A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings
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. Relaxase...
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| Veröffentlicht in: | PloS one 2012-07, Vol.7 (7), p.e40438-e40438 |
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| creator | Alvarado, Andrés Garcillán-Barcia, M Pilar de la Cruz, Fernando |
| description | 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. |
| doi_str_mv | 10.1371/journal.pone.0040438 |
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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0040438</identifier><identifier>PMID: 22792321</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amino Acid Sequence ; Amino acids ; Antibiotic resistance ; Antibiotics ; Bacterial Proteins - genetics ; Base Sequence ; Biology ; Clinical isolates ; Deoxyribonucleic acid ; DNA ; DNA Primers - genetics ; Ecological effects ; Endodeoxyribonucleases - genetics ; Environmental Microbiology ; Epidemiology ; Escherichia coli - enzymology ; Escherichia coli - genetics ; Escherichia coli - isolation & purification ; Escherichia coli Infections - microbiology ; Female ; Genomes ; Humans ; Hybridization ; Identification ; Lactobacillus casei ; Methods ; Microbial drug resistance ; Molecular Typing - methods ; Molecular Typing - standards ; Multilocus sequence typing ; Phylogenetics ; Phylogeny ; Plasmids ; Plasmids - classification ; Plasmids - genetics ; Polymerase Chain Reaction - standards ; Primers ; Protein families ; Proteins ; Proteobacteria ; Reference Standards ; Relaxase ; Trans-Activators - genetics ; Urinary Tract Infections - microbiology ; Veterinary Science ; Virulence ; Virulence (Microbiology)</subject><ispartof>PloS one, 2012-07, Vol.7 (7), p.e40438-e40438</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Alvarado et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Alvarado et al. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c659t-402e1c18d850aa1db2d61d8e93dac0efc3638c9246e0f29c7692c3e63a06a2553</citedby><cites>FETCH-LOGICAL-c659t-402e1c18d850aa1db2d61d8e93dac0efc3638c9246e0f29c7692c3e63a06a2553</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394729/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394729/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23847,27903,27904,53769,53771,79346,79347</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22792321$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Cloeckaert, Axel</contributor><creatorcontrib>Alvarado, Andrés</creatorcontrib><creatorcontrib>Garcillán-Barcia, M Pilar</creatorcontrib><creatorcontrib>de la Cruz, Fernando</creatorcontrib><title>A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>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. 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Alvarado, Andrés</au><au>Garcillán-Barcia, M Pilar</au><au>de la Cruz, Fernando</au><au>Cloeckaert, Axel</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2012-07-11</date><risdate>2012</risdate><volume>7</volume><issue>7</issue><spage>e40438</spage><epage>e40438</epage><pages>e40438-e40438</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22792321</pmid><doi>10.1371/journal.pone.0040438</doi><oa>free_for_read</oa></addata></record> |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; Full-Text Journals in Chemistry (Open access); DOAJ Directory of Open Access Journals; PubMed Central; EZB Electronic Journals Library |
| subjects | Amino Acid Sequence Amino acids Antibiotic resistance Antibiotics Bacterial Proteins - genetics Base Sequence Biology Clinical isolates Deoxyribonucleic acid DNA DNA Primers - genetics Ecological effects Endodeoxyribonucleases - genetics Environmental Microbiology Epidemiology Escherichia coli - enzymology Escherichia coli - genetics Escherichia coli - isolation & purification Escherichia coli Infections - microbiology Female Genomes Humans Hybridization Identification Lactobacillus casei Methods Microbial drug resistance Molecular Typing - methods Molecular Typing - standards Multilocus sequence typing Phylogenetics Phylogeny Plasmids Plasmids - classification Plasmids - genetics Polymerase Chain Reaction - standards Primers Protein families Proteins Proteobacteria Reference Standards Relaxase Trans-Activators - genetics Urinary Tract Infections - microbiology Veterinary Science Virulence Virulence (Microbiology) |
| title | A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings |
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