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International Society of Human and Animal Mycology Downloaded from https://academic.oup.com/mmy/article-abstract/53/4/313/977005 by Fundação Oswaldo Cruz-Biblioteca de Manguinhos/Oswaldo Cruz Foundation-Manguinhos Library user on 26 March 2019 Medical Mycology, 2015, 53, 313–337 doi: 10.1093/mmy/myv008 Review Article Review Article 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 Laszlo Irinyi1, Carolina Serena1,22,DeaGarcia-Hermoso2, Michael Arabatzis3,MarieDesnos-Ollivier2, Duong Vu4, Gianluigi Cardinali5,IanArthur6, Anne-Cecile´ Normand7, Alejandra Giraldo8, Keith Cassia da Cunha8,MarceloSandoval-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 eFerreira13, Mauro de Medeiros Muniz14, Laura Rosio Castan˜ on-Olivares´ 15, Daniel Estrada-Barcenas15, Carole Cassagne7, Charles Mary7, Shu Yao Duan1, Fanrong Kong16, Annie Ying Sun17,XianyuZeng16, Zuotao Zhao16, Nausicaa Gantois18, Franc¸oise Botterel19, Barbara Robbertse20, Conrad Schoch20,WalterGams4,DavidEllis21, Catriona Halliday16, Sharon Chen1,16, Tania C. Sorrell1, Renaud Piarroux7, Arnaldo L. Colombo10,Celia´ Pais12, Sybren de Hoog4, Rosely Maria Zancope-Oliveira´ 14, Maria Lucia Taylor15, Conchita Toriello15,Celia´ Maria de Almeida Soares11, Laurence Delhaes18, Dirk Stubbe9, Franc¸oise Dromer2,Stephane´ Ranque7, Josep Guarro8, Jose F. Cano-Lira8, Vincent Robert4,AristeaVelegraki3 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, Uni- versity of Sydney, Westmead Millennium Institute, Sydney, Australia, 2Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit; CNRS URA3012, Paris, France, 3Mycology 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, 4CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands, 5Department of Pharmaceutical Sciences-Universita` degli Studi di Perugia, Perugia, Italy, 6Mycology Laboratory, De- partment of Microbiology and Infectious Diseases, PathWest Laboratory Medicine WA, QEII Medical C The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. 313 All rights reserved. For permissions, please e-mail: [email protected] Downloaded from https://academic.oup.com/mmy/article-abstract/53/4/313/977005 by Fundação Oswaldo Cruz-Biblioteca de Manguinhos/Oswaldo Cruz Foundation-Manguinhos Library user on 26 March 2019 314 Medical Mycology, 2015, Vol. 53, No. 4 Centre, Nedlands, Western Australia, Australia, 7Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France, 8Unitat de Micro- biologia, Facultat de Medicina i Ciencies` de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain, 9BCCM/IHEM, Biomedical fungi and yeasts collection, Scientific Institute of Public Health, Brussels, Belgium, 10Laboratorio´ Especial de Micologia, Escola Paulista de Medicina, Universidade Federal de Sao˜ Paulo, Sao˜ Paulo, Brazil, 11Universidade Federal de Goias,´ Instituto de Cienciasˆ Biologicas,´ Labo- ratorio´ de Biologia Molecular, Goiania,ˆ Goias,´ Brazil, 12Centre of Molecular and Environmental Biology (CBMA), Biology Department, School of Sciences, University of Minho, Braga, Portugal, 13Laboratorio´ de Genomicaˆ e Biocomplexidade Evolutiva, Escola Paulista de Medicina, Universidade Federal de Sao˜ Paulo, Sao˜ Paulo, Brazil, 14Instituto de Pesquisa Cl´ınica Evandro Chagas (IPEC), Fundac¸ao˜ Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil, 15Facultad de Medicina, Departamento de Microbiolog´ıa y Parasitolog´ıa (Unidad de Micolog´ıa), Universidad Nacional Autonoma´ de Mexico,´ Ciudad de Mexico,´ Mexico,´ 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, Universite´ de Lille2, Lille, France, 19Unite´ 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 *To whom correspondence should be addressed. Prof. Wieland Meyer, Molecular Mycology Research Laboratory, MBI, CIDM, Level 4, Room O.4.04, 176 Hawkesbury Road, Westmead, SW 2145, Australia, Tel: +61-2-86273430; Fax +61-2-98915317; E-mail: [email protected] Received 6 October 2014; Revised 22 December 2014; Accepted 19 January 2015 Abstract Human and animal fungal pathogens are a growing threat worldwide leading to emerg- ing 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 tar- geted 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, of- fer 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, provid- ing 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 eval- uate 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 Downloaded from https://academic.oup.com/mmy/article-abstract/53/4/313/977005 by Fundação Oswaldo Cruz-Biblioteca de Manguinhos/Oswaldo Cruz Foundation-Manguinhos Library user on 26 March 2019 Irinyi et al. 315 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are re- quired for their reliable identification from clinical and veterinary specimens. Key words: fungal identification, DNA barcoding, ITS region, reference ITS database, intraspecies/interspecies genetic diversity. Introduction cation is straightforward when a sequence is unique to a single species and constant within each species [8,11,12]. The number of human and animal fungal infections, rang- The most important question in barcoding is: How ing from superficial infections of the nails and skin, through accurate and reliable are the delineation and identification mucocutaneous candidiasis to invasive fungal infections, of a species using a single gene? have significantly increased over the last three decades, The correct identification of fungi is essential for many causing serious public health burdens and increased risk of biological purposes, such as the assessment of biodiversity, biodiversity loss among animal species [1,2]. In humans, su- taxonomy and species conservation [9,13]. It is manda- perficial infections affect an estimated 25% ( = 1.7 billion) tory for clinical diagnosis and early initiation of appropri- individuals world-wide. Oropharyngeal or genital mucosal ate antifungal therapy. Traditional identification based on infections are also common and can be disabling. For exam- morphology and biochemistry of pathogenic fungi is time- ple, an estimated 75% of women of childbearing age suffer- consuming and requires a certain level of morphological ing from vulvovaginitis, mainly caused by Candida species and taxonomical expertise. To overcome these limitations, [3], which are the third most common opportunistic fungal DNA barcoding was evaluated in fungi, targeting numer- disease agents after Aspergillus spp. worldwide [1]. Inva- ous genetic loci, including COX1 [14], protein-coding genes sive fungal diseases are of great concern, due to their high like RNA polymerase I and II [15–19], partial translation mortality that can exceed 50%. More than 90% of fungal- elongation factor 1-α [20–22], β-tubulin [23], and the in- related deaths are caused by four fungal genera: Aspergillus, ternal transcribed spacer (ITS) regions [24,25]. The protein Candida, Cryptococcus, and Pneumocystis [1,4,5]. Delays coding genes
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