Author
Affilliation
Abstract
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.
Publisher
Frontiers Media
Citation
HOANG, Minh Thuy Vi et al. Dual DNA barcoding for the molecular identification of the agents of invasive fungal infections. Frontiers in Microbiology, v. 10, p. 1-13, July 2019.
DOI
10.3389/fmicb.2019.01647
ISSN
1664-302X
Notes
Rosely Maria Zancopé-Oliveira. Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta a informação no documento.
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. DATA AVAILABILITY The primary and secondary fungal barcodes generated and analyzed for this study are available in the ISHAM Barcoding Database (http://its.mycologylab.org/).
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