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INTERNATIONAL SOCIETY OF HUMAN AND ANIMAL MYCOLOGY (ISHAM)-ITS REFERENCE DNA BARCODING DATABASE--THE QUALITY CONTROLLED STANDARD TOOL FOR ROUTINE IDENTIFICATION OF HUMAN AND ANIMAL PATHOGENIC FUNGI
DNA barcoding
ITS region
Reference ITS database
Intraspecies/interspecies genetic diversity
Laszlo Irinyi1, Carolina Serena1,22, Dea Garcia-Hermoso2, Michael Arabatzis3, Marie Desnos-Ollivier2, Duong Vu4, Gianluigi Cardinali5, Ian Arthur6, Anne-Cécile Normand7, Alejandra Giraldo8, Keith Cassia da Cunha8, Marcelo Sandoval-Denis8, Marijke Hendrickx9, Angela Satie Nishikaku10, Analy Salles de Azevedo Melo10, Karina Bellinghausen Merseguel10, Aziza Khan1, Juliana Alves Parente Rocha11, Paula Sampaio12, Marcelo Ribeiro da Silva Briones13, Renata Carmona e Ferreira13, Mauro de Medeiros Muniz14, Laura Rosio Castañón-Olivares15, Daniel Estrada-Barcenas15, Carole Cassagne7, Charles Mary7, Shu Yao Duan1, Fanrong Kong16, Annie Ying Sun17, Xianyu Zeng16, Zuotao Zhao16, Nausicaa Gantois18, Françoise Botterel19, Barbara Robbertse20, Conrad Schoch20, Walter Gams4, David Ellis21, Catriona Halliday16, Sharon Chen1,16, Tania C. Sorrell1, Renaud Piarroux7, Arnaldo L. Colombo10, Célia Pais12, Sybren de Hoog4, Rosely Maria Zancope-Oliveira ´ 14, Maria Lucia Taylor15, Conchita Toriello15, Célia Maria de Almeida Soares11, Laurence Delhaes18, Dirk Stubbe9, Françoise Dromer2, Stéphane Ranque7, Josep Guarro8, Jose F. Cano-Lira8, Vincent Robert4, Aristea Velegraki3 and Wieland Meyer1* 1Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney,WestmeadMillenniumInstitute, Sydney, Australia, 2Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit; CNRS URA3012, Paris, France, 3 Mycology Research Laboratory, Department of Microbiology, Medical School, the University of Athens Hellenic Collection of Pathogenic Fungi (UOA/HCPF), National and Kapodistrian University of Athens, Athens, Greece, 4 CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands, 5 Department of Pharmaceutical Sciences-Università degli Studi di Perugia, Perugia, Italy, ` 6 Mycology Laboratory, Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands, Western Australia, Australia, 7 Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France, 8 Unitat de Microbiologia, Facultat de Medicina i Ciencies de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain, 9 BCCM/IHEM, Biomedical fungi and yeasts collection, Scientific Institute of Public Health, Brussels, Belgium, 10Laboratório Especial de Micologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil, 11Universidade Federal de Goiás, Instituto de Ciências Biolóogicas, Laboratório de Biologia Molecular, Goiânia, Goiás, Brazil, 12Centre of Molecular and Environmental Biology (CBMA), Biology Department, School of Sciences, University of Minho, Braga, Portugal, 13Laboratório de Genômica e Biocomplexidade Evolutiva, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil, 14Instituto de Pesquisa Clíınica Evandro Chagas (IPEC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil, 15Facultad de Medicina, Departamento de Microbiología y Parasitología (Unidad de Micología), Universidad Nacional Autonóma de México, Ciudad de México, México, 16Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia, 17School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA, Australia; Robinson Institute, University of Adelaide, Adelaide, SA, Australia, 18BDEEP-EA4547, CIIL, Institut Pasteur de Lille, CHU de Lille, Université de Lille2, Lille, France, 19Unité de Parasitologie – Mycologie, Dynamyc Team, CHU Henri Mondor, AP-HP, Creteil, France, 20National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, 21Mycology and Infectious Diseases, SA Pathology, University of Adelaide, Adelaide, SA, Australia and 22Unitat de Recerca, Hospital Joan XXIII, Institut de Investigacio Sanitaria Rovira I Virgili (IISPV), Universitat Rovira i Virgili, Tarragona, Spain.
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Abstract
Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.
Keywords
Fungal identificationDNA barcoding
ITS region
Reference ITS database
Intraspecies/interspecies genetic diversity
Publisher
Oxford
Citation
IRINYI, Laszlo et al. International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database: the quality controlled standard tool for routine identification of human and animal pathogenic fungi. Medical Mycology, v. 53, n. 4, p. 313-337, May 2015.DOI
10.1093/mmy/myv008ISSN
1369-3786Notes
Mauro de Medeiros Muniz e Rosely Maria Zancope-Oliveira - Fundação Oswaldo Cruz. Instituto de Pesquisa Clínica Evandro Chagas. Rio de Janeiro, RJ, Brasil.Laszlo Irinyi1, Carolina Serena1,22, Dea Garcia-Hermoso2, Michael Arabatzis3, Marie Desnos-Ollivier2, Duong Vu4, Gianluigi Cardinali5, Ian Arthur6, Anne-Cécile Normand7, Alejandra Giraldo8, Keith Cassia da Cunha8, Marcelo Sandoval-Denis8, Marijke Hendrickx9, Angela Satie Nishikaku10, Analy Salles de Azevedo Melo10, Karina Bellinghausen Merseguel10, Aziza Khan1, Juliana Alves Parente Rocha11, Paula Sampaio12, Marcelo Ribeiro da Silva Briones13, Renata Carmona e Ferreira13, Mauro de Medeiros Muniz14, Laura Rosio Castañón-Olivares15, Daniel Estrada-Barcenas15, Carole Cassagne7, Charles Mary7, Shu Yao Duan1, Fanrong Kong16, Annie Ying Sun17, Xianyu Zeng16, Zuotao Zhao16, Nausicaa Gantois18, Françoise Botterel19, Barbara Robbertse20, Conrad Schoch20, Walter Gams4, David Ellis21, Catriona Halliday16, Sharon Chen1,16, Tania C. Sorrell1, Renaud Piarroux7, Arnaldo L. Colombo10, Célia Pais12, Sybren de Hoog4, Rosely Maria Zancope-Oliveira ´ 14, Maria Lucia Taylor15, Conchita Toriello15, Célia Maria de Almeida Soares11, Laurence Delhaes18, Dirk Stubbe9, Françoise Dromer2, Stéphane Ranque7, Josep Guarro8, Jose F. Cano-Lira8, Vincent Robert4, Aristea Velegraki3 and Wieland Meyer1* 1Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney,WestmeadMillenniumInstitute, Sydney, Australia, 2Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit; CNRS URA3012, Paris, France, 3 Mycology Research Laboratory, Department of Microbiology, Medical School, the University of Athens Hellenic Collection of Pathogenic Fungi (UOA/HCPF), National and Kapodistrian University of Athens, Athens, Greece, 4 CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands, 5 Department of Pharmaceutical Sciences-Università degli Studi di Perugia, Perugia, Italy, ` 6 Mycology Laboratory, Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands, Western Australia, Australia, 7 Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France, 8 Unitat de Microbiologia, Facultat de Medicina i Ciencies de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain, 9 BCCM/IHEM, Biomedical fungi and yeasts collection, Scientific Institute of Public Health, Brussels, Belgium, 10Laboratório Especial de Micologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil, 11Universidade Federal de Goiás, Instituto de Ciências Biolóogicas, Laboratório de Biologia Molecular, Goiânia, Goiás, Brazil, 12Centre of Molecular and Environmental Biology (CBMA), Biology Department, School of Sciences, University of Minho, Braga, Portugal, 13Laboratório de Genômica e Biocomplexidade Evolutiva, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil, 14Instituto de Pesquisa Clíınica Evandro Chagas (IPEC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil, 15Facultad de Medicina, Departamento de Microbiología y Parasitología (Unidad de Micología), Universidad Nacional Autonóma de México, Ciudad de México, México, 16Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia, 17School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA, Australia; Robinson Institute, University of Adelaide, Adelaide, SA, Australia, 18BDEEP-EA4547, CIIL, Institut Pasteur de Lille, CHU de Lille, Université de Lille2, Lille, France, 19Unité de Parasitologie – Mycologie, Dynamyc Team, CHU Henri Mondor, AP-HP, Creteil, France, 20National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, 21Mycology and Infectious Diseases, SA Pathology, University of Adelaide, Adelaide, SA, Australia and 22Unitat de Recerca, Hospital Joan XXIII, Institut de Investigacio Sanitaria Rovira I Virgili (IISPV), Universitat Rovira i Virgili, Tarragona, Spain.
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