Application of multiplex single nucleotide primer extension (mSNuPE) to the identification of bacteria: The Burkholderia cepacia complex case
Burkholderia cepacia complex (BCC) is characterized by a complex taxonomy constituted by seventeen closely related species of both biotechnological and clinical importance. Several molecular methods have been developed to accurately identify BCC species but simpler and effective strategies for BCC c...
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| Veröffentlicht in: | Journal of microbiological methods 2010-03, Vol.80 (3), p.251-256 |
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| creator | Ferri, L. Perrin, E. Campana, S. Tabacchioni, S. Taccetti, G. Cocchi, P. Ravenni, N. Dalmastri, C. Chiarini, L. Bevivino, A. Manno, G. Mentasti, M. Fani, R. |
| description | Burkholderia cepacia complex (BCC) is characterized by a complex taxonomy constituted by seventeen closely related species of both biotechnological and clinical importance. Several molecular methods have been developed to accurately identify BCC species but simpler and effective strategies for BCC classification are still needed.
A single nucleotide primer extension (SNuPE) assay using
gyrB as a target gene was developed to identify bacteria belonging to the
B. cepacia (BCC) complex. This technique allows the successful detection and distinction of single nucleotide polymorphisms (SNPs) and is effectively applied in routine medical diagnosis since it permits to analyze routinely many samples in a few times.
Seven SNuPE primers were designed analyzing the conserved regions of the BCC
gyrB sequences currently available in databases. The specificity of the assay was evaluated using reference strains of some BCC species. Data obtained enabled to discriminate bacteria belonging to the species
B. multivorans,
B. cenocepacia (including bacteria belonging to
recA lineages III-A, III-C, and III-D),
B. vietnamiensis,
B. dolosa,
B. ambifaria,
B. anthina and
B. pyrrocinia. Conversely, identification failed for
B. cepacia,
B. cenocepacia III-B and
B. stabilis. This study demonstrates the efficacy of SNuPE technique for the identification of bacteria characterized by a complex taxonomical organization as BCC bacteria. |
| doi_str_mv | 10.1016/j.mimet.2010.01.008 |
| format | Article |
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A single nucleotide primer extension (SNuPE) assay using
gyrB as a target gene was developed to identify bacteria belonging to the
B. cepacia (BCC) complex. This technique allows the successful detection and distinction of single nucleotide polymorphisms (SNPs) and is effectively applied in routine medical diagnosis since it permits to analyze routinely many samples in a few times.
Seven SNuPE primers were designed analyzing the conserved regions of the BCC
gyrB sequences currently available in databases. The specificity of the assay was evaluated using reference strains of some BCC species. Data obtained enabled to discriminate bacteria belonging to the species
B. multivorans,
B. cenocepacia (including bacteria belonging to
recA lineages III-A, III-C, and III-D),
B. vietnamiensis,
B. dolosa,
B. ambifaria,
B. anthina and
B. pyrrocinia. Conversely, identification failed for
B. cepacia,
B. cenocepacia III-B and
B. stabilis. This study demonstrates the efficacy of SNuPE technique for the identification of bacteria characterized by a complex taxonomical organization as BCC bacteria.</description><identifier>ISSN: 0167-7012</identifier><identifier>EISSN: 1872-8359</identifier><identifier>DOI: 10.1016/j.mimet.2010.01.008</identifier><identifier>PMID: 20079386</identifier><identifier>CODEN: JMIMDQ</identifier><language>eng</language><publisher>Amsterdam: Elsevier B.V</publisher><subject>Bacterial Typing Techniques - methods ; Bacteriological methods and techniques used in bacteriology ; Bacteriology ; Biological and medical sciences ; Burkholderia cepacia ; Burkholderia cepacia complex ; Burkholderia cepacia complex - classification ; Burkholderia cepacia complex - genetics ; Burkholderia cepacia complex - isolation & purification ; Burkholderia Infections - diagnosis ; Burkholderia Infections - microbiology ; DNA Gyrase - analysis ; DNA Gyrase - genetics ; DNA Primers ; DNA, Bacterial - analysis ; DNA, Bacterial - genetics ; Fundamental and applied biological sciences. Psychology ; Genetic Variation ; Humans ; Identification ; Microbiology ; Polymorphism, Single Nucleotide ; Sensitivity and Specificity ; Sequence Analysis, DNA - methods ; Single nucleotide polymorphisms ; Species Specificity</subject><ispartof>Journal of microbiological methods, 2010-03, Vol.80 (3), p.251-256</ispartof><rights>2010 Elsevier B.V.</rights><rights>2015 INIST-CNRS</rights><rights>Copyright 2010 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c420t-d1842ac6d777e40e67f5346e99279e9c736bad7b6921c66162427827f7fedfb13</citedby><cites>FETCH-LOGICAL-c420t-d1842ac6d777e40e67f5346e99279e9c736bad7b6921c66162427827f7fedfb13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.mimet.2010.01.008$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3536,27903,27904,45974</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22525878$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20079386$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ferri, L.</creatorcontrib><creatorcontrib>Perrin, E.</creatorcontrib><creatorcontrib>Campana, S.</creatorcontrib><creatorcontrib>Tabacchioni, S.</creatorcontrib><creatorcontrib>Taccetti, G.</creatorcontrib><creatorcontrib>Cocchi, P.</creatorcontrib><creatorcontrib>Ravenni, N.</creatorcontrib><creatorcontrib>Dalmastri, C.</creatorcontrib><creatorcontrib>Chiarini, L.</creatorcontrib><creatorcontrib>Bevivino, A.</creatorcontrib><creatorcontrib>Manno, G.</creatorcontrib><creatorcontrib>Mentasti, M.</creatorcontrib><creatorcontrib>Fani, R.</creatorcontrib><title>Application of multiplex single nucleotide primer extension (mSNuPE) to the identification of bacteria: The Burkholderia cepacia complex case</title><title>Journal of microbiological methods</title><addtitle>J Microbiol Methods</addtitle><description>Burkholderia cepacia complex (BCC) is characterized by a complex taxonomy constituted by seventeen closely related species of both biotechnological and clinical importance. Several molecular methods have been developed to accurately identify BCC species but simpler and effective strategies for BCC classification are still needed.
A single nucleotide primer extension (SNuPE) assay using
gyrB as a target gene was developed to identify bacteria belonging to the
B. cepacia (BCC) complex. This technique allows the successful detection and distinction of single nucleotide polymorphisms (SNPs) and is effectively applied in routine medical diagnosis since it permits to analyze routinely many samples in a few times.
Seven SNuPE primers were designed analyzing the conserved regions of the BCC
gyrB sequences currently available in databases. The specificity of the assay was evaluated using reference strains of some BCC species. Data obtained enabled to discriminate bacteria belonging to the species
B. multivorans,
B. cenocepacia (including bacteria belonging to
recA lineages III-A, III-C, and III-D),
B. vietnamiensis,
B. dolosa,
B. ambifaria,
B. anthina and
B. pyrrocinia. Conversely, identification failed for
B. cepacia,
B. cenocepacia III-B and
B. stabilis. This study demonstrates the efficacy of SNuPE technique for the identification of bacteria characterized by a complex taxonomical organization as BCC bacteria.</description><subject>Bacterial Typing Techniques - methods</subject><subject>Bacteriological methods and techniques used in bacteriology</subject><subject>Bacteriology</subject><subject>Biological and medical sciences</subject><subject>Burkholderia cepacia</subject><subject>Burkholderia cepacia complex</subject><subject>Burkholderia cepacia complex - classification</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>DNA Gyrase - analysis</subject><subject>DNA Gyrase - genetics</subject><subject>DNA Primers</subject><subject>DNA, Bacterial - analysis</subject><subject>DNA, Bacterial - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genetic Variation</subject><subject>Humans</subject><subject>Identification</subject><subject>Microbiology</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Sensitivity and Specificity</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Single nucleotide polymorphisms</subject><subject>Species Specificity</subject><issn>0167-7012</issn><issn>1872-8359</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkctu1TAQhi0EoofCEyAhbxCwyMGXxE4qsShVuUgVIFHWluOMqQ9OHGwHlYfgnXF6DpcVrEaa-eafy4_QQ0q2lFDxfLcd3Qh5y0jJELolpL2FNrSVrGp5091Gm0LJShLKjtC9lHaE0IbX7V10xAiRHW_FBv04nWfvjM4uTDhYPC4-u9nDNU5u-uwBT4vxELIbAM-xzIsYrjNMaeWfjh_fLR_On-EccL4CXKApO_uXXK9Nhuj0Cb4s9ZdL_HIV_LBmsIFZmzWG8Wae0QnuoztW-wQPDvEYfXp1fnn2prp4__rt2elFZWpGcjXQtmbaiEFKCTUBIW05TEDXMdlBZyQXvR5kLzpGjRBUsJrJlkkrLQy2p_wYPdnrzjF8XSBlNbpkwHs9QViSknUjOONt_X-Sc055R1aS70kTQ0oRrFr_peN3RYlaDVM7dWOYWg1ThKpiWOl6dNBf-hGG3z2_HCrA4wOgk9HeRj0Zl_5wrGFNK1ehF3sOyt--OYgqGQeTgcFFMFkNwf1zkZ_aPbY9</recordid><startdate>20100301</startdate><enddate>20100301</enddate><creator>Ferri, L.</creator><creator>Perrin, E.</creator><creator>Campana, S.</creator><creator>Tabacchioni, S.</creator><creator>Taccetti, G.</creator><creator>Cocchi, P.</creator><creator>Ravenni, N.</creator><creator>Dalmastri, C.</creator><creator>Chiarini, L.</creator><creator>Bevivino, A.</creator><creator>Manno, G.</creator><creator>Mentasti, M.</creator><creator>Fani, R.</creator><general>Elsevier B.V</general><general>Elsevier</general><scope>IQODW</scope><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>7TM</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>L.G</scope><scope>P64</scope></search><sort><creationdate>20100301</creationdate><title>Application of multiplex single nucleotide primer extension (mSNuPE) to the identification of bacteria: The Burkholderia cepacia complex case</title><author>Ferri, L. ; Perrin, E. ; Campana, S. ; Tabacchioni, S. ; Taccetti, G. ; Cocchi, P. ; Ravenni, N. ; Dalmastri, C. ; Chiarini, L. ; Bevivino, A. ; Manno, G. ; Mentasti, M. ; Fani, R.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c420t-d1842ac6d777e40e67f5346e99279e9c736bad7b6921c66162427827f7fedfb13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Bacterial Typing Techniques - methods</topic><topic>Bacteriological methods and techniques used in bacteriology</topic><topic>Bacteriology</topic><topic>Biological and medical sciences</topic><topic>Burkholderia cepacia</topic><topic>Burkholderia cepacia complex</topic><topic>Burkholderia cepacia complex - classification</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>DNA Gyrase - analysis</topic><topic>DNA Gyrase - genetics</topic><topic>DNA Primers</topic><topic>DNA, Bacterial - analysis</topic><topic>DNA, Bacterial - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genetic Variation</topic><topic>Humans</topic><topic>Identification</topic><topic>Microbiology</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Sensitivity and Specificity</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Single nucleotide polymorphisms</topic><topic>Species Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ferri, L.</creatorcontrib><creatorcontrib>Perrin, E.</creatorcontrib><creatorcontrib>Campana, S.</creatorcontrib><creatorcontrib>Tabacchioni, S.</creatorcontrib><creatorcontrib>Taccetti, G.</creatorcontrib><creatorcontrib>Cocchi, P.</creatorcontrib><creatorcontrib>Ravenni, N.</creatorcontrib><creatorcontrib>Dalmastri, C.</creatorcontrib><creatorcontrib>Chiarini, L.</creatorcontrib><creatorcontrib>Bevivino, A.</creatorcontrib><creatorcontrib>Manno, G.</creatorcontrib><creatorcontrib>Mentasti, M.</creatorcontrib><creatorcontrib>Fani, R.</creatorcontrib><collection>Pascal-Francis</collection><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>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><jtitle>Journal of microbiological methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ferri, L.</au><au>Perrin, E.</au><au>Campana, S.</au><au>Tabacchioni, S.</au><au>Taccetti, G.</au><au>Cocchi, P.</au><au>Ravenni, N.</au><au>Dalmastri, C.</au><au>Chiarini, L.</au><au>Bevivino, A.</au><au>Manno, G.</au><au>Mentasti, M.</au><au>Fani, R.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Application of multiplex single nucleotide primer extension (mSNuPE) to the identification of bacteria: The Burkholderia cepacia complex case</atitle><jtitle>Journal of microbiological methods</jtitle><addtitle>J Microbiol Methods</addtitle><date>2010-03-01</date><risdate>2010</risdate><volume>80</volume><issue>3</issue><spage>251</spage><epage>256</epage><pages>251-256</pages><issn>0167-7012</issn><eissn>1872-8359</eissn><coden>JMIMDQ</coden><abstract>Burkholderia cepacia complex (BCC) is characterized by a complex taxonomy constituted by seventeen closely related species of both biotechnological and clinical importance. Several molecular methods have been developed to accurately identify BCC species but simpler and effective strategies for BCC classification are still needed.
A single nucleotide primer extension (SNuPE) assay using
gyrB as a target gene was developed to identify bacteria belonging to the
B. cepacia (BCC) complex. This technique allows the successful detection and distinction of single nucleotide polymorphisms (SNPs) and is effectively applied in routine medical diagnosis since it permits to analyze routinely many samples in a few times.
Seven SNuPE primers were designed analyzing the conserved regions of the BCC
gyrB sequences currently available in databases. The specificity of the assay was evaluated using reference strains of some BCC species. Data obtained enabled to discriminate bacteria belonging to the species
B. multivorans,
B. cenocepacia (including bacteria belonging to
recA lineages III-A, III-C, and III-D),
B. vietnamiensis,
B. dolosa,
B. ambifaria,
B. anthina and
B. pyrrocinia. Conversely, identification failed for
B. cepacia,
B. cenocepacia III-B and
B. stabilis. This study demonstrates the efficacy of SNuPE technique for the identification of bacteria characterized by a complex taxonomical organization as BCC bacteria.</abstract><cop>Amsterdam</cop><pub>Elsevier B.V</pub><pmid>20079386</pmid><doi>10.1016/j.mimet.2010.01.008</doi><tpages>6</tpages></addata></record> |
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| ispartof | Journal of microbiological methods, 2010-03, Vol.80 (3), p.251-256 |
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| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | Bacterial Typing Techniques - methods Bacteriological methods and techniques used in bacteriology Bacteriology Biological and medical sciences Burkholderia cepacia Burkholderia cepacia complex Burkholderia cepacia complex - classification Burkholderia cepacia complex - genetics Burkholderia cepacia complex - isolation & purification Burkholderia Infections - diagnosis Burkholderia Infections - microbiology DNA Gyrase - analysis DNA Gyrase - genetics DNA Primers DNA, Bacterial - analysis DNA, Bacterial - genetics Fundamental and applied biological sciences. Psychology Genetic Variation Humans Identification Microbiology Polymorphism, Single Nucleotide Sensitivity and Specificity Sequence Analysis, DNA - methods Single nucleotide polymorphisms Species Specificity |
| title | Application of multiplex single nucleotide primer extension (mSNuPE) to the identification of bacteria: The Burkholderia cepacia complex case |
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