Ligation-mediated PCR, a fast and reliable technique for insertion sequence-based typing of Xanthomonas citri pv. citri
Asiatic citrus canker, caused by Xanthomonas citri pv. citri, is a major disease threatening citrus crops throughout the world. The most common methods for strain differentiation of this pathogen are repetitive element sequence-based PCR (rep-PCR) and pulsed field gel electrophoresis (PFGE), using r...
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| Veröffentlicht in: | FEMS microbiology letters 2008-11, Vol.288 (1), p.33-39 |
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| creator | Bui Thi Ngoc, Lan Vernière, Christian Belasque, José Jr Vital, Karine Boutry, Sébastien Gagnevin, Lionel Pruvost, Olivier |
| description | Asiatic citrus canker, caused by Xanthomonas citri pv. citri, is a major disease threatening citrus crops throughout the world. The most common methods for strain differentiation of this pathogen are repetitive element sequence-based PCR (rep-PCR) and pulsed field gel electrophoresis (PFGE), using rare-cutting restriction enzyme analysis. We developed a ligation-mediated PCR targeting three insertion sequences (IS-LM-PCR) present as several copies in the genome of the fully sequenced strain 306 of X. citri pv. citri. This technique amplifies DNA fragments between an insertion sequence element and an MspI restriction site. The analysis of strains can be conducted within 24 h, starting from very small amounts of bacterial DNA, which makes IS-LM-PCR much less labor-intensive than PFGE. We used IS-LM-PCR to analyze a collection of 66 strains of X. citri pv. citri from around the world. The overall reproducibility of IS-LM-PCR reached 98% in this data set and its discriminatory power was markedly superior than rep-PCR. We suggest that IS-LM-PCR could be used for the global surveillance of nonepidemiologically related strains of X. citri pv. citri. |
| doi_str_mv | 10.1111/j.1574-6968.2008.01331.x |
| format | Article |
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The most common methods for strain differentiation of this pathogen are repetitive element sequence-based PCR (rep-PCR) and pulsed field gel electrophoresis (PFGE), using rare-cutting restriction enzyme analysis. We developed a ligation-mediated PCR targeting three insertion sequences (IS-LM-PCR) present as several copies in the genome of the fully sequenced strain 306 of X. citri pv. citri. This technique amplifies DNA fragments between an insertion sequence element and an MspI restriction site. The analysis of strains can be conducted within 24 h, starting from very small amounts of bacterial DNA, which makes IS-LM-PCR much less labor-intensive than PFGE. We used IS-LM-PCR to analyze a collection of 66 strains of X. citri pv. citri from around the world. The overall reproducibility of IS-LM-PCR reached 98% in this data set and its discriminatory power was markedly superior than rep-PCR. We suggest that IS-LM-PCR could be used for the global surveillance of nonepidemiologically related strains of X. citri pv. citri.</description><identifier>ISSN: 0378-1097</identifier><identifier>EISSN: 1574-6968</identifier><identifier>DOI: 10.1111/j.1574-6968.2008.01331.x</identifier><identifier>PMID: 18771421</identifier><identifier>CODEN: FMLED7</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>Asiatic citrus canker ; Bacterial Typing Techniques - methods ; Bacteriological methods and techniques used in bacteriology ; Bacteriology ; Biological and medical sciences ; Canker ; Citrus ; Citrus - microbiology ; Deoxyribonucleic acid ; DNA ; DNA Transposable Elements ; Electrophoresis ; Fundamental and applied biological sciences. Psychology ; Gel electrophoresis ; Gene sequencing ; Genomes ; Insertion ; insertion sequence ; Insertion sequences ; Ligase Chain Reaction - methods ; Microbiology ; molecular epidemiology ; monitoring ; Nucleotide sequence ; Phylogeny ; Plant Diseases - microbiology ; Polymerase chain reaction ; Rutaceae ; Strains (organisms) ; surveillance ; Xanthomonas ; Xanthomonas - classification ; Xanthomonas - genetics ; Xanthomonas - isolation & purification ; Xanthomonas citri ; Xanthomonas citri pv. citri</subject><ispartof>FEMS microbiology letters, 2008-11, Vol.288 (1), p.33-39</ispartof><rights>2008 Federation of European Microbiological Societies 2008</rights><rights>2008 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved</rights><rights>2009 INIST-CNRS</rights><rights>2008 Federation of European Microbiological Societies</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5241-1c8f551c9d1f66e5fa4ff27a3735898c49f44f6d260dcefb3637a3a04f77da473</citedby><cites>FETCH-LOGICAL-c5241-1c8f551c9d1f66e5fa4ff27a3735898c49f44f6d260dcefb3637a3a04f77da473</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1574-6968.2008.01331.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1574-6968.2008.01331.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=20747867$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18771421$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bui Thi Ngoc, Lan</creatorcontrib><creatorcontrib>Vernière, Christian</creatorcontrib><creatorcontrib>Belasque, José Jr</creatorcontrib><creatorcontrib>Vital, Karine</creatorcontrib><creatorcontrib>Boutry, Sébastien</creatorcontrib><creatorcontrib>Gagnevin, Lionel</creatorcontrib><creatorcontrib>Pruvost, Olivier</creatorcontrib><title>Ligation-mediated PCR, a fast and reliable technique for insertion sequence-based typing of Xanthomonas citri pv. citri</title><title>FEMS microbiology letters</title><addtitle>FEMS Microbiol Lett</addtitle><description>Asiatic citrus canker, caused by Xanthomonas citri pv. citri, is a major disease threatening citrus crops throughout the world. The most common methods for strain differentiation of this pathogen are repetitive element sequence-based PCR (rep-PCR) and pulsed field gel electrophoresis (PFGE), using rare-cutting restriction enzyme analysis. We developed a ligation-mediated PCR targeting three insertion sequences (IS-LM-PCR) present as several copies in the genome of the fully sequenced strain 306 of X. citri pv. citri. This technique amplifies DNA fragments between an insertion sequence element and an MspI restriction site. The analysis of strains can be conducted within 24 h, starting from very small amounts of bacterial DNA, which makes IS-LM-PCR much less labor-intensive than PFGE. We used IS-LM-PCR to analyze a collection of 66 strains of X. citri pv. citri from around the world. The overall reproducibility of IS-LM-PCR reached 98% in this data set and its discriminatory power was markedly superior than rep-PCR. We suggest that IS-LM-PCR could be used for the global surveillance of nonepidemiologically related strains of X. citri pv. citri.</description><subject>Asiatic citrus canker</subject><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>Canker</subject><subject>Citrus</subject><subject>Citrus - microbiology</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Transposable Elements</subject><subject>Electrophoresis</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gel electrophoresis</subject><subject>Gene sequencing</subject><subject>Genomes</subject><subject>Insertion</subject><subject>insertion sequence</subject><subject>Insertion sequences</subject><subject>Ligase Chain Reaction - methods</subject><subject>Microbiology</subject><subject>molecular epidemiology</subject><subject>monitoring</subject><subject>Nucleotide sequence</subject><subject>Phylogeny</subject><subject>Plant Diseases - microbiology</subject><subject>Polymerase chain reaction</subject><subject>Rutaceae</subject><subject>Strains (organisms)</subject><subject>surveillance</subject><subject>Xanthomonas</subject><subject>Xanthomonas - classification</subject><subject>Xanthomonas - genetics</subject><subject>Xanthomonas - isolation & purification</subject><subject>Xanthomonas citri</subject><subject>Xanthomonas citri pv. citri</subject><issn>0378-1097</issn><issn>1574-6968</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkV1rFDEUhgdRbK3-BQ2IXjljvibJXHghi1VhRVEL3oWzmWSbZTbZJrO2--_NOEsFUTQ3CTnPk5zDW1WI4IaU9XLTkFbyWnRCNRRj1WDCGGlu7lSnt4W71SlmUtUEd_KkepDzBmPMKRb3qxOipCScktPqeunXMPoY6q3tPYy2R58Wn18gQA7yiCD0KNnBw2qwaLTmMvirvUUuJuRDtmkyUbblLhhbryAXfzzsfFij6NA3CONl3MYAGRk_Jo9235v59LC652DI9tFxP6suzt98Xbyrlx_fvl-8XtampZzUxCjXtsR0PXFC2NYBd45KYJK1qlOGd45zJ3oqcG-sWzHBShEwd1L2wCU7q57P7-5SLF3mUW99NnYYINi4z1p0HRWcdf8EKeatahku4NPfwE3cp1CG0JRh0VLFO14oNVMmxZyTdXqX_BbSQROspwz1Rk9R6SkqPWWof2aob4r6-PjBflVC-SUeQyvAsyMA2cDgEgTj8y1HseRSiWn2VzN37Qd7-O8G9PmH5XQqPpv9uN_9xa7_1P6T2XIQNaxT6eziCy1VTFpOlOrYD5cIz14</recordid><startdate>200811</startdate><enddate>200811</enddate><creator>Bui Thi Ngoc, Lan</creator><creator>Vernière, Christian</creator><creator>Belasque, José Jr</creator><creator>Vital, Karine</creator><creator>Boutry, Sébastien</creator><creator>Gagnevin, Lionel</creator><creator>Pruvost, Olivier</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><general>Wiley-Blackwell</general><general>Oxford University Press</general><scope>FBQ</scope><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>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>200811</creationdate><title>Ligation-mediated PCR, a fast and reliable technique for insertion sequence-based typing of Xanthomonas citri pv. citri</title><author>Bui Thi Ngoc, Lan ; Vernière, Christian ; Belasque, José Jr ; Vital, Karine ; Boutry, Sébastien ; Gagnevin, Lionel ; Pruvost, Olivier</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5241-1c8f551c9d1f66e5fa4ff27a3735898c49f44f6d260dcefb3637a3a04f77da473</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Asiatic citrus canker</topic><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>Canker</topic><topic>Citrus</topic><topic>Citrus - microbiology</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Transposable Elements</topic><topic>Electrophoresis</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gel electrophoresis</topic><topic>Gene sequencing</topic><topic>Genomes</topic><topic>Insertion</topic><topic>insertion sequence</topic><topic>Insertion sequences</topic><topic>Ligase Chain Reaction - methods</topic><topic>Microbiology</topic><topic>molecular epidemiology</topic><topic>monitoring</topic><topic>Nucleotide sequence</topic><topic>Phylogeny</topic><topic>Plant Diseases - microbiology</topic><topic>Polymerase chain reaction</topic><topic>Rutaceae</topic><topic>Strains (organisms)</topic><topic>surveillance</topic><topic>Xanthomonas</topic><topic>Xanthomonas - classification</topic><topic>Xanthomonas - genetics</topic><topic>Xanthomonas - isolation & purification</topic><topic>Xanthomonas citri</topic><topic>Xanthomonas citri pv. citri</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bui Thi Ngoc, Lan</creatorcontrib><creatorcontrib>Vernière, Christian</creatorcontrib><creatorcontrib>Belasque, José Jr</creatorcontrib><creatorcontrib>Vital, Karine</creatorcontrib><creatorcontrib>Boutry, Sébastien</creatorcontrib><creatorcontrib>Gagnevin, Lionel</creatorcontrib><creatorcontrib>Pruvost, Olivier</creatorcontrib><collection>AGRIS</collection><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>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>FEMS microbiology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bui Thi Ngoc, Lan</au><au>Vernière, Christian</au><au>Belasque, José Jr</au><au>Vital, Karine</au><au>Boutry, Sébastien</au><au>Gagnevin, Lionel</au><au>Pruvost, Olivier</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Ligation-mediated PCR, a fast and reliable technique for insertion sequence-based typing of Xanthomonas citri pv. citri</atitle><jtitle>FEMS microbiology letters</jtitle><addtitle>FEMS Microbiol Lett</addtitle><date>2008-11</date><risdate>2008</risdate><volume>288</volume><issue>1</issue><spage>33</spage><epage>39</epage><pages>33-39</pages><issn>0378-1097</issn><eissn>1574-6968</eissn><coden>FMLED7</coden><abstract>Asiatic citrus canker, caused by Xanthomonas citri pv. citri, is a major disease threatening citrus crops throughout the world. The most common methods for strain differentiation of this pathogen are repetitive element sequence-based PCR (rep-PCR) and pulsed field gel electrophoresis (PFGE), using rare-cutting restriction enzyme analysis. We developed a ligation-mediated PCR targeting three insertion sequences (IS-LM-PCR) present as several copies in the genome of the fully sequenced strain 306 of X. citri pv. citri. This technique amplifies DNA fragments between an insertion sequence element and an MspI restriction site. The analysis of strains can be conducted within 24 h, starting from very small amounts of bacterial DNA, which makes IS-LM-PCR much less labor-intensive than PFGE. We used IS-LM-PCR to analyze a collection of 66 strains of X. citri pv. citri from around the world. The overall reproducibility of IS-LM-PCR reached 98% in this data set and its discriminatory power was markedly superior than rep-PCR. We suggest that IS-LM-PCR could be used for the global surveillance of nonepidemiologically related strains of X. citri pv. citri.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>18771421</pmid><doi>10.1111/j.1574-6968.2008.01331.x</doi><tpages>7</tpages></addata></record> |
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| subjects | Asiatic citrus canker Bacterial Typing Techniques - methods Bacteriological methods and techniques used in bacteriology Bacteriology Biological and medical sciences Canker Citrus Citrus - microbiology Deoxyribonucleic acid DNA DNA Transposable Elements Electrophoresis Fundamental and applied biological sciences. Psychology Gel electrophoresis Gene sequencing Genomes Insertion insertion sequence Insertion sequences Ligase Chain Reaction - methods Microbiology molecular epidemiology monitoring Nucleotide sequence Phylogeny Plant Diseases - microbiology Polymerase chain reaction Rutaceae Strains (organisms) surveillance Xanthomonas Xanthomonas - classification Xanthomonas - genetics Xanthomonas - isolation & purification Xanthomonas citri Xanthomonas citri pv. citri |
| title | Ligation-mediated PCR, a fast and reliable technique for insertion sequence-based typing of Xanthomonas citri pv. citri |
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