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Determining the analytical specificity of PCR-based assays for the diagnosis of IA: What is Aspergillus?

Identifieur interne : 000E53 ( PubMed/Checkpoint ); précédent : 000E52; suivant : 000E54

Determining the analytical specificity of PCR-based assays for the diagnosis of IA: What is Aspergillus?

Auteurs : C Oliver Morton [Australie] ; P Lewis White [Royaume-Uni] ; Rosemary A. Barnes ; Lena Klingspor [Suède] ; Manuel Cuenca-Estrella [Espagne] ; Katrien Lagrou [Belgique] ; Stéphane Bretagne [France] ; Willem Melchers [Pays-Bas] ; Carlo Mengoli [Italie] ; Angela M. Caliendo [États-Unis] ; Massimo Cogliati [Italie] ; Yvette Debets-Ossenkopp [Pays-Bas] ; Rebecca Gorton [Royaume-Uni] ; Ferry Hagen [Pays-Bas] ; Catriona Halliday [Australie] ; Petr Hamal [République tchèque] ; Kathleen Harvey-Wood [Royaume-Uni] ; Katia Jaton [Suisse] ; Gemma Johnson [Royaume-Uni] ; Sarah Kidd ; Martina Lengerova [République tchèque] ; Cornelia Lass-Florl [Autriche] ; Chris Linton [Royaume-Uni] ; Laurence Millon [France] ; C Orla Morrissey [Australie] ; Melinda Paholcsek ; Alida Fe Talento [Irlande (pays)] ; Markus Ruhnke [Allemagne] ; Birgit Willinger [Autriche] ; J Peter Donnelly [Pays-Bas] ; Juergen Loeffler [Allemagne]

Source :

RBID : pubmed:28339744

Abstract

A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help exclude IA. Conversely, when testing more invasive samples (BAL, biopsy, CSF) emphasis is placed on confirming disease, so analytical specificity is paramount. This multicenter study examined the analytical specificity of PCR methods for detecting IA by blind testing a panel of DNA extracted from a various fungal species to explore the range of Aspergillus species that could be detected, but also potential cross reactivity with other fungal species. Positivity rates were calculated and regression analysis was performed to determine any associations between technical specifications and performance. The accuracy of Aspergillus genus specific assays was 71.8%, significantly greater (P < .0001) than assays specific for individual Aspergillus species (47.2%). For genus specific assays the most often missed species were A. lentulus (25.0%), A. versicolor (24.1%), A. terreus (16.1%), A. flavus (15.2%), A. niger (13.4%), and A. fumigatus (6.2%). There was a significant positive association between accuracy and using an Aspergillus genus PCR assay targeting the rRNA genes (P = .0011). Conversely, there was a significant association between rRNA PCR targets and false positivity (P = .0032). To conclude current Aspergillus PCR assays are better suited for detecting A. fumigatus, with inferior detection of most other Aspergillus species. The use of an Aspergillus genus specific PCR assay targeting the rRNA genes is preferential.

DOI: 10.1093/mmy/myw093
PubMed: 28339744


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pubmed:28339744

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<name sortKey="Hagen, Ferry" sort="Hagen, Ferry" uniqKey="Hagen F" first="Ferry" last="Hagen">Ferry Hagen</name>
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<settlement type="city">Nimègue</settlement>
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<name sortKey="Kidd, Sarah" sort="Kidd, Sarah" uniqKey="Kidd S" first="Sarah" last="Kidd">Sarah Kidd</name>
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<name sortKey="Lass Florl, Cornelia" sort="Lass Florl, Cornelia" uniqKey="Lass Florl C" first="Cornelia" last="Lass-Florl">Cornelia Lass-Florl</name>
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<nlm:affiliation>Innsbruck Medical University, Innsbruck, Austria.</nlm:affiliation>
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<wicri:regionArea>Innsbruck Medical University, Innsbruck</wicri:regionArea>
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<name sortKey="Linton, Chris" sort="Linton, Chris" uniqKey="Linton C" first="Chris" last="Linton">Chris Linton</name>
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<wicri:regionArea>UK Mycology Reference Lab, Public Health England, Bristol</wicri:regionArea>
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<author>
<name sortKey="Millon, Laurence" sort="Millon, Laurence" uniqKey="Millon L" first="Laurence" last="Millon">Laurence Millon</name>
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<nlm:affiliation>Laboratoire de Parasitologie-Mycologie Centre Hospitalier Universitaire, Besançon, France.</nlm:affiliation>
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<wicri:regionArea>Laboratoire de Parasitologie-Mycologie Centre Hospitalier Universitaire, Besançon</wicri:regionArea>
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<region type="region">Bourgogne-Franche-Comté</region>
<region type="old region">Franche-Comté</region>
<settlement type="city">Besançon</settlement>
</placeName>
</affiliation>
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<name sortKey="Morrissey, C Orla" sort="Morrissey, C Orla" uniqKey="Morrissey C" first="C Orla" last="Morrissey">C Orla Morrissey</name>
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<nlm:affiliation>Alfred Health and Monash University, Melbourne, Australia.</nlm:affiliation>
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<placeName>
<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
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<author>
<name sortKey="Paholcsek, Melinda" sort="Paholcsek, Melinda" uniqKey="Paholcsek M" first="Melinda" last="Paholcsek">Melinda Paholcsek</name>
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<wicri:noCountry code="subField">Debrecen</wicri:noCountry>
</affiliation>
</author>
<author>
<name sortKey="Talento, Alida Fe" sort="Talento, Alida Fe" uniqKey="Talento A" first="Alida Fe" last="Talento">Alida Fe Talento</name>
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<nlm:affiliation>Department of Clinical Microbiology, Trinity College, Dublin, Ireland.</nlm:affiliation>
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<wicri:regionArea>Department of Clinical Microbiology, Trinity College, Dublin</wicri:regionArea>
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<name sortKey="Ruhnke, Markus" sort="Ruhnke, Markus" uniqKey="Ruhnke M" first="Markus" last="Ruhnke">Markus Ruhnke</name>
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<nlm:affiliation>Charité Medical School, University of Berlin, Berlin. Germany.</nlm:affiliation>
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</placeName>
<wicri:orgArea>Charité Medical School, University of Berlin</wicri:orgArea>
</affiliation>
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<name sortKey="Willinger, Birgit" sort="Willinger, Birgit" uniqKey="Willinger B" first="Birgit" last="Willinger">Birgit Willinger</name>
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<name sortKey="Donnelly, J Peter" sort="Donnelly, J Peter" uniqKey="Donnelly J" first="J Peter" last="Donnelly">J Peter Donnelly</name>
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<nlm:affiliation>Radboud University Medical Centre, Nijmegen, Netherlands.</nlm:affiliation>
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<name sortKey="Loeffler, Juergen" sort="Loeffler, Juergen" uniqKey="Loeffler J" first="Juergen" last="Loeffler">Juergen Loeffler</name>
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<nlm:affiliation>Wuerzburg University, Wuerzburg, Germany.</nlm:affiliation>
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<title level="j">Medical mycology</title>
<idno type="eISSN">1460-2709</idno>
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<div type="abstract" xml:lang="en">A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help exclude IA. Conversely, when testing more invasive samples (BAL, biopsy, CSF) emphasis is placed on confirming disease, so analytical specificity is paramount. This multicenter study examined the analytical specificity of PCR methods for detecting IA by blind testing a panel of DNA extracted from a various fungal species to explore the range of Aspergillus species that could be detected, but also potential cross reactivity with other fungal species. Positivity rates were calculated and regression analysis was performed to determine any associations between technical specifications and performance. The accuracy of Aspergillus genus specific assays was 71.8%, significantly greater (P < .0001) than assays specific for individual Aspergillus species (47.2%). For genus specific assays the most often missed species were A. lentulus (25.0%), A. versicolor (24.1%), A. terreus (16.1%), A. flavus (15.2%), A. niger (13.4%), and A. fumigatus (6.2%). There was a significant positive association between accuracy and using an Aspergillus genus PCR assay targeting the rRNA genes (P = .0011). Conversely, there was a significant association between rRNA PCR targets and false positivity (P = .0032). To conclude current Aspergillus PCR assays are better suited for detecting A. fumigatus, with inferior detection of most other Aspergillus species. The use of an Aspergillus genus specific PCR assay targeting the rRNA genes is preferential.</div>
</front>
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<DateCreated>
<Year>2017</Year>
<Month>03</Month>
<Day>24</Day>
</DateCreated>
<DateRevised>
<Year>2017</Year>
<Month>05</Month>
<Day>16</Day>
</DateRevised>
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<Journal>
<ISSN IssnType="Electronic">1460-2709</ISSN>
<JournalIssue CitedMedium="Internet">
<Volume>55</Volume>
<Issue>4</Issue>
<PubDate>
<Year>2017</Year>
<Month>Jun</Month>
<Day>01</Day>
</PubDate>
</JournalIssue>
<Title>Medical mycology</Title>
<ISOAbbreviation>Med. Mycol.</ISOAbbreviation>
</Journal>
<ArticleTitle>Determining the analytical specificity of PCR-based assays for the diagnosis of IA: What is Aspergillus?</ArticleTitle>
<Pagination>
<MedlinePgn>402-413</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1093/mmy/myw093</ELocationID>
<Abstract>
<AbstractText>A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help exclude IA. Conversely, when testing more invasive samples (BAL, biopsy, CSF) emphasis is placed on confirming disease, so analytical specificity is paramount. This multicenter study examined the analytical specificity of PCR methods for detecting IA by blind testing a panel of DNA extracted from a various fungal species to explore the range of Aspergillus species that could be detected, but also potential cross reactivity with other fungal species. Positivity rates were calculated and regression analysis was performed to determine any associations between technical specifications and performance. The accuracy of Aspergillus genus specific assays was 71.8%, significantly greater (P < .0001) than assays specific for individual Aspergillus species (47.2%). For genus specific assays the most often missed species were A. lentulus (25.0%), A. versicolor (24.1%), A. terreus (16.1%), A. flavus (15.2%), A. niger (13.4%), and A. fumigatus (6.2%). There was a significant positive association between accuracy and using an Aspergillus genus PCR assay targeting the rRNA genes (P = .0011). Conversely, there was a significant association between rRNA PCR targets and false positivity (P = .0032). To conclude current Aspergillus PCR assays are better suited for detecting A. fumigatus, with inferior detection of most other Aspergillus species. The use of an Aspergillus genus specific PCR assay targeting the rRNA genes is preferential.</AbstractText>
<CopyrightInformation>© The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation>
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</AffiliationInfo>
</Author>
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<LastName>White</LastName>
<ForeName>P Lewis</ForeName>
<Initials>PL</Initials>
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<Affiliation>Public Health Wales Microbiology Cardiff, UK.</Affiliation>
</AffiliationInfo>
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<LastName>Barnes</LastName>
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</AffiliationInfo>
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