or PromA. Several of them were persistent in their new hosts when grown in the absence of antibiotics, suggesting that the newly acquired drug resistance traits would be sustained over time. This study highlights the role of BHRs in the spread of ARG between environmental bacteria and human pathogens and commensals, where they may persist. The work further emphasizes biosolids as potential vehicles of highly mobile plasmid-borne antibiotic resistance genes.
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Affiliation(s)
- Aaron Law
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Olubunmi Solano
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Celeste J. Brown
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Samuel S. Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
- UC-Davis Genome Center, Davis, CA, United States
| | - Matt Fagnan
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Eva M. Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
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4
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Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes. ISME JOURNAL 2020; 14:1170-1181. [PMID: 32020051 DOI: 10.1038/s41396-020-0596-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 01/19/2020] [Accepted: 01/21/2020] [Indexed: 12/18/2022]
Abstract
The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Enterobacteriaceae, and Pseudomonas, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in high-throughput without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognised potential to maintain plasmids for long-term community-wide access.
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5
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Nguyen TPO, Hansen MA, Hansen LH, Horemans B, Sørensen SJ, De Mot R, Springael D. Intra- and inter-field diversity of 2,4-dichlorophenoxyacetic acid-degradative plasmids and their tfd catabolic genes in rice fields of the Mekong delta in Vietnam. FEMS Microbiol Ecol 2019; 95:5149497. [PMID: 30380047 DOI: 10.1093/femsec/fiy214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/29/2018] [Indexed: 11/14/2022] Open
Abstract
The tfd genes mediating degradation of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) differ in composition and organization in bacterial isolates from different geographical origin and are carried by different types of mobile genetic elements (MGE). It is not known whether such global diversity of 2,4-D-catabolic MGE and their tfd gene cargo is reflected in the diversity at field scale. The genomic context of the 2,4-D catabolic genes of 2,4-D-degrading isolates from two rice fields with a 2,4-D application history, located in two distant provinces of the Vietnam Mekong delta, was compared. All isolates were β-proteobacteria, were unique for each rice field and carried the catabolic genes on MGE and especially plasmids. Most plasmids were IncP-1β plasmids and carried tfd clusters highly similar to those of the IncP-1β plasmid pJP4, typified by two chlorophenol catabolic gene modules (tfd-I and tfd-II). IncP-1β plasmids from the same field showed small deletions and/or insertions in accessory metabolic genes. One plasmid belonged to an unclassified plasmid group and carries a copy of both tfdA and tfd-II identical to those in the IncP-1β plasmids. Our results indicate intra-field evolution and inter-field exchange of 2,4-D-catabolic IncP-1β plasmids as well as the exchange of tfd genes between different plasmids within a confined local environment.
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Affiliation(s)
- Thi Phi Oanh Nguyen
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, Heverlee-Leuven B-3001, Belgium.,Department of Biology, College of Natural Sciences, Can Tho University, Campus II, 3/2 street, Ninh Kieu district, Can Tho City, Vietnam
| | - Martin Asser Hansen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen DK-2100, Denmark
| | - Lars Hestbjerg Hansen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen DK-2100, Denmark.,Department of Environmental Science - Environmental Microbiology & Biotechnology, Aarhus University, Frederiksborgvej 399, Building 7411 B2.12, Roskilde DK-4000, Denmark
| | - Benjamin Horemans
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, Heverlee-Leuven B-3001, Belgium
| | - Søren Johannes Sørensen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen DK-2100, Denmark
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Heverlee-Leuven B-3001, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, Heverlee-Leuven B-3001, Belgium
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6
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Yanagiya K, Maejima Y, Nakata H, Tokuda M, Moriuchi R, Dohra H, Inoue K, Ohkuma M, Kimbara K, Shintani M. Novel Self-Transmissible and Broad-Host-Range Plasmids Exogenously Captured From Anaerobic Granules or Cow Manure. Front Microbiol 2018; 9:2602. [PMID: 30459733 PMCID: PMC6232296 DOI: 10.3389/fmicb.2018.02602] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/11/2018] [Indexed: 11/29/2022] Open
Abstract
Novel self-transmissible plasmids were exogenously captured from environmental samples by triparental matings with pBBR1MCS-2 as a mobilizable plasmid and Pseudomonas resinovorans as a recipient. A total of 272 recipients were successfully obtained as plasmid host candidates from granules of an anaerobic methane fermentation plant and from cow manure. The whole nucleotide sequences of six plasmids were determined, including one IncP-1 plasmid (pSN1104-59), four PromA-like plasmids (pSN1104-11, pSN1104-34, pSN0729-62, and pSN0729-70), and one novel plasmid (pSN1216-29), whose incompatibility group has not been previously identified. No previously known antibiotic resistance genes were found in these plasmids. In-depth phylogenetic analyses showed that the PromA-like plasmids belong to subgroups of PromA (designated as PromAγ and PromAδ) different from previously proposed subgroups PromAα and PromAβ. Twenty-four genes were identified as backbone genes by comparisons with other PromA plasmids. The nucleotide sequences of pSN1216-29 share high identity with those found in clinical isolates. A minireplicon of pSN1216-29 was successfully constructed from repA encoding a replication initiation protein and oriV. All the captured plasmids were found to have a broad host range and could be transferred to and replicated in different classes of Proteobacteria. Notably, repA and oriV of pSN1216-29 showed high similarity with one of two replication systems of pSRC119-A/C, known as a plasmid with multidrug resistance genes found in Salmonella enterica serovar Senftenberg. Our findings suggest that these “cryptic” but broad-host-range plasmids may be important for spreading several genes as “vehicles” in a wider range of bacteria in natural environments.
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Affiliation(s)
- Kosuke Yanagiya
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Yoshiaki Maejima
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hiroki Nakata
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Maho Tokuda
- Faculty of Engineering, Shizuoka University, Shizuoka, Japan
| | - Ryota Moriuchi
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hideo Dohra
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Kengo Inoue
- Department of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Kazuhide Kimbara
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Faculty of Engineering, Shizuoka University, Shizuoka, Japan
| | - Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Faculty of Engineering, Shizuoka University, Shizuoka, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan.,Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
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7
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Dias ACF, Cotta SR, Andreote FD, van Elsas JD. The parA Region of Broad-Host-Range PromA Plasmids Is a Carrier of Mobile Genes. MICROBIAL ECOLOGY 2018; 75:479-486. [PMID: 28875307 DOI: 10.1007/s00248-017-1059-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
The ecological competences in microbiomes are driven by the adaptive capabilities present within microbiome members. Horizontal gene transfer (HGT) promoted by plasmids provides a rapid adaptive strategy to microbiomes, an interesting feature considering the constantly changing conditions in most environments. This study examined the parA locus, found in the highly promiscuous PromA class of plasmids, as the insertion site for incoming genes. A novel PCR system was designed that enabled examining insertions into this locus. Microbiomes of mangrove sediments, salt marsh, mycosphere, and bulk soil revealed habitat-specific sets of insertions in this plasmid region. Furthermore, such habitats could be differentiated based on patterns of parA-inserted genes, and the genes carried by these plasmids. Thus, a suite of dioxygenase-related genes and transposase elements were found in oil-affected mangroves, whereas genes involved in nitrogen and carbon cycling were detected in salt marsh and soils. All genes detected could be associated with capabilities of members of the microbiome to adapt to and survive in each habitat. The methodology developed in this work was effective, sensitive, and practical, allowing detection of mobilized genes between microorganisms.
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Affiliation(s)
- Armando Cavalcante Franco Dias
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Av Padua Dias, 11, Piracicaba, SP, 13418-900, Brazil.
- Microbial Ecology Group, Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), Groningen, Netherlands.
| | - Simone Raposo Cotta
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Av Padua Dias, 11, Piracicaba, SP, 13418-900, Brazil
- Microbial Ecology Group, Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), Groningen, Netherlands
| | - Fernando Dini Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Av Padua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology Group, Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), Groningen, Netherlands
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8
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Abstract
Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid carriage, only a fraction of a local population carries plasmids or is permissive to plasmid uptake. Plasmids provide various accessory traits which might be beneficial under particular conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness toward environmental changes. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens. Here we summarize the state-of-the-art methods to study the occurrence, abundance, and diversity of plasmids in environmental bacteria. Increasingly, cultivation-independent total-community DNA-based methods are being used to characterize and quantify the diversity and abundance of plasmids in relation to various biotic and abiotic factors. An improved understanding of the ecology of plasmids and their hosts is crucial in the development of intervention strategies for antibiotic-resistance-gene spread. We discuss the potentials and limitations of methods used to determine the host range of plasmids, as the ecology of plasmids is tightly linked to their hosts. The recent advances in sequencing technologies provide an enormous potential for plasmid classification, diversity, and evolution studies, but numerous challenges still exist.
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9
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Conjugative transfer of broad host range plasmids to an acidobacterial strain, Edaphobacter aggregans. J Biotechnol 2016; 221:107-13. [DOI: 10.1016/j.jbiotec.2016.01.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 01/19/2023]
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10
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Li X, Wang Y, Brown CJ, Yao F, Jiang Y, Top EM, Li H. Diversification of broad host range plasmids correlates with the presence of antibiotic resistance genes. FEMS Microbiol Ecol 2015; 92:fiv151. [PMID: 26635412 DOI: 10.1093/femsec/fiv151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2015] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Xiaobin Li
- 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
| | - Yafei Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Celeste J Brown
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA
| | - Fei Yao
- 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
| | - Yong Jiang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Eva M Top
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA
| | - Hui Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
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11
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Li X, Top EM, Wang Y, Brown CJ, Yao F, Yang S, Jiang Y, Li H. The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family. Front Microbiol 2015; 5:777. [PMID: 25628616 PMCID: PMC4290620 DOI: 10.3389/fmicb.2014.00777] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/18/2014] [Indexed: 11/13/2022] Open
Abstract
A self-transmissible broad-host-range (BHR) plasmid pSFA231 was isolated from petroleum-contaminated sediment in Shen-fu wastewater irrigation zone, China, using the triparental mating exogenous plasmid capture method. Based on its complete sequence the plasmid has a size of 41.5 kb and codes for 50 putative open reading frames (orfs), 29 of which represent genes involved in replication, partitioning and transfer functions of the plasmid. Phylogenetic analysis grouped pSFA231 into the newly defined PromA plasmid family, which currently includes five members. Further comparative genomic analysis shows that pSFA231 shares the common backbone regions with the other PromA plasmids, i.e., genes involved in replication, maintenance and control, and conjugative transfer. Nevertheless, phylogenetic divergence was found in specific gene products. We propose to divide the PromA group into two subgroups, PromA-α (pMRAD02, pSB102) and PromA-β (pMOL98, pIPO2T, pSFA231, pTer331), based on the splits network analysis of the RepA protein. Interestingly, a cluster of hypothetical orfs located between parA and traA of pSFA231 shows high similarity with the corresponding regions on pMOL98, pIPO2T, and pTer331, suggesting these hypothetical orfs may represent “essential” plasmid backbone genes for the PromA-β subgroup. Alternatively, they may also be accessory genes that were first acquired and then stayed as the plasmid diverged. Our study increases the available collection of complete genome sequences of BHR plasmids, and since pSFA231 is the only characterized PromA plasmid from China, our findings also enhance our understanding of the genetic diversity of this plasmid group in different parts of the world.
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Affiliation(s)
- Xiaobin Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China ; College of Resources and Environment, University of Chinese Academy of Sciences Beijing, China
| | - Eva M Top
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho Moscow, ID, USA
| | - Yafei Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China
| | - Celeste J Brown
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho Moscow, ID, USA
| | - Fei Yao
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China ; College of Resources and Environment, University of Chinese Academy of Sciences Beijing, China
| | - Shan Yang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China
| | - Yong Jiang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China
| | - Hui Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China
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12
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Sen D, Brown CJ, Top EM, Sullivan J. Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol Biol Evol 2013; 30:154-66. [PMID: 22936717 PMCID: PMC3525142 DOI: 10.1093/molbev/mss210] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Plasmids of the incompatibility group IncP-1 can transfer and replicate in many genera of the Proteobacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. Although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of IncP-1 plasmids. As a consequence, phylogeny estimation based on backbone genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer the evolutionary history of IncP-1 plasmids in the presence of both vertical and horizontal gene transfer. This was achieved by quantifying the incongruence among gene trees and attributing it to known causes such as 1) phylogenetic uncertainty, 2) coalescent stochasticity, and 3) horizontal inheritance. Topologies of gene trees exhibited more incongruence than could be attributed to phylogenetic uncertainty alone. Species-tree estimation using a Bayesian framework that takes coalescent stochasticity into account was well supported, but it differed slightly from the maximum-likelihood tree estimated by concatenation of backbone genes. After removal of the gene that demonstrated a signal of intergroup recombination, the concatenated tree was congruent with the species-tree estimate, which itself was robust to inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene exchange both within and among IncP-1 subgroups, the backbone genome of these IncP-1 plasmids retains a detectable vertical evolutionary history.
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Affiliation(s)
- Diya Sen
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
- Bioinformatics and Computational Biology Graduate Program, University of Idaho
| | - Celeste J. Brown
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
- Bioinformatics and Computational Biology Graduate Program, University of Idaho
- Department of Biological Sciences, University of Idaho
| | - Eva M. Top
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
- Bioinformatics and Computational Biology Graduate Program, University of Idaho
- Department of Biological Sciences, University of Idaho
| | - Jack Sullivan
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho
- Bioinformatics and Computational Biology Graduate Program, University of Idaho
- Department of Biological Sciences, University of Idaho
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Heuer H, Smalla K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev 2012; 36:1083-104. [DOI: 10.1111/j.1574-6976.2012.00337.x] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 10/15/2011] [Accepted: 02/24/2012] [Indexed: 11/26/2022] Open
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Alvarado A, Garcillán-Barcia MP, de la Cruz F. A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings. PLoS One 2012; 7:e40438. [PMID: 22792321 PMCID: PMC3394729 DOI: 10.1371/journal.pone.0040438] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 06/07/2012] [Indexed: 11/18/2022] Open
Abstract
Transmissible plasmids are responsible for the spread of genetic determinants, such as antibiotic resistance or virulence traits, causing a large ecological and epidemiological impact. Transmissible plasmids, either conjugative or mobilizable, have in common the presence of a relaxase gene. Relaxases were previously classified in six protein families according to their phylogeny. Degenerate primers hybridizing to coding sequences of conserved amino acid motifs were designed to amplify related relaxase genes from γ-Proteobacterial plasmids. Specificity and sensitivity of a selected set of 19 primer pairs were first tested using a collection of 33 reference relaxases, representing the diversity of γ-Proteobacterial plasmids. The validated set was then applied to the analysis of two plasmid collections obtained from clinical isolates. The relaxase screening method, which we call “Degenerate Primer MOB Typing” or DPMT, detected not only most known Inc/Rep groups, but also a plethora of plasmids not previously assigned to any Inc group or Rep-type.
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Affiliation(s)
- Andrés Alvarado
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, Santander, Spain
| | - M. Pilar Garcillán-Barcia
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, Santander, Spain
| | - Fernando de la Cruz
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, Santander, Spain
- * E-mail:
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Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Appl Environ Microbiol 2011; 77:7975-83. [PMID: 21948829 DOI: 10.1128/aem.05439-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Broad-host-range plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to antibiotics and heavy metals or degradation of pollutants. Although some broad-host-range plasmids have been extensively studied, their evolutionary history and genetic diversity remain largely unknown. The goal of this study was to analyze and compare the genomes of 12 broad-host-range plasmids that were previously isolated from Norwegian soils by exogenous plasmid isolation and that encode mercury resistance. Complete nucleotide sequencing followed by phylogenetic analyses based on the relaxase gene traI showed that all the plasmids belong to one of two subgroups (β and ε) of the well-studied incompatibility group IncP-1. A diverse array of accessory genes was found to be involved in resistance to antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic acid), and a putative new catabolic pathway. Intramolecular transposition of insertion sequences followed by deletion was found to contribute to the diversity of some of these plasmids. The previous observation that the insertion sites of a Tn501-related element are identical in four IncP-1β plasmids (pJP4, pB10, R906, and R772) was further extended to three more IncP-1β plasmids (pAKD15, pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these Tn501-bearing IncP-1β plasmids that predicts recent diversification followed by worldwide spread. Our study increases the available collection of complete IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our understanding of the evolution and function of this important plasmid family.
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Anjum R, Grohmann E, Malik A. Molecular characterization of conjugative plasmids in pesticide tolerant and multi-resistant bacterial isolates from contaminated alluvial soil. CHEMOSPHERE 2011; 84:175-181. [PMID: 21376364 DOI: 10.1016/j.chemosphere.2011.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 01/29/2011] [Accepted: 02/02/2011] [Indexed: 05/30/2023]
Abstract
A total of 35 bacteria from contaminated soil (cultivated fields) near pesticide industry from Chinhat, Lucknow, (India) were isolated and tested for their tolerance/resistance to pesticides, heavy metals and antibiotics. Bacterial isolates were identified by 16S rDNA sequencing. Gas Chromatography analysis of the soil samples revealed the presence of lindane at a concentration of 547 ng g(-1) and α-endosulfan and β-endosulfan of 422 ng g(-1) and 421 ng g(-1) respectively. Atomic Absorption Spectrophotometry analysis of the test sample was done and Cr, Zn, Ni, Fe, Cu and Cd were detected at concentrations of 36.2, 42.5, 43.2, 241, 13.3 and 11.20 mg kg(-1) respectively. Minimum inhibitory concentrations of all the isolates were determined for pesticides and heavy metals. All the multi-resistant/tolerant bacterial isolates were also tested for the presence of incompatibility (Inc) group IncP, IncN, IncW, IncQ plasmids and for rolling circle plasmids of the pMV158-family by PCR. Total community DNA was extracted from pesticide contaminated soil. PCR amplification of the bacterial isolates and soil DNA revealed the presence of IncP-specific sequences (trfA2 and oriT) which was confirmed by dot blot hybridization with RP4-derived DIG-labelled probes. Plasmids belonging to IncN, IncW and IncQ group were neither detected in the bacterial isolates nor in total soil DNA. The presence of conjugative or mobilizable IncP plasmids in the isolates indicate that these bacteria have gene transfer capacity with implications for dissemination of heavy metal and antibiotic resistance genes. We propose that IncP plasmids are mainly responsible for the spread of multi-resistant bacteria in the contaminated soils.
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Affiliation(s)
- Reshma Anjum
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202 002, India
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Molina L, Duque E, Gómez MJ, Krell T, Lacal J, García-Puente A, García V, Matilla MA, Ramos JL, Segura A. The pGRT1 plasmid of Pseudomonas putida DOT-T1E encodes functions relevant for survival under harsh conditions in the environment. Environ Microbiol 2011; 13:2315-27. [PMID: 21605303 DOI: 10.1111/j.1462-2920.2011.02492.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Pseudomonas putida DOT-T1E has the capacity to grow in the presence of high concentrations of toluene. This ability is mainly conferred by an efflux pump encoded in a self-transmissible 133 kb plasmid named pGRT1. Sequence analysis of the pGRT1 plasmid revealed several key features. Most of the genes related to the plasmid maintenance functions show similarity with those encoded on pBVIE04 from Burkholderia vietnamensis G4, and knock-out mutants in several of these genes confirmed their roles. Two additional plasmid DNA fragments were incorporated into the plasmid backbone by recombination and/or transposition; in these DNA regions, apart from multiple recombinases and transposases, several stress-related and environmentally relevant functions are encoded. We report that plasmid pGRT1 not only confers the cells with tolerance to toluene but also resistance to ultraviolet light. We show here the implication of a new protein in solvent tolerance which controls the level of expression of the TtgGHI efflux pump, as well as the implication of a protein with homology to the universal stress protein in solvent tolerance and ultraviolet light resistance. Furthermore, this plasmid encodes functions that allow the cells to chemotactically respond to toluene and participate in iron scavenging.
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Affiliation(s)
- Lázaro Molina
- Environmental Protection Department, Estación Experimental del Zaidín, CSIC, C/ Profesor Albareda 1,18008-Granada, Spain
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Ryan MP, Pembroke JT, Adley CC. Novel Tn4371-ICE like element in Ralstonia pickettii and genome mining for comparative elements. BMC Microbiol 2009; 9:242. [PMID: 19941653 PMCID: PMC2789088 DOI: 10.1186/1471-2180-9-242] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 11/26/2009] [Indexed: 11/22/2022] Open
Abstract
Background Integrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements. A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element. Results Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several β and γ- Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371- like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type. Conclusion All elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water.
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Affiliation(s)
- Michael P Ryan
- Microbiology Laboratory, Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland.
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Bahl MI, Burmølle M, Meisner A, Hansen LH, Sørensen SJ. All IncP-1 plasmid subgroups, including the novel ε subgroup, are prevalent in the influent of a Danish wastewater treatment plant. Plasmid 2009; 62:134-9. [DOI: 10.1016/j.plasmid.2009.05.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 05/27/2009] [Accepted: 05/29/2009] [Indexed: 11/26/2022]
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Van der Auwera GA, Król JE, Suzuki H, Foster B, Van Houdt R, Brown CJ, Mergeay M, Top EM. Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids. Antonie van Leeuwenhoek 2009; 96:193-204. [PMID: 19259779 DOI: 10.1007/s10482-009-9316-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 02/08/2009] [Indexed: 11/29/2022]
Abstract
The self-transmissible, broad-host-range (BHR) plasmid pMOL98 was previously isolated from polluted soil using a triparental plasmid capture approach and shown to possess a replicon similar to that of the BHR plasmids pSB102 and pIPO2. Here, complete sequence analysis and comparative genomics reveal that the 55.5 kb nucleotide sequence of pMOL98 shows extensive sequence similarity and synteny with the BHR plasmid family that now includes pIPO2, pSB102, pTER331, and pMRAD02. They share a plasmid backbone comprising replication, partitioning and conjugative transfer functions. Comparison of the variable accessory regions of these plasmids shows that the majority of natural transposons, as well as the mini-transposon used to mark the plasmids, are inserted in the parA locus. The transposon unique to pMOL98 appears to have inserted from the chromosome of the recipient strain used in the plasmid capture procedure. This demonstrates the necessity for careful screening of plasmids and host chromosomes to avoid mis-interpretation of plasmid genome content. The presence of very similar BHR plasmids with different accessory genes in geographically distinct locations suggests an important role in horizontal gene exchange and bacterial adaptation for this recently defined plasmid group, which we propose to name "PromA".
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Mela F, Fritsche K, Boersma H, van Elsas JD, Bartels D, Meyer F, de Boer W, van Veen JA, Leveau JHJ. Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiol Ecol 2008; 66:45-62. [PMID: 18355297 DOI: 10.1111/j.1574-6941.2008.00472.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Plasmid pTer331 from the bacterium Collimonas fungivorans Ter331 is a new member of the pIPO2/pSB102 family of environmental plasmids. The 40 457-bp sequence of pTer331 codes for 44 putative ORFs, most of which represent genes involved in replication, partitioning and transfer of the plasmid. We confirmed that pTer331 is stably maintained in its native host. Deletion analysis identified a mini-replicon capable of replicating autonomously in Escherichia coli and Pseudomonas putida. Furthermore, plasmid pTer331 was able to mobilize and retromobilize IncQ plasmid pSM1890 at typical rates of 10(-4) and 10(-8), respectively. Analysis of the 91% DNA sequence identity between pTer331 and pIPO2 revealed functional conservation of coding sequences, the deletion of DNA fragments flanked by short direct repeats (DR), and sequence preservation of long DRs. In addition, we experimentally established that pTer331 has no obvious contribution in several of the phenotypes that are characteristic of its host C. fungivorans Ter331, including the ability to efficiently colonize plant roots. Based on our findings, we hypothesize that cryptic plasmids such as pTer331 and pIPO2 might not confer an individual advantage to bacteria, but, due to their broad-host-range and ability to retromobilize, benefit bacterial populations by accelerating the intracommunal dissemination of the mobile gene pool.
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Affiliation(s)
- Francesca Mela
- Centre for Terrestrial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Heteren, The Netherlands
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Ansari MI, Grohmann E, Malik A. Conjugative plasmids in multi-resistant bacterial isolates from Indian soil. J Appl Microbiol 2008; 104:1774-81. [PMID: 18284489 DOI: 10.1111/j.1365-2672.2008.03736.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Determination of heavy metal and antibiotic resistance and presence of conjugative plasmids in bacteria isolated from soil irrigated with wastewater. METHODS AND RESULTS Composite soil samples were collected from Ghaziabad, Uttar Pradesh, India. Forty different bacteria were selected from nutrient agar and characterized by morphological, cultural and biochemical tests. All the isolates were tested for their resistance to different heavy metals and antibiotics. The DNA derived from multiple metal and antibiotic-resistant bacterial isolates was PCR amplified and plasmid-specific sequences (IncP, IncN, IncW, IncQ and pMV158-type) were analysed by dot blot hybridization. All isolates gave PCR products with trfA2 and oriT primers of the IncP group. These PCR products also hybridized with the RP4-derived probes. However, the samples were negative for all the other investigated plasmids as proved by PCR and dot blots. CONCLUSIONS The presence of conjugative/mobilizable IncP plasmids in the isolates indicates that these bacteria have gene-mobilizing capacity with implications for potential dissemination of introduced recombinant DNA. SIGNIFICANCE AND IMPACT OF THE STUDY The detection of IncP plasmids in all the bacterial isolates is another proof for the prevalence of these plasmids. We propose that IncP plasmids are mainly responsible for the spread of multi-resistant bacteria in these soils.
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Affiliation(s)
- M I Ansari
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
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Malik A, Ãelik EK, Bohn C, Böckelmann U, Knobel K, Grohmann E. Detection of conjugative plasmids and antibiotic resistance genes in anthropogenic soils from Germany and India. FEMS Microbiol Lett 2008; 279:207-16. [DOI: 10.1111/j.1574-6968.2007.01030.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Abstract
The 2.1-kb cryptic plasmid pCIBAO89 from Bifidobacterium asteroides harbors a 1.4-kb segment which is sufficient for its autonomous replication. The segment is divided into two parts, the presumed replication origin, ori89, and the rep gene encoding the putative 41-kDa Rep89 replication initiation protein. This minimal replication region of pCIBAO89 was functionally dissected by transcriptional analyses as well as by DNA-binding studies, and the information obtained was exploited to create a number of Escherichia coli-Bifidobacterium shuttle vectors capable of transforming various bifidobacteria with an efficiency of up to 10(6) transformants/mug DNA.
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Schlüter A, Szczepanowski R, Pühler A, Top EM. Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiol Rev 2007; 31:449-77. [PMID: 17553065 DOI: 10.1111/j.1574-6976.2007.00074.x] [Citation(s) in RCA: 286] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The dramatic spread of antibiotic resistance is a crisis in the treatment of infectious diseases that affect humans. Several studies suggest that wastewater treatment plants (WWTP) are reservoirs for diverse mobile antibiotic resistance elements. This review summarizes findings derived from genomic analysis of IncP-1 resistance plasmids isolated from WWTP bacteria. Plasmids that belong to the IncP-1 group are self-transmissible, and transfer to and replicate in a wide range of hosts. Their backbone functions are described with respect to their impact on vegetative replication, stable maintenance and inheritance, mobility and plasmid control. Accessory genetic modules, mainly representing mobile genetic elements, are integrated in-between functional plasmid backbone modules. These elements carry determinants conferring resistance to nearly all clinically relevant antimicrobial drug classes, to heavy metals, and quaternary ammonium compounds used as disinfectants. All plasmids analysed here contain integrons that potentially facilitate integration, exchange and dissemination of resistance gene cassettes. Comparative genomics of accessory modules located on plasmids from WWTP and corresponding modules previously identified in other bacterial genomes revealed that animal, human and plant pathogens and other bacteria isolated from different habitats share a common pool of resistance determinants.
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Affiliation(s)
- Andreas Schlüter
- Fakultät für Biologie, Lehrstuhl für Genetik, Universität Bielefeld, Bielefeld, Germany
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Bahl MI, Hansen LH, Goesmann A, Sørensen SJ. The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established α, β and δ sub-groups. Plasmid 2007; 58:31-43. [PMID: 17306874 DOI: 10.1016/j.plasmid.2006.11.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Revised: 11/07/2006] [Accepted: 11/29/2006] [Indexed: 10/23/2022]
Abstract
The 54,383bp plasmid pKJK5 was recovered from a soil environment by exogenous plasmid isolation and conveys resistance towards tetracycline and trimethoprim. Sequencing and annotation revealed a high level of structural similarity of the backbone genes to other IncP-1 plasmids containing a Tra1 and Tra2 region, a central control module and a replication initiation module. A considerable degree of divergence was associated with the backbone genes of pKJK5 as compared to homologous genes in the alpha, beta and delta subgroups, which indicates that pKJK5 may belong to a novel subgroup of IncP-1 plasmids, which may also accommodate the partially sequenced non-subgroup classified plasmid pEMT3. Individual backbone genes in pKJK5 have a GC-content, which is consistently lower (average 6.3%) than the homologous genes from the archetype IncP-1beta plasmid R751 indicating homogenous amelioration of IncP-1 plasmid backbone genes. Two discrete accessory elements of 2145bp (load 1) and 11678bp (load 2) respectively are situated between the Tra1 and Tra2 regions of pKJK5, both bounded by inverted repeats and direct flanking repeats indicative of transposon-mediated insertion. Load 1 consists of an insertion sequence ISPa17 and load 2 is a Tn402-derivative containing a class 1 integron, IS1326 and a fragment identical to a region of plasmid pTB11 harboring a tetracycline resistance determinant and part of an IncP-1alphaoriV region.
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Affiliation(s)
- Martin Iain Bahl
- Department of Microbiology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen K, Denmark
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Vedler E, Vahter M, Heinaru A. The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol 2004; 186:7161-74. [PMID: 15489427 PMCID: PMC523222 DOI: 10.1128/jb.186.21.7161-7174.2004] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains plasmid pEST4011. This plasmid ensures its host a stable 2,4-D(+) phenotype. We determined the complete 76,958-bp nucleotide sequence of pEST4011. This plasmid is a deletion and duplication derivative of pD2M4, the 95-kb highly unstable laboratory ancestor of pEST4011, and was self-generated during different laboratory manipulations performed to increase the stability of the 2,4-D(+) phenotype of the original strain, strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a transposon-like structure with identical copies of the hybrid insertion element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011 and pJP4, the best-studied 2,4-D-degradative plasmid, both contain homologous, tfd-like genes for complete 2,4-D degradation, but they have little sequence similarity other than that. The backbone genes of pEST4011 are most similar to the corresponding genes of broad-host-range self-transmissible IncP1 plasmids. The backbones of the other three IncP1 catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazine-catabolic plasmid pADP-1) are nearly identical to the backbone of R751, the archetype plasmid of the IncP1 beta subgroup. We show that despite the overall similarity in plasmid organization, the pEST4011 backbone is sufficiently different (51 to 86% amino acid sequence identity between individual backbone genes) from the backbones of members of the three IncP1 subgroups (the alpha, beta, and gamma subgroups) that it belongs to a new IncP1subgroup, the delta subgroup. This conclusion was also supported by a phylogenetic analysis of the trfA2, korA, and traG gene products of different IncP1 plasmids.
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Affiliation(s)
- Eve Vedler
- Department of Genetics, Institute of Molecular and Cell Biology, 23 Riia Street, Tartu 51010, Estonia.
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