In Situ Processing and Efficient Environmental Detection (iSPEED) of tree pests and pathogens using point-of-use real-time PCR.
Identifieur interne : 000154 ( Main/Exploration ); précédent : 000153; suivant : 000155In Situ Processing and Efficient Environmental Detection (iSPEED) of tree pests and pathogens using point-of-use real-time PCR.
Auteurs : Arnaud Capron [Canada] ; Don Stewart [Canada] ; Kelly Hrywkiw [Canada] ; Kiah Allen [Canada] ; Nicolas Feau [Canada] ; Guillaume Bilodeau [Canada] ; Philippe Tanguay [Canada] ; Michel Cusson [Canada] ; Richard C. Hamelin [Canada]Source :
- PloS one [ 1932-6203 ] ; 2020.
Descripteurs français
- KwdFr :
- Arbres (croissance et développement), Arbres (génétique), Arbres (microbiologie), Champignons (génétique), Champignons (isolement et purification), Champignons (pathogénicité), Changement climatique (MeSH), Espèce introduite (MeSH), Forêts (MeSH), Humains (MeSH), Lutte contre les nuisibles (méthodes), Réaction de polymérisation en chaîne (MeSH), Surveillance de l'environnement (MeSH), Écosystème (MeSH).
- MESH :
- croissance et développement : Arbres.
- génétique : Arbres, Champignons.
- isolement et purification : Champignons.
- microbiologie : Arbres.
- méthodes : Lutte contre les nuisibles.
- pathogénicité : Champignons.
- Changement climatique, Espèce introduite, Forêts, Humains, Réaction de polymérisation en chaîne, Surveillance de l'environnement, Écosystème.
English descriptors
- KwdEn :
- Climate Change (MeSH), Ecosystem (MeSH), Environmental Monitoring (MeSH), Forests (MeSH), Fungi (genetics), Fungi (isolation & purification), Fungi (pathogenicity), Humans (MeSH), Introduced Species (MeSH), Pest Control (methods), Polymerase Chain Reaction (MeSH), Trees (genetics), Trees (growth & development), Trees (microbiology).
- MESH :
- genetics : Fungi, Trees.
- growth & development : Trees.
- isolation & purification : Fungi.
- methods : Pest Control.
- microbiology : Trees.
- pathogenicity : Fungi.
- Climate Change, Ecosystem, Environmental Monitoring, Forests, Humans, Introduced Species, Polymerase Chain Reaction.
Abstract
Global trade and climate change are responsible for a surge in foreign invasive species and emerging pests and pathogens across the world. Early detection and surveillance activities are essential to monitor the environment and prevent or mitigate future ecosystem impacts. Molecular diagnostics by DNA testing has become an integral part of this process. However, for environmental applications, there is a need for cost-effective and efficient point-of-use DNA testing to obtain accurate results from remote sites in real-time. This requires the development of simple and fast sample processing and DNA extraction, room-temperature stable reagents and a portable instrument. We developed a point-of-use real-time Polymerase Chain Reaction system using a crude buffer-based DNA extraction protocol and lyophilized, pre-made, reactions for on-site applications. We demonstrate the use of this approach with pathogens and pests covering a broad spectrum of known undesirable forest enemies: the fungi Sphaerulina musiva, Cronartium ribicola and Cronartium comandrae, the oomycete Phytophthora ramorum and the insect Lymantria dispar. We obtained positive DNA identification from a variety of different tissues, including infected leaves, pathogen spores, or insect legs and antenna. The assays were accurate and yielded no false positive nor negative. The shelf-life of the lyophilized reactions was confirmed after one year at room temperature. Finally, successful tests conducted with portable thermocyclers and disposable instruments demonstrate the suitability of the method, named in Situ Processing and Efficient Environmental Detection (iSPEED), for field testing. This kit fits in a backpack and can be carried to remote locations for accurate and rapid detection of pests and pathogens.
DOI: 10.1371/journal.pone.0226863
PubMed: 32240194
PubMed Central: PMC7117680
Affiliations:
- Canada
- Colombie-Britannique , Québec
- Québec (ville), Vancouver
- Université Laval, Université de la Colombie-Britannique
Links toward previous steps (curation, corpus...)
Le document en format XML
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Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Stewart, Don" sort="Stewart, Don" uniqKey="Stewart D" first="Don" last="Stewart">Don Stewart</name><affiliation wicri:level="1"><nlm:affiliation>Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec</wicri:regionArea><wicri:noRegion>Québec</wicri:noRegion></affiliation></author><author><name sortKey="Hrywkiw, Kelly" sort="Hrywkiw, Kelly" uniqKey="Hrywkiw K" first="Kelly" last="Hrywkiw">Kelly Hrywkiw</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Allen, Kiah" sort="Allen, Kiah" uniqKey="Allen K" first="Kiah" last="Allen">Kiah Allen</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Feau, Nicolas" sort="Feau, Nicolas" uniqKey="Feau N" first="Nicolas" last="Feau">Nicolas Feau</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Bilodeau, Guillaume" sort="Bilodeau, Guillaume" uniqKey="Bilodeau G" first="Guillaume" last="Bilodeau">Guillaume Bilodeau</name><affiliation wicri:level="1"><nlm:affiliation>Canadian Food Inspection Agency, Ottawa, Ontario, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Canadian Food Inspection Agency, Ottawa, Ontario</wicri:regionArea><wicri:noRegion>Ontario</wicri:noRegion></affiliation></author><author><name sortKey="Tanguay, Philippe" sort="Tanguay, Philippe" uniqKey="Tanguay P" first="Philippe" last="Tanguay">Philippe Tanguay</name><affiliation wicri:level="1"><nlm:affiliation>Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec</wicri:regionArea><wicri:noRegion>Québec</wicri:noRegion></affiliation></author><author><name sortKey="Cusson, Michel" sort="Cusson, Michel" uniqKey="Cusson M" first="Michel" last="Cusson">Michel Cusson</name><affiliation wicri:level="1"><nlm:affiliation>Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec</wicri:regionArea><wicri:noRegion>Québec</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:affiliation>Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author><author><name sortKey="Hamelin, Richard C" sort="Hamelin, Richard C" uniqKey="Hamelin R" first="Richard C" last="Hamelin">Richard C. Hamelin</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Département des sciences du bois et de la forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Département des sciences du bois et de la forêt, Faculté de Foresterie et Géographie, Université Laval, Québec</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Climate Change (MeSH)</term><term>Ecosystem (MeSH)</term><term>Environmental Monitoring (MeSH)</term><term>Forests (MeSH)</term><term>Fungi (genetics)</term><term>Fungi (isolation & purification)</term><term>Fungi (pathogenicity)</term><term>Humans (MeSH)</term><term>Introduced Species (MeSH)</term><term>Pest Control (methods)</term><term>Polymerase Chain Reaction (MeSH)</term><term>Trees (genetics)</term><term>Trees (growth & development)</term><term>Trees (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Arbres (croissance et développement)</term><term>Arbres (génétique)</term><term>Arbres (microbiologie)</term><term>Champignons (génétique)</term><term>Champignons (isolement et purification)</term><term>Champignons (pathogénicité)</term><term>Changement climatique (MeSH)</term><term>Espèce introduite (MeSH)</term><term>Forêts (MeSH)</term><term>Humains (MeSH)</term><term>Lutte contre les nuisibles (méthodes)</term><term>Réaction de polymérisation en chaîne (MeSH)</term><term>Surveillance de l'environnement (MeSH)</term><term>Écosystème (MeSH)</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Arbres</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fungi</term><term>Trees</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Trees</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arbres</term><term>Champignons</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Fungi</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Champignons</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Pest Control</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Arbres</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Trees</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Lutte contre les nuisibles</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Fungi</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Champignons</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Climate Change</term><term>Ecosystem</term><term>Environmental Monitoring</term><term>Forests</term><term>Humans</term><term>Introduced Species</term><term>Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Changement climatique</term><term>Espèce introduite</term><term>Forêts</term><term>Humains</term><term>Réaction de polymérisation en chaîne</term><term>Surveillance de l'environnement</term><term>Écosystème</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Global trade and climate change are responsible for a surge in foreign invasive species and emerging pests and pathogens across the world. Early detection and surveillance activities are essential to monitor the environment and prevent or mitigate future ecosystem impacts. Molecular diagnostics by DNA testing has become an integral part of this process. However, for environmental applications, there is a need for cost-effective and efficient point-of-use DNA testing to obtain accurate results from remote sites in real-time. This requires the development of simple and fast sample processing and DNA extraction, room-temperature stable reagents and a portable instrument. We developed a point-of-use real-time Polymerase Chain Reaction system using a crude buffer-based DNA extraction protocol and lyophilized, pre-made, reactions for on-site applications. We demonstrate the use of this approach with pathogens and pests covering a broad spectrum of known undesirable forest enemies: the fungi Sphaerulina musiva, Cronartium ribicola and Cronartium comandrae, the oomycete Phytophthora ramorum and the insect Lymantria dispar. We obtained positive DNA identification from a variety of different tissues, including infected leaves, pathogen spores, or insect legs and antenna. The assays were accurate and yielded no false positive nor negative. The shelf-life of the lyophilized reactions was confirmed after one year at room temperature. Finally, successful tests conducted with portable thermocyclers and disposable instruments demonstrate the suitability of the method, named in Situ Processing and Efficient Environmental Detection (iSPEED), for field testing. This kit fits in a backpack and can be carried to remote locations for accurate and rapid detection of pests and pathogens.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32240194</PMID><DateCompleted><Year>2020</Year><Month>07</Month><Day>06</Day></DateCompleted><DateRevised><Year>2020</Year><Month>07</Month><Day>06</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><Issue>4</Issue><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>In Situ Processing and Efficient Environmental Detection (iSPEED) of tree pests and pathogens using point-of-use real-time PCR.</ArticleTitle><Pagination><MedlinePgn>e0226863</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0226863</ELocationID><Abstract><AbstractText>Global trade and climate change are responsible for a surge in foreign invasive species and emerging pests and pathogens across the world. Early detection and surveillance activities are essential to monitor the environment and prevent or mitigate future ecosystem impacts. Molecular diagnostics by DNA testing has become an integral part of this process. However, for environmental applications, there is a need for cost-effective and efficient point-of-use DNA testing to obtain accurate results from remote sites in real-time. This requires the development of simple and fast sample processing and DNA extraction, room-temperature stable reagents and a portable instrument. We developed a point-of-use real-time Polymerase Chain Reaction system using a crude buffer-based DNA extraction protocol and lyophilized, pre-made, reactions for on-site applications. We demonstrate the use of this approach with pathogens and pests covering a broad spectrum of known undesirable forest enemies: the fungi Sphaerulina musiva, Cronartium ribicola and Cronartium comandrae, the oomycete Phytophthora ramorum and the insect Lymantria dispar. We obtained positive DNA identification from a variety of different tissues, including infected leaves, pathogen spores, or insect legs and antenna. The assays were accurate and yielded no false positive nor negative. The shelf-life of the lyophilized reactions was confirmed after one year at room temperature. Finally, successful tests conducted with portable thermocyclers and disposable instruments demonstrate the suitability of the method, named in Situ Processing and Efficient Environmental Detection (iSPEED), for field testing. This kit fits in a backpack and can be carried to remote locations for accurate and rapid detection of pests and pathogens.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Capron</LastName><ForeName>Arnaud</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stewart</LastName><ForeName>Don</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hrywkiw</LastName><ForeName>Kelly</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Allen</LastName><ForeName>Kiah</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Feau</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bilodeau</LastName><ForeName>Guillaume</ForeName><Initials>G</Initials><Identifier Source="ORCID">0000-0003-1766-229X</Identifier><AffiliationInfo><Affiliation>Canadian Food Inspection Agency, Ottawa, Ontario, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tanguay</LastName><ForeName>Philippe</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cusson</LastName><ForeName>Michel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hamelin</LastName><ForeName>Richard C</ForeName><Initials>RC</Initials><Identifier Source="ORCID">0000-0003-4006-532X</Identifier><AffiliationInfo><Affiliation>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Département des sciences du bois et de la forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, Canada.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D057231" MajorTopicYN="N">Climate Change</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017753" MajorTopicYN="N">Ecosystem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004784" MajorTopicYN="Y">Environmental Monitoring</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D065928" MajorTopicYN="N">Forests</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005658" MajorTopicYN="N">Fungi</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName><QualifierName UI="Q000472" MajorTopicYN="N">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058865" MajorTopicYN="Y">Introduced Species</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010571" MajorTopicYN="N">Pest Control</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014197" MajorTopicYN="N">Trees</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading></MeshHeadingList><CoiStatement>The authors have no competing interests exist.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>12</Month><Day>08</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>16</Day></PubMedPubDate><PubMedPubDate 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