The Fungal PCR Initiative's evaluation of in-house and commercial Pneumocystis jirovecii qPCR assays: Toward a standard for a diagnostics assay: Toward a standard for a diagnostics assay
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| Titel: | The Fungal PCR Initiative's evaluation of in-house and commercial Pneumocystis jirovecii qPCR assays: Toward a standard for a diagnostics assay: Toward a standard for a diagnostics assay |
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| Autoren: | Stéphane Bretagne, Emeline Scherer, Martina Lengerová, Maud Gits-Muselli, Lily Novak-Frazer, Juergen Loeffler, Willem J. G. Melchers, Alexandre Alanio, P. Lewis White, Joerg Steinmann, Carlo Mengoli, Malcom Guiver, Mario Cruciani, Riina Rautemaa-Richardson, Brendan Crowley, Rebecca Gorton, Gijs Dingemans, J. Peter Donnelly, Catriona Halliday, Ferry Hagen, Katrien Lagrou, Sharon C.-A. Chen, Emilie Fréalle, Rosemary Ann Barnes, Gemma Johnson |
| Weitere Verfasser: | Laboratoire de Parasitologie-Mycologie CHU Saint Louis, Paris, Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal Paris, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de parasitologie et mycologie CHRU de Besançon, Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté COMUE (UBFC)-Université Bourgogne Franche-Comté COMUE (UBFC) |
| Quelle: | Medical Mycology, 58, 6, pp. 779-788 Gits-muselli, M, White, P L, Mengoli, C, Chen, S, Crowley, B, Dingemans, G, Fréalle, E, L Gorton, R, Guiver, M, Hagen, F, Halliday, C, Johnson, G, Lagrou, K, Lengerova, M, Melchers, W J G, Novak-frazer, L, Rautemaa-richardson, R, Scherer, E, Steinmann, J, Cruciani, M, Barnes, R, Donnelly, J P, Loeffler, J, Bretagne, S & Alanio, A 2020, 'The Fungal PCR Initiative's evaluation of in-house and commercial Pneumocystis jirovecii qPCR assays: Toward a standard for a diagnostics assay', Medical Mycology, vol. 58, no. 6, pp. 779-788. https://doi.org/10.1093/mmy/myz115 |
| Verlagsinformationen: | Oxford University Press (OUP), 2019. |
| Publikationsjahr: | 2019 |
| Schlagwörter: | Medical Microbiology - Radboud University Medical Center, 0301 basic medicine, MESH: Pneumonia, diagnosis, Medizin, MESH: Molecular Diagnostic Techniques, Pneumocystis carinii, Real-Time Polymerase Chain Reaction, Sensitivity and Specificity, pneumocystosis, 03 medical and health sciences, Cq, environment/Health, threshold, Humans, DNA, Fungal, Pneumocystis jirovecii, panel specimens, standardization, 0303 health sciences, MESH: Humans, MESH: Bronchoalveolar Lavage Fluid, Pneumocystis, MESH: Real-Time Polymerase Chain Reaction, Pneumonia, Pneumocystis, MESH: DNA, DNA, quantification, quantification cycles, MESH: Pneumocystis carinii, MESH: Sensitivity and Specificity, Radboudumc 17: Women's cancers RIMLS: Radboud Institute for Molecular Life Sciences, 3. Good health, PCP, qPCR, whole nucleic acids, Fungal, Molecular Diagnostic Techniques, efficiency, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, Bronchoalveolar Lavage Fluid |
| Beschreibung: | Quantitative real-time PCR (qPCR) is increasingly used to detect Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia (PCP), but there are differences in the nucleic acids targeted, DNA only versus whole nucleic acid (WNA), and also the target genes for amplification. Through the Fungal PCR Initiative, a working group of the International Society for Human and Animal Mycology, a multicenter and monocenter evaluation of PCP qPCR assays was performed. For the multicenter study, 16 reference laboratories from eight different countries, performing 20 assays analyzed a panel consisting of two negative and three PCP positive samples. Aliquots were prepared by pooling residual material from 20 negative or positive- P. jirovecii bronchoalveolar lavage fluids (BALFs). The positive pool was diluted to obtain three concentrations (pure 1:1; 1:100; and 1:1000 to mimic high, medium, and low fungal loads, respectively). The monocenter study compared five in-house and five commercial qPCR assays testing 19 individual BALFs on the same amplification platform. Across both evaluations and for all fungal loads, targeting WNA and the mitochondrial small sub-unit (mtSSU) provided the earliest Cq values, compared to only targeting DNA and the mitochondrial large subunit, the major surface glycoprotein or the beta-tubulin genes. Thus, reverse transcriptase-qPCR targeting the mtSSU gene could serve as a basis for standardizing the P. jirovecii load, which is essential if qPCR is to be incorporated into clinical care pathways as the reference method, accepting that additional parameters such as amplification platforms still need evaluation. |
| Publikationsart: | Article |
| Dateibeschreibung: | application/vnd.openxmlformats-officedocument.wordprocessingml.document |
| Sprache: | English |
| ISSN: | 1460-2709 1369-3786 |
| DOI: | 10.1093/mmy/myz115 |
| Zugangs-URL: | https://academic.oup.com/mmy/article-pdf/58/6/779/33530836/myz115.pdf https://pubmed.ncbi.nlm.nih.gov/31758173 https://pure.knaw.nl/portal/en/publications/3195bed0-1968-4f3a-90e0-3b292e5a2a08 https://doi.org/10.1093/mmy/myz115 https://hdl.handle.net/20.500.11755/3195bed0-1968-4f3a-90e0-3b292e5a2a08 https://www.research.manchester.ac.uk/portal/en/publications/the-fungal-pcr-initiatives-evaluation-of-inhouse-and-commercial-pneumocystis-jirovecii-qpcr-assays-toward-a-standard-for-a-diagnostics-assay(2142b246-c1a9-4ac0-aade-47866c6afa06).html https://www.ncbi.nlm.nih.gov/pubmed/31758173 https://www.narcis.nl/publication/RecordID/oai%3Apure.knaw.nl%3Apublications%2F3195bed0-1968-4f3a-90e0-3b292e5a2a08 https://pure.knaw.nl/portal/en/publications/the-fungal-pcr-initiatives-evaluation-of-in-house-and-commercial- https://academic.oup.com/mmy/article/58/6/779/5638040 https://khepri-node.dev.meta-infra.org/papers/the-fungal-pcr-initiatives-evaluation-of-in-house/31758173 https://repository.ubn.ru.nl//bitstream/handle/2066/226024/226024.pdf https://hdl.handle.net/2066/226024 https://pure.manchester.ac.uk/ws/files/175442537/FPCRI_PCP_lab_200519concat_AA.docx https://academic.oup.com/mmy/article/58/6/779/5638040 https://doi.org/10.1093/mmy/myz115 https://research.manchester.ac.uk/en/publications/2142b246-c1a9-4ac0-aade-47866c6afa06 https://www.ncbi.nlm.nih.gov/pubmed/31758173 https://doi.org/10.1093/mmy/myz115 https://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&origin=inward&scp=85089127409 |
| Rights: | OUP Standard Publication Reuse |
| Dokumentencode: | edsair.doi.dedup.....27a23d4765e71dd5a8129329b51a3cc4 |
| Datenbank: | OpenAIRE |
Nájsť tento článok vo Web of Science | Abstract: | Quantitative real-time PCR (qPCR) is increasingly used to detect Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia (PCP), but there are differences in the nucleic acids targeted, DNA only versus whole nucleic acid (WNA), and also the target genes for amplification. Through the Fungal PCR Initiative, a working group of the International Society for Human and Animal Mycology, a multicenter and monocenter evaluation of PCP qPCR assays was performed. For the multicenter study, 16 reference laboratories from eight different countries, performing 20 assays analyzed a panel consisting of two negative and three PCP positive samples. Aliquots were prepared by pooling residual material from 20 negative or positive- P. jirovecii bronchoalveolar lavage fluids (BALFs). The positive pool was diluted to obtain three concentrations (pure 1:1; 1:100; and 1:1000 to mimic high, medium, and low fungal loads, respectively). The monocenter study compared five in-house and five commercial qPCR assays testing 19 individual BALFs on the same amplification platform. Across both evaluations and for all fungal loads, targeting WNA and the mitochondrial small sub-unit (mtSSU) provided the earliest Cq values, compared to only targeting DNA and the mitochondrial large subunit, the major surface glycoprotein or the beta-tubulin genes. Thus, reverse transcriptase-qPCR targeting the mtSSU gene could serve as a basis for standardizing the P. jirovecii load, which is essential if qPCR is to be incorporated into clinical care pathways as the reference method, accepting that additional parameters such as amplification platforms still need evaluation. |
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| ISSN: | 14602709 13693786 |
| DOI: | 10.1093/mmy/myz115 |