Loading…
Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers
The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex...
Saved in:
| Published in: | Journal of microbiological methods 2015-10, Vol.117, p.108-112 |
|---|---|
| Main Authors: | , , , , , , , , , , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that this one cites Items that cite this one |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | cdi_FETCH-LOGICAL-c392t-7ba2b5a727f3c849380390c48cda93f061834374414f8e22da917f62b10c96293 |
|---|---|
| cites | cdi_FETCH-LOGICAL-c392t-7ba2b5a727f3c849380390c48cda93f061834374414f8e22da917f62b10c96293 |
| container_end_page | 112 |
| container_issue | |
| container_start_page | 108 |
| container_title | Journal of microbiological methods |
| container_volume | 117 |
| creator | Perrin, Elena Fondi, Marco Maida, Isabel Mengoni, Alessio Chiellini, Carolina Mocali, Stefano Cocchi, Priscilla Campana, Silvia Taccetti, Giovanni Vaneechoutte, Mario Fani, Renato |
| description | The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex as a model, genomic analyses were performed to check the phylogenetic distribution of an overlap between marC and hisH genes and then, a PCR specific for Burkholderia was designed, set up and tested on a panel of strains and on DNA extracted from the sputum of cystic fibrosis patients. Results obtained revealed the usefulness of this approach, which could then be used to develop PCR for the identification of specific bacteria species or genera.
•Comparative microbial genomes analysis could be used in the field of microbial identification.•The use of overlapping genes for this purpose was evaluated.•The phylogenetic distribution of an overlap between marC and hisH genes was analyzed.•A PCR on this overlap, specific for Burkholderia, was designed, set up and tested. |
| doi_str_mv | 10.1016/j.mimet.2015.07.025 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1746895214</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0167701215300336</els_id><sourcerecordid>1746895214</sourcerecordid><originalsourceid>FETCH-LOGICAL-c392t-7ba2b5a727f3c849380390c48cda93f061834374414f8e22da917f62b10c96293</originalsourceid><addsrcrecordid>eNqNkU1LxDAQhoMouq7-AkFy9NKarzap4EEWv2DBi55Dmk41a9usSSv478266lE8zTA8877MvAidUJJTQsvzVd67HsacEVrkROaEFTtoRpVkmeJFtYtmiZKZJJQdoMMYVySBXKh9dMBKxotC8BnStzD4HiI2g-k-ots0Da6NHSE4g10Dw-haZ83o_HCBH18ATxGwb7F_h9CZ9doNz_gZho1ExL3vwE6dCbg34RVCPEJ7rekiHH_XOXq6uX5c3GXLh9v7xdUys7xiYyZrw-rCSCZbbpWouCK8IlYo25iKt6SkigsuhaCiVcBYmlLZlqymxFYlq_gcnW1118G_TRBH3btooevMAH6KmkpRqqpgVPwDpTyRBaUJ5VvUBh9jgFavg0uXfWhK9CYEvdJfIehNCJpInUJIW6ffBlPdQ_O78_P1BFxuAUgfeXcQdLQOBguNC2BH3Xj3p8EnsyuYcg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1713952511</pqid></control><display><type>article</type><title>Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers</title><source>Elsevier</source><creator>Perrin, Elena ; Fondi, Marco ; Maida, Isabel ; Mengoni, Alessio ; Chiellini, Carolina ; Mocali, Stefano ; Cocchi, Priscilla ; Campana, Silvia ; Taccetti, Giovanni ; Vaneechoutte, Mario ; Fani, Renato</creator><creatorcontrib>Perrin, Elena ; Fondi, Marco ; Maida, Isabel ; Mengoni, Alessio ; Chiellini, Carolina ; Mocali, Stefano ; Cocchi, Priscilla ; Campana, Silvia ; Taccetti, Giovanni ; Vaneechoutte, Mario ; Fani, Renato</creatorcontrib><description>The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex as a model, genomic analyses were performed to check the phylogenetic distribution of an overlap between marC and hisH genes and then, a PCR specific for Burkholderia was designed, set up and tested on a panel of strains and on DNA extracted from the sputum of cystic fibrosis patients. Results obtained revealed the usefulness of this approach, which could then be used to develop PCR for the identification of specific bacteria species or genera.
•Comparative microbial genomes analysis could be used in the field of microbial identification.•The use of overlapping genes for this purpose was evaluated.•The phylogenetic distribution of an overlap between marC and hisH genes was analyzed.•A PCR on this overlap, specific for Burkholderia, was designed, set up and tested.</description><identifier>ISSN: 0167-7012</identifier><identifier>EISSN: 1872-8359</identifier><identifier>DOI: 10.1016/j.mimet.2015.07.025</identifier><identifier>PMID: 26235543</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Bacteria ; Burkholderia cepacia ; Burkholderia cepacia complex ; Burkholderia cepacia complex - genetics ; Burkholderia cepacia complex - isolation & purification ; Burkholderia Infections - diagnosis ; Burkholderia Infections - microbiology ; Cystic Fibrosis - microbiology ; DNA, Bacterial - genetics ; Genes, Overlapping - genetics ; Genetic Markers - genetics ; Genome, Bacterial - genetics ; Genomes ; Humans ; Identification ; marC–hisH ; Molecular Typing - methods ; Overlapping genes ; Polymerase Chain Reaction</subject><ispartof>Journal of microbiological methods, 2015-10, Vol.117, p.108-112</ispartof><rights>2015 Elsevier B.V.</rights><rights>Copyright © 2015 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c392t-7ba2b5a727f3c849380390c48cda93f061834374414f8e22da917f62b10c96293</citedby><cites>FETCH-LOGICAL-c392t-7ba2b5a727f3c849380390c48cda93f061834374414f8e22da917f62b10c96293</cites><orcidid>0000-0001-9114-2335</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26235543$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Perrin, Elena</creatorcontrib><creatorcontrib>Fondi, Marco</creatorcontrib><creatorcontrib>Maida, Isabel</creatorcontrib><creatorcontrib>Mengoni, Alessio</creatorcontrib><creatorcontrib>Chiellini, Carolina</creatorcontrib><creatorcontrib>Mocali, Stefano</creatorcontrib><creatorcontrib>Cocchi, Priscilla</creatorcontrib><creatorcontrib>Campana, Silvia</creatorcontrib><creatorcontrib>Taccetti, Giovanni</creatorcontrib><creatorcontrib>Vaneechoutte, Mario</creatorcontrib><creatorcontrib>Fani, Renato</creatorcontrib><title>Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers</title><title>Journal of microbiological methods</title><addtitle>J Microbiol Methods</addtitle><description>The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex as a model, genomic analyses were performed to check the phylogenetic distribution of an overlap between marC and hisH genes and then, a PCR specific for Burkholderia was designed, set up and tested on a panel of strains and on DNA extracted from the sputum of cystic fibrosis patients. Results obtained revealed the usefulness of this approach, which could then be used to develop PCR for the identification of specific bacteria species or genera.
•Comparative microbial genomes analysis could be used in the field of microbial identification.•The use of overlapping genes for this purpose was evaluated.•The phylogenetic distribution of an overlap between marC and hisH genes was analyzed.•A PCR on this overlap, specific for Burkholderia, was designed, set up and tested.</description><subject>Bacteria</subject><subject>Burkholderia cepacia</subject><subject>Burkholderia cepacia complex</subject><subject>Burkholderia cepacia complex - genetics</subject><subject>Burkholderia cepacia complex - isolation & purification</subject><subject>Burkholderia Infections - diagnosis</subject><subject>Burkholderia Infections - microbiology</subject><subject>Cystic Fibrosis - microbiology</subject><subject>DNA, Bacterial - genetics</subject><subject>Genes, Overlapping - genetics</subject><subject>Genetic Markers - genetics</subject><subject>Genome, Bacterial - genetics</subject><subject>Genomes</subject><subject>Humans</subject><subject>Identification</subject><subject>marC–hisH</subject><subject>Molecular Typing - methods</subject><subject>Overlapping genes</subject><subject>Polymerase Chain Reaction</subject><issn>0167-7012</issn><issn>1872-8359</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><recordid>eNqNkU1LxDAQhoMouq7-AkFy9NKarzap4EEWv2DBi55Dmk41a9usSSv478266lE8zTA8877MvAidUJJTQsvzVd67HsacEVrkROaEFTtoRpVkmeJFtYtmiZKZJJQdoMMYVySBXKh9dMBKxotC8BnStzD4HiI2g-k-ots0Da6NHSE4g10Dw-haZ83o_HCBH18ATxGwb7F_h9CZ9doNz_gZho1ExL3vwE6dCbg34RVCPEJ7rekiHH_XOXq6uX5c3GXLh9v7xdUys7xiYyZrw-rCSCZbbpWouCK8IlYo25iKt6SkigsuhaCiVcBYmlLZlqymxFYlq_gcnW1118G_TRBH3btooevMAH6KmkpRqqpgVPwDpTyRBaUJ5VvUBh9jgFavg0uXfWhK9CYEvdJfIehNCJpInUJIW6ffBlPdQ_O78_P1BFxuAUgfeXcQdLQOBguNC2BH3Xj3p8EnsyuYcg</recordid><startdate>201510</startdate><enddate>201510</enddate><creator>Perrin, Elena</creator><creator>Fondi, Marco</creator><creator>Maida, Isabel</creator><creator>Mengoni, Alessio</creator><creator>Chiellini, Carolina</creator><creator>Mocali, Stefano</creator><creator>Cocchi, Priscilla</creator><creator>Campana, Silvia</creator><creator>Taccetti, Giovanni</creator><creator>Vaneechoutte, Mario</creator><creator>Fani, Renato</creator><general>Elsevier B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7QL</scope><scope>7T7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><orcidid>https://orcid.org/0000-0001-9114-2335</orcidid></search><sort><creationdate>201510</creationdate><title>Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers</title><author>Perrin, Elena ; Fondi, Marco ; Maida, Isabel ; Mengoni, Alessio ; Chiellini, Carolina ; Mocali, Stefano ; Cocchi, Priscilla ; Campana, Silvia ; Taccetti, Giovanni ; Vaneechoutte, Mario ; Fani, Renato</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c392t-7ba2b5a727f3c849380390c48cda93f061834374414f8e22da917f62b10c96293</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Bacteria</topic><topic>Burkholderia cepacia</topic><topic>Burkholderia cepacia complex</topic><topic>Burkholderia cepacia complex - genetics</topic><topic>Burkholderia cepacia complex - isolation & purification</topic><topic>Burkholderia Infections - diagnosis</topic><topic>Burkholderia Infections - microbiology</topic><topic>Cystic Fibrosis - microbiology</topic><topic>DNA, Bacterial - genetics</topic><topic>Genes, Overlapping - genetics</topic><topic>Genetic Markers - genetics</topic><topic>Genome, Bacterial - genetics</topic><topic>Genomes</topic><topic>Humans</topic><topic>Identification</topic><topic>marC–hisH</topic><topic>Molecular Typing - methods</topic><topic>Overlapping genes</topic><topic>Polymerase Chain Reaction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Perrin, Elena</creatorcontrib><creatorcontrib>Fondi, Marco</creatorcontrib><creatorcontrib>Maida, Isabel</creatorcontrib><creatorcontrib>Mengoni, Alessio</creatorcontrib><creatorcontrib>Chiellini, Carolina</creatorcontrib><creatorcontrib>Mocali, Stefano</creatorcontrib><creatorcontrib>Cocchi, Priscilla</creatorcontrib><creatorcontrib>Campana, Silvia</creatorcontrib><creatorcontrib>Taccetti, Giovanni</creatorcontrib><creatorcontrib>Vaneechoutte, Mario</creatorcontrib><creatorcontrib>Fani, Renato</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Journal of microbiological methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Perrin, Elena</au><au>Fondi, Marco</au><au>Maida, Isabel</au><au>Mengoni, Alessio</au><au>Chiellini, Carolina</au><au>Mocali, Stefano</au><au>Cocchi, Priscilla</au><au>Campana, Silvia</au><au>Taccetti, Giovanni</au><au>Vaneechoutte, Mario</au><au>Fani, Renato</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers</atitle><jtitle>Journal of microbiological methods</jtitle><addtitle>J Microbiol Methods</addtitle><date>2015-10</date><risdate>2015</risdate><volume>117</volume><spage>108</spage><epage>112</epage><pages>108-112</pages><issn>0167-7012</issn><eissn>1872-8359</eissn><abstract>The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex as a model, genomic analyses were performed to check the phylogenetic distribution of an overlap between marC and hisH genes and then, a PCR specific for Burkholderia was designed, set up and tested on a panel of strains and on DNA extracted from the sputum of cystic fibrosis patients. Results obtained revealed the usefulness of this approach, which could then be used to develop PCR for the identification of specific bacteria species or genera.
•Comparative microbial genomes analysis could be used in the field of microbial identification.•The use of overlapping genes for this purpose was evaluated.•The phylogenetic distribution of an overlap between marC and hisH genes was analyzed.•A PCR on this overlap, specific for Burkholderia, was designed, set up and tested.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>26235543</pmid><doi>10.1016/j.mimet.2015.07.025</doi><tpages>5</tpages><orcidid>https://orcid.org/0000-0001-9114-2335</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0167-7012 |
| ispartof | Journal of microbiological methods, 2015-10, Vol.117, p.108-112 |
| issn | 0167-7012 1872-8359 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1746895214 |
| source | Elsevier |
| subjects | Bacteria Burkholderia cepacia Burkholderia cepacia complex Burkholderia cepacia complex - genetics Burkholderia cepacia complex - isolation & purification Burkholderia Infections - diagnosis Burkholderia Infections - microbiology Cystic Fibrosis - microbiology DNA, Bacterial - genetics Genes, Overlapping - genetics Genetic Markers - genetics Genome, Bacterial - genetics Genomes Humans Identification marC–hisH Molecular Typing - methods Overlapping genes Polymerase Chain Reaction |
| title | Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-05T02%3A08%3A20IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genomes%20analysis%20and%20bacteria%20identification:%20The%20use%20of%20overlapping%20genes%20as%20molecular%20markers&rft.jtitle=Journal%20of%20microbiological%20methods&rft.au=Perrin,%20Elena&rft.date=2015-10&rft.volume=117&rft.spage=108&rft.epage=112&rft.pages=108-112&rft.issn=0167-7012&rft.eissn=1872-8359&rft_id=info:doi/10.1016/j.mimet.2015.07.025&rft_dat=%3Cproquest_cross%3E1746895214%3C/proquest_cross%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c392t-7ba2b5a727f3c849380390c48cda93f061834374414f8e22da917f62b10c96293%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=1713952511&rft_id=info:pmid/26235543&rfr_iscdi=true |