Real-time loop-mediated isothermal amplification: an early-warning tool for quarantine plant pathogen detection.
Identifieur interne : 000398 ( Main/Exploration ); précédent : 000397; suivant : 000399Real-time loop-mediated isothermal amplification: an early-warning tool for quarantine plant pathogen detection.
Auteurs : Chiara Aglietti [Italie] ; Nicola Luchi [Italie] ; Alessia Lucia Pepori [Italie] ; Paola Bartolini [Italie] ; Francesco Pecori [Italie] ; Aida Raio [Italie] ; Paolo Capretti [Italie] ; Alberto Santini [Italie]Source :
- AMB Express [ 2191-0855 ] ; 2019.
Abstract
An effective framework for early warning and rapid response is a crucial element to prevent or mitigate the impact of biological invasions of plant pathogens, especially at ports of entry. Molecular detection of pathogens by using PCR-based methods usually requires a well-equipped laboratory. Rapid detection tools that can be applied as point-of-care diagnostics are highly desirable, especially to intercept quarantine plant pathogens such as Xylella fastidiosa, Ceratocystis platani and Phytophthora ramorum, three of the most devastating pathogens of trees and ornamental plants in Europe and North America. To this aim, in this study we developed three different loop mediated isothermal amplification (LAMP) assays able to detect each target pathogen both in DNA extracted from axenic culture and in infected plant tissues. By using the portable instrument Genie® II, the LAMP assay was able to recognize X. fastidiosa, C. platani and P. ramorum DNA within 30 min of isothermal amplification reaction, with high levels of specificity and sensitivity (up to 0.02 pg µL-1 of DNA). These new LAMP-based tools, allowing an on-site rapid detection of pathogens, are especially suited for being used at ports of entry, but they can be also profitably used to monitor and prevent the possible spread of invasive pathogens in natural ecosystems.
DOI: 10.1186/s13568-019-0774-9
PubMed: 31016406
PubMed Central: PMC6478783
Affiliations:
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sortKey="Bartolini, Paola" sort="Bartolini, Paola" uniqKey="Bartolini P" first="Paola" last="Bartolini">Paola Bartolini</name><affiliation wicri:level="1"><nlm:affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze</wicri:regionArea><wicri:noRegion>Firenze</wicri:noRegion></affiliation></author><author><name sortKey="Pecori, Francesco" sort="Pecori, Francesco" uniqKey="Pecori F" first="Francesco" last="Pecori">Francesco Pecori</name><affiliation wicri:level="1"><nlm:affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze</wicri:regionArea><wicri:noRegion>Firenze</wicri:noRegion></affiliation></author><author><name sortKey="Raio, Aida" sort="Raio, Aida" uniqKey="Raio A" first="Aida" last="Raio">Aida Raio</name><affiliation wicri:level="1"><nlm:affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze</wicri:regionArea><wicri:noRegion>Firenze</wicri:noRegion></affiliation></author><author><name sortKey="Capretti, Paolo" sort="Capretti, Paolo" uniqKey="Capretti P" first="Paolo" last="Capretti">Paolo Capretti</name><affiliation wicri:level="1"><nlm:affiliation>Department of Agrifood Production and Environmental Sciences (DISPAA), University of Florence, Piazzale delle Cascine 28, 50144, Firenze, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Agrifood Production and Environmental Sciences (DISPAA), University of Florence, Piazzale delle Cascine 28, 50144, Firenze</wicri:regionArea><wicri:noRegion>Firenze</wicri:noRegion></affiliation></author><author><name sortKey="Santini, Alberto" sort="Santini, Alberto" uniqKey="Santini A" first="Alberto" last="Santini">Alberto Santini</name><affiliation wicri:level="1"><nlm:affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze</wicri:regionArea><wicri:noRegion>Firenze</wicri:noRegion></affiliation></author></analytic><series><title level="j">AMB Express</title><idno type="ISSN">2191-0855</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">An effective framework for early warning and rapid response is a crucial element to prevent or mitigate the impact of biological invasions of plant pathogens, especially at ports of entry. Molecular detection of pathogens by using PCR-based methods usually requires a well-equipped laboratory. Rapid detection tools that can be applied as point-of-care diagnostics are highly desirable, especially to intercept quarantine plant pathogens such as Xylella fastidiosa, Ceratocystis platani and Phytophthora ramorum, three of the most devastating pathogens of trees and ornamental plants in Europe and North America. To this aim, in this study we developed three different loop mediated isothermal amplification (LAMP) assays able to detect each target pathogen both in DNA extracted from axenic culture and in infected plant tissues. By using the portable instrument Genie<sup>®</sup> II, the LAMP assay was able to recognize X. fastidiosa, C. platani and P. ramorum DNA within 30 min of isothermal amplification reaction, with high levels of specificity and sensitivity (up to 0.02 pg µL<sup>-1</sup> of DNA). These new LAMP-based tools, allowing an on-site rapid detection of pathogens, are especially suited for being used at ports of entry, but they can be also profitably used to monitor and prevent the possible spread of invasive pathogens in natural ecosystems.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">31016406</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>01</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Print">2191-0855</ISSN><JournalIssue CitedMedium="Print"><Volume>9</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>Apr</Month><Day>24</Day></PubDate></JournalIssue><Title>AMB Express</Title><ISOAbbreviation>AMB Express</ISOAbbreviation></Journal><ArticleTitle>Real-time loop-mediated isothermal amplification: an early-warning tool for quarantine plant pathogen detection.</ArticleTitle><Pagination><MedlinePgn>50</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13568-019-0774-9</ELocationID><Abstract><AbstractText>An effective framework for early warning and rapid response is a crucial element to prevent or mitigate the impact of biological invasions of plant pathogens, especially at ports of entry. Molecular detection of pathogens by using PCR-based methods usually requires a well-equipped laboratory. Rapid detection tools that can be applied as point-of-care diagnostics are highly desirable, especially to intercept quarantine plant pathogens such as Xylella fastidiosa, Ceratocystis platani and Phytophthora ramorum, three of the most devastating pathogens of trees and ornamental plants in Europe and North America. To this aim, in this study we developed three different loop mediated isothermal amplification (LAMP) assays able to detect each target pathogen both in DNA extracted from axenic culture and in infected plant tissues. By using the portable instrument Genie<sup>®</sup> II, the LAMP assay was able to recognize X. fastidiosa, C. platani and P. ramorum DNA within 30 min of isothermal amplification reaction, with high levels of specificity and sensitivity (up to 0.02 pg µL<sup>-1</sup> of DNA). These new LAMP-based tools, allowing an on-site rapid detection of pathogens, are especially suited for being used at ports of entry, but they can be also profitably used to monitor and prevent the possible spread of invasive pathogens in natural ecosystems.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Aglietti</LastName><ForeName>Chiara</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Agrifood Production and Environmental Sciences (DISPAA), University of Florence, Piazzale delle Cascine 28, 50144, Firenze, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luchi</LastName><ForeName>Nicola</ForeName><Initials>N</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-3119-7574</Identifier><AffiliationInfo><Affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy. nicola.luchi@ipsp.cnr.it.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pepori</LastName><ForeName>Alessia Lucia</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bartolini</LastName><ForeName>Paola</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pecori</LastName><ForeName>Francesco</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Raio</LastName><ForeName>Aida</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Capretti</LastName><ForeName>Paolo</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Agrifood Production and Environmental Sciences (DISPAA), University of Florence, Piazzale delle Cascine 28, 50144, Firenze, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Santini</LastName><ForeName>Alberto</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>255</GrantID><Agency>Fondazione Cassa di Risparmio di Pistoia e Pescia</Agency><Country></Country></Grant><Grant><GrantID>771271</GrantID><Agency>Horizon 2020 research and innovation programme</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>04</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>AMB Express</MedlineTA><NlmUniqueID>101561785</NlmUniqueID><ISSNLinking>2191-0855</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Alien pathogens</Keyword><Keyword MajorTopicYN="N">Canker Stain Disease</Keyword><Keyword MajorTopicYN="N">Isothermal amplification</Keyword><Keyword MajorTopicYN="N">LAMP</Keyword><Keyword MajorTopicYN="N">Olive Quick Decline Syndrome</Keyword><Keyword MajorTopicYN="N">Portable diagnostics</Keyword><Keyword MajorTopicYN="N">Sudden Oak Death</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>01</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>04</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>4</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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first="Paolo" last="Capretti">Paolo Capretti</name><name sortKey="Luchi, Nicola" sort="Luchi, Nicola" uniqKey="Luchi N" first="Nicola" last="Luchi">Nicola Luchi</name><name sortKey="Pecori, Francesco" sort="Pecori, Francesco" uniqKey="Pecori F" first="Francesco" last="Pecori">Francesco Pecori</name><name sortKey="Pepori, Alessia Lucia" sort="Pepori, Alessia Lucia" uniqKey="Pepori A" first="Alessia Lucia" last="Pepori">Alessia Lucia Pepori</name><name sortKey="Raio, Aida" sort="Raio, Aida" uniqKey="Raio A" first="Aida" last="Raio">Aida Raio</name><name sortKey="Santini, Alberto" sort="Santini, Alberto" uniqKey="Santini A" first="Alberto" last="Santini">Alberto Santini</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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