Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens.
Identifieur interne : 002137 ( PubMed/Corpus ); précédent : 002136; suivant : 002138Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens.
Auteurs : A. Petrich ; J. Mahony ; S. Chong ; G. Broukhanski ; F. Gharabaghi ; G. Johnson ; L. Louie ; K. Luinstra ; B. Willey ; P. Akhaven ; L. Chui ; F. Jamieson ; M. Louie ; T. Mazzulli ; R. Tellier ; M. Smieja ; W. Cai ; M. Chernesky ; S E RichardsonSource :
- Journal of clinical microbiology [ 0095-1137 ] ; 2006.
English descriptors
- KwdEn :
- Feces (virology), Humans, Molecular Diagnostic Techniques, RNA, Viral (analysis), RNA, Viral (genetics), RNA, Viral (isolation & purification), Reverse Transcriptase Polymerase Chain Reaction, SARS Virus (genetics), SARS Virus (isolation & purification), Sensitivity and Specificity, Severe Acute Respiratory Syndrome (diagnosis), Severe Acute Respiratory Syndrome (virology).
- MESH :
- chemical , analysis : RNA, Viral.
- chemical , genetics : RNA, Viral.
- chemical , isolation & purification : RNA, Viral.
- diagnosis : Severe Acute Respiratory Syndrome.
- genetics : SARS Virus.
- isolation & purification : SARS Virus.
- virology : Feces, Severe Acute Respiratory Syndrome.
- Humans, Molecular Diagnostic Techniques, Reverse Transcriptase Polymerase Chain Reaction, Sensitivity and Specificity.
Abstract
The emergence of a novel coronavirus (CoV) as the cause of severe acute respiratory syndrome (SARS) catalyzed the development of rapid diagnostic tests. Stool samples have been shown to be appropriate for diagnostic testing for SARS CoV, although it has been recognized to be a heterogeneous and difficult sample that contains amplification inhibitors. Limited information on the efficiency of extraction methods for the purification and concentration of SARS CoV RNA from stool samples is available. Our study objectives were to determine the optimal extraction method for SARS CoV RNA detection and to examine the effect of increased specimen volume for the detection of SARS CoV RNA in stool specimens. We conducted a multicenter evaluation of four automated and four manual extraction methods using dilutions of viral lysate in replicate mock stool samples, followed by quantitation of SARS CoV RNA using real-time reverse transcriptase PCR. The sensitivities of the manual methods ranged from 50% to 100%, with the Cortex Biochem Magazorb method, a magnetic bead isolation method, allowing detection of all 12 positive samples. The sensitivities of the automated methods ranged from 75% to 100%. The bioMérieux NucliSens automated extractor and miniMag extraction methods each had a sensitivity of 100%. Examination of the copy numbers detected and the generation of 10-fold dilutions of the extracted material indicated that a number of extraction methods retained inhibitory substances that prevented optimal amplification. Increasing the volume of sample input did improve detection. This information could be useful for the extraction of other RNA viruses from stool samples and demonstrates the need to evaluate extraction methods for different specimen types.
DOI: 10.1128/JCM.02460-05
PubMed: 16891478
Links to Exploration step
pubmed:16891478Le document en format XML
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Broukhanski</name></author><author><name sortKey="Gharabaghi, F" sort="Gharabaghi, F" uniqKey="Gharabaghi F" first="F" last="Gharabaghi">F. Gharabaghi</name></author><author><name sortKey="Johnson, G" sort="Johnson, G" uniqKey="Johnson G" first="G" last="Johnson">G. Johnson</name></author><author><name sortKey="Louie, L" sort="Louie, L" uniqKey="Louie L" first="L" last="Louie">L. Louie</name></author><author><name sortKey="Luinstra, K" sort="Luinstra, K" uniqKey="Luinstra K" first="K" last="Luinstra">K. Luinstra</name></author><author><name sortKey="Willey, B" sort="Willey, B" uniqKey="Willey B" first="B" last="Willey">B. Willey</name></author><author><name sortKey="Akhaven, P" sort="Akhaven, P" uniqKey="Akhaven P" first="P" last="Akhaven">P. Akhaven</name></author><author><name sortKey="Chui, L" sort="Chui, L" uniqKey="Chui L" first="L" last="Chui">L. Chui</name></author><author><name sortKey="Jamieson, F" sort="Jamieson, F" uniqKey="Jamieson F" first="F" last="Jamieson">F. Jamieson</name></author><author><name sortKey="Louie, M" sort="Louie, M" uniqKey="Louie M" first="M" last="Louie">M. Louie</name></author><author><name sortKey="Mazzulli, T" sort="Mazzulli, T" uniqKey="Mazzulli T" first="T" last="Mazzulli">T. Mazzulli</name></author><author><name sortKey="Tellier, R" sort="Tellier, R" uniqKey="Tellier R" first="R" last="Tellier">R. Tellier</name></author><author><name sortKey="Smieja, M" sort="Smieja, M" uniqKey="Smieja M" first="M" last="Smieja">M. Smieja</name></author><author><name sortKey="Cai, W" sort="Cai, W" uniqKey="Cai W" first="W" last="Cai">W. Cai</name></author><author><name sortKey="Chernesky, M" sort="Chernesky, M" uniqKey="Chernesky M" first="M" last="Chernesky">M. Chernesky</name></author><author><name sortKey="Richardson, S E" sort="Richardson, S E" uniqKey="Richardson S" first="S E" last="Richardson">S E Richardson</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16891478</idno><idno type="pmid">16891478</idno><idno type="doi">10.1128/JCM.02460-05</idno><idno type="wicri:Area/PubMed/Corpus">002137</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002137</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens.</title><author><name sortKey="Petrich, A" sort="Petrich, A" uniqKey="Petrich A" first="A" last="Petrich">A. Petrich</name><affiliation><nlm:affiliation>St. Joseph's Healthcare, L424, Microbiology, 50 Charlton Ave. East, Hamilton, ON L8N 4A6, Canada. petricha@mcmaster.ca</nlm:affiliation></affiliation></author><author><name sortKey="Mahony, J" sort="Mahony, J" uniqKey="Mahony J" first="J" last="Mahony">J. Mahony</name></author><author><name sortKey="Chong, S" sort="Chong, S" uniqKey="Chong S" first="S" last="Chong">S. Chong</name></author><author><name sortKey="Broukhanski, G" sort="Broukhanski, G" uniqKey="Broukhanski G" first="G" last="Broukhanski">G. Broukhanski</name></author><author><name sortKey="Gharabaghi, F" sort="Gharabaghi, F" uniqKey="Gharabaghi F" first="F" last="Gharabaghi">F. Gharabaghi</name></author><author><name sortKey="Johnson, G" sort="Johnson, G" uniqKey="Johnson G" first="G" last="Johnson">G. Johnson</name></author><author><name sortKey="Louie, L" sort="Louie, L" uniqKey="Louie L" first="L" last="Louie">L. Louie</name></author><author><name sortKey="Luinstra, K" sort="Luinstra, K" uniqKey="Luinstra K" first="K" last="Luinstra">K. Luinstra</name></author><author><name sortKey="Willey, B" sort="Willey, B" uniqKey="Willey B" first="B" last="Willey">B. Willey</name></author><author><name sortKey="Akhaven, P" sort="Akhaven, P" uniqKey="Akhaven P" first="P" last="Akhaven">P. Akhaven</name></author><author><name sortKey="Chui, L" sort="Chui, L" uniqKey="Chui L" first="L" last="Chui">L. Chui</name></author><author><name sortKey="Jamieson, F" sort="Jamieson, F" uniqKey="Jamieson F" first="F" last="Jamieson">F. Jamieson</name></author><author><name sortKey="Louie, M" sort="Louie, M" uniqKey="Louie M" first="M" last="Louie">M. Louie</name></author><author><name sortKey="Mazzulli, T" sort="Mazzulli, T" uniqKey="Mazzulli T" first="T" last="Mazzulli">T. Mazzulli</name></author><author><name sortKey="Tellier, R" sort="Tellier, R" uniqKey="Tellier R" first="R" last="Tellier">R. Tellier</name></author><author><name sortKey="Smieja, M" sort="Smieja, M" uniqKey="Smieja M" first="M" last="Smieja">M. Smieja</name></author><author><name sortKey="Cai, W" sort="Cai, W" uniqKey="Cai W" first="W" last="Cai">W. Cai</name></author><author><name sortKey="Chernesky, M" sort="Chernesky, M" uniqKey="Chernesky M" first="M" last="Chernesky">M. Chernesky</name></author><author><name sortKey="Richardson, S E" sort="Richardson, S E" uniqKey="Richardson S" first="S E" last="Richardson">S E Richardson</name></author></analytic><series><title level="j">Journal of clinical microbiology</title><idno type="ISSN">0095-1137</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Feces (virology)</term><term>Humans</term><term>Molecular Diagnostic Techniques</term><term>RNA, Viral (analysis)</term><term>RNA, Viral (genetics)</term><term>RNA, Viral (isolation & purification)</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>SARS Virus (genetics)</term><term>SARS Virus (isolation & purification)</term><term>Sensitivity and Specificity</term><term>Severe Acute Respiratory Syndrome (diagnosis)</term><term>Severe Acute Respiratory Syndrome (virology)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Feces</term><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Humans</term><term>Molecular Diagnostic Techniques</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>Sensitivity and Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The emergence of a novel coronavirus (CoV) as the cause of severe acute respiratory syndrome (SARS) catalyzed the development of rapid diagnostic tests. Stool samples have been shown to be appropriate for diagnostic testing for SARS CoV, although it has been recognized to be a heterogeneous and difficult sample that contains amplification inhibitors. Limited information on the efficiency of extraction methods for the purification and concentration of SARS CoV RNA from stool samples is available. Our study objectives were to determine the optimal extraction method for SARS CoV RNA detection and to examine the effect of increased specimen volume for the detection of SARS CoV RNA in stool specimens. We conducted a multicenter evaluation of four automated and four manual extraction methods using dilutions of viral lysate in replicate mock stool samples, followed by quantitation of SARS CoV RNA using real-time reverse transcriptase PCR. The sensitivities of the manual methods ranged from 50% to 100%, with the Cortex Biochem Magazorb method, a magnetic bead isolation method, allowing detection of all 12 positive samples. The sensitivities of the automated methods ranged from 75% to 100%. The bioMérieux NucliSens automated extractor and miniMag extraction methods each had a sensitivity of 100%. Examination of the copy numbers detected and the generation of 10-fold dilutions of the extracted material indicated that a number of extraction methods retained inhibitory substances that prevented optimal amplification. Increasing the volume of sample input did improve detection. This information could be useful for the extraction of other RNA viruses from stool samples and demonstrates the need to evaluate extraction methods for different specimen types.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16891478</PMID><DateCompleted><Year>2006</Year><Month>11</Month><Day>02</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0095-1137</ISSN><JournalIssue CitedMedium="Print"><Volume>44</Volume><Issue>8</Issue><PubDate><Year>2006</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Journal of clinical microbiology</Title><ISOAbbreviation>J. Clin. Microbiol.</ISOAbbreviation></Journal><ArticleTitle>Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens.</ArticleTitle><Pagination><MedlinePgn>2681-8</MedlinePgn></Pagination><Abstract><AbstractText>The emergence of a novel coronavirus (CoV) as the cause of severe acute respiratory syndrome (SARS) catalyzed the development of rapid diagnostic tests. Stool samples have been shown to be appropriate for diagnostic testing for SARS CoV, although it has been recognized to be a heterogeneous and difficult sample that contains amplification inhibitors. Limited information on the efficiency of extraction methods for the purification and concentration of SARS CoV RNA from stool samples is available. Our study objectives were to determine the optimal extraction method for SARS CoV RNA detection and to examine the effect of increased specimen volume for the detection of SARS CoV RNA in stool specimens. We conducted a multicenter evaluation of four automated and four manual extraction methods using dilutions of viral lysate in replicate mock stool samples, followed by quantitation of SARS CoV RNA using real-time reverse transcriptase PCR. The sensitivities of the manual methods ranged from 50% to 100%, with the Cortex Biochem Magazorb method, a magnetic bead isolation method, allowing detection of all 12 positive samples. The sensitivities of the automated methods ranged from 75% to 100%. The bioMérieux NucliSens automated extractor and miniMag extraction methods each had a sensitivity of 100%. Examination of the copy numbers detected and the generation of 10-fold dilutions of the extracted material indicated that a number of extraction methods retained inhibitory substances that prevented optimal amplification. Increasing the volume of sample input did improve detection. This information could be useful for the extraction of other RNA viruses from stool samples and demonstrates the need to evaluate extraction methods for different specimen types.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Petrich</LastName><ForeName>A</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>St. Joseph's Healthcare, L424, Microbiology, 50 Charlton Ave. East, Hamilton, ON L8N 4A6, Canada. petricha@mcmaster.ca</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mahony</LastName><ForeName>J</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Chong</LastName><ForeName>S</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Broukhanski</LastName><ForeName>G</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Gharabaghi</LastName><ForeName>F</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Johnson</LastName><ForeName>G</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Louie</LastName><ForeName>L</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Luinstra</LastName><ForeName>K</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Willey</LastName><ForeName>B</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Akhaven</LastName><ForeName>P</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Chui</LastName><ForeName>L</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Jamieson</LastName><ForeName>F</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Louie</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Mazzulli</LastName><ForeName>T</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Tellier</LastName><ForeName>R</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Smieja</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Cai</LastName><ForeName>W</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Chernesky</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Richardson</LastName><ForeName>S E</ForeName><Initials>SE</Initials></Author><Author ValidYN="Y"><CollectiveName>Ontario Laboratory Working Group for the Rapid Diagnosis of Emerging Infections</CollectiveName></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D016448">Multicenter Study</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Clin Microbiol</MedlineTA><NlmUniqueID>7505564</NlmUniqueID><ISSNLinking>0095-1137</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012367">RNA, Viral</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005243" MajorTopicYN="N">Feces</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D025202" MajorTopicYN="Y">Molecular Diagnostic Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012367" MajorTopicYN="N">RNA, Viral</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020133" MajorTopicYN="N">Reverse Transcriptase Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012680" MajorTopicYN="N">Sensitivity and Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D045169" MajorTopicYN="N">Severe Acute Respiratory Syndrome</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="Y">diagnosis</QualifierName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>8</Month><Day>8</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>11</Month><Day>3</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>8</Month><Day>8</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16891478</ArticleId><ArticleId IdType="pii">44/8/2681</ArticleId><ArticleId IdType="doi">10.1128/JCM.02460-05</ArticleId><ArticleId IdType="pmc">PMC1594626</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>J Clin Microbiol. 2000 Sep;38(9):3274-9</Citation><ArticleIdList><ArticleId IdType="pubmed">10970370</ArticleId></ArticleIdList></Reference><Reference><Citation>J Clin Microbiol. 2001 May;39(5):1796-801</Citation><ArticleIdList><ArticleId 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