1. Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections
- Author
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Minh Thuy Vi Hoang, Laszlo Irinyi, Sharon C. A. Chen, Tania C. Sorrell, The ISHAM Barcoding of Medical Fungi Working Group, Wieland Meyer, Michael Arabatzis, Ian Arthur, Jose F. Cano-Lira, Gianluigi Cardinali, Laura Rosio Castañón, Sharon Chen, Wen Chen, Ariya Chindamporn, Arnaldo L. Colombo, Marie Desnos-Ollivier, Wilhelm de Beer, Sybren de Hoog, Françoise Dromer, Dea Garcia-Hermoso, Marieka Gryzenhout, Josep Guarro, Catriona Halliday, Marijke Hendrickx, Sabine Huhndorf, C. Andre Levesque, Maria Luiza Moretti, Mauro de Medeiros Muniz, Analy Salles de Azevedo Melo, Angela Satie Nishikaku, Anne-Cécile Normand, Célia Pais, Renaud Piarroux, Stéphane Ranque, Barbara Robbertse, Vincent Robert, Conrad L. Schoch, Keith A. Seifert, Célia Maria de Almeida Soares, John L. Spouge, Dirk Stubbe, Maria Lucia Taylor, Conchita Toriello, Aristea Velegraki, Chompoonek Yurayart, Rosely Maria Zancopé-Oliveira, The University of Sydney, Centre for Infectious Disease and Microbiology (CIDM), The Westmead Institute for Medical Research, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), National Health and Medical Research Council of Australia (NH & MRC) grant (#APP1121936), Members of the Isham Barcoding of Medical Fungi Working Group : Michael Arabatzis, National and Kapodistrian University of Athens, Athens, Greece, Ian Arthur, PathWest Laboratory Medicine, Nedlands, WA, Australia, Jose F. Cano-Lira, Universitat Rovira i Virgili, Reus, Spain, Gianluigi Cardinali, Università degli Studi di Perugia, Perugia, Italy, Laura Rosio Castañón, Universidad Nacional Autónoma de México, Mexico City, Mexico, Sharon Chen, Westmead Hospital, University of Sydney, Sydney, NSW, Australia, Wen Chen, Agriculture and Agri-Food Canada, Ottawa, ON, Canada, Ariya Chindamporn, Chulalongkorn University, Bangkok, Thailand, Arnaldo L. Colombo, Universidade Federal de São Paulo, São Paulo, Brazil, Marie Desnos-Ollivier, Institut Pasteur, Paris, France, Wilhelm de Beer, FABI, Pretoria, South Africa, Sybren de Hoog, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands, Françoise Dromer, Institut Pasteur, Paris, France, Dea Garcia-Hermoso, Institut Pasteur, Paris, France, Marieka Gryzenhout, University of the Free State, Bloemfontein, South Africa, Josep Guarro, Universitat Rovira i Virgili, Reus, Spain, Catriona Halliday, University of Sydney/Westmead Hospital, Sydney, NSW, Australia, Marijke Hendrickx, BCCM/IHEM, Scientific Institute of Public Health, Brussels, Belgium, Sabine Huhndorf, The Field Museum, Chicago, IL, United States, Laszlo Irinyi, Westmead Hospital, University of Sydney, Sydney, NSW, Australia, C. Andre Levesque, Agriculture and Agri-Food Canada, Ottawa, ON, Canada, Wieland Meyer, Westmead Hospital, University of Sydney, Sydney, NSW, Australia, Maria Luiza Moretti, University of Campinas, Campinas, Brazil, Mauro de Medeiros Muniz, Instituto de Pesquisa Clínica Evandro Chagas (IPEC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil, Analy Salles de Azevedo Melo, Universidade Federal de São Paulo, São Paulo, Brazil, Angela Satie Nishikaku, Universidade Federal de São Paulo, São Paulo, Brazil, Anne-Cécile Normand, Aix-Marseille University, Marseille, France, Célia Pais, University of Minho, Braga, Portugal, Renaud Piarroux, Aix-Marseille University, Marseille, France, Stéphane Ranque, Aix-Marseille University, Marseille, France, Barbara Robbertse, National Center for Biotechnology Information, Bethesda, MD, United States, Vincent Robert, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands, Conrad L. Schoch, National Center for Biotechnology Information, Bethesda, MD, United States, Keith A. Seifert, Agriculture and Agri-Food Canada, Ottawa, ON, Canada, Célia Maria de Almeida Soares, Universidade Federal de Goiás, Goiânia, Brazil, Tania C. Sorrell, Westmead Hospital, University of Sydney, Sydney, NSW, Australia, John L. Spouge, National Center for Biotechnology Information, Bethesda, MD, United States, Dirk Stubbe, BCCM/IHEM, Scientific Institute of Public Health, Brussels, Belgium, Maria Lucia Taylor, Universidad Nacional Autónoma de México, Mexico City, Mexico, Conchita Toriello, Universidad Nacional Autónoma de México, Mexico City, Mexico, Aristea Velegraki, National and Kapodistrian University of Athens, Athens, Greece, Chompoonek Yurayart, Kasetsart University, Bangkok, Thailand, Rosely Maria Zancopé-Oliveira, Instituto de Pesquisa Clínica Evandro Chagas (IPEC), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil., Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Westerdijk Fungal Biodiversity Institute - Medical Mycology, Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Software and Databasing
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Microbiology (medical) ,invasive fungal diseases ,lcsh:QR1-502 ,ISHAM Barcoding Database ,Computational biology ,Biology ,Barcode ,Microbiology ,DNA barcoding ,lcsh:Microbiology ,law.invention ,dual barcoding system ,03 medical and health sciences ,[SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,law ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Internal transcribed spacer ,Original Research ,030304 developmental biology ,Molecular identification ,internal transcribed spacer region ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,0303 health sciences ,030306 microbiology ,Fungal DNA ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,fungal DNA barcoding ,Clinical Practice ,translational elongation factor 1α ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,identification ,Identification (biology) ,Translational elongation - Abstract
International audience; Invasive fungal infections, such as aspergillosis, candidiasis, and cryptococcosis, have significantly increased among immunocompromised people. To tackle these infections the first and most decisive step is the accurate identification of the causal pathogen. Routine identification of invasive fungal infections has progressed away from culture-dependent methods toward molecular techniques, including DNA barcoding, a highly efficient and widely used diagnostic technique. Fungal DNA barcoding previously relied on a single barcoding region, the internal transcribed spacer (ITS) region. However, this allowed only for 75% of all fungi to be correctly identified. As such, the translational elongation factor 1α (TEF1α) was recently introduced as the secondary barcode region to close the gap. Both loci together form the dual fungal DNA barcoding scheme. As a result, the ISHAM Barcoding Database has been expanded to include sequences for both barcoding regions to enable practical implementation of the dual barcoding scheme into clinical practice. The present study investigates the impact of the secondary barcode on the identification of clinically important fungal taxa, that have been demonstrated to cause severe invasive disease. Analysis of the barcoding regions was performed using barcoding gap analysis based on the genetic distances generated with the Kimura 2-parameter model. The secondary barcode demonstrated an improvement in identification for all taxa that were unidentifiable with the primary barcode, and when combined with the primary barcode ensured accurate identification for all taxa analyzed, making DNA barcoding an important, efficient and reliable addition to the diagnostic toolset of invasive fungal infections.
- Published
- 2019