DESCRIPTIONS OF MEDICAL FUNGI THIRD EDITION (revised November 2017) SARAH KIDD1,3, CATRIONA HALLIDAY2, HELEN ALEXIOU1 and DAVID ELLIS1,3 1NaTIONal MycOlOgy REfERENcE cENTRE Sa PaTHOlOgy, aDElaIDE, SOUTH aUSTRalIa 2clINIcal MycOlOgy REfERENcE labORatory cENTRE fOR INfEcTIOUS DISEaSES aND MIcRObIOlOgy labORatory SERvIcES, PaTHOlOgy WEST, IcPMR, WESTMEaD HOSPITal, WESTMEaD, NEW SOUTH WalES 3 DEPaRTMENT Of MOlEcUlaR & cEllUlaR bIOlOgy ScHOOl Of bIOlOgIcal ScIENcES UNIvERSITy Of aDElaIDE, aDElaIDE aUSTRalIa 2016 We thank Pfizera ustralia for an unrestricted educational grant to the australian and New Zealand Mycology Interest group to cover the cost of the printing. Published by the authors contact: Dr. Sarah E. Kidd Head, National Mycology Reference centre Microbiology & Infectious Diseases Sa Pathology frome Rd, adelaide, Sa 5000 Email: [email protected] Phone: (08) 8222 3571 fax: (08) 8222 3543 www.mycology.adelaide.edu.au © copyright 2016 The National Library of Australia Cataloguing-in-Publication entry: creator: Kidd, Sarah, author. Title: Descriptions of medical fungi / Sarah Kidd, catriona Halliday, Helen alexiou, David Ellis. Edition: Third edition. ISbN: 9780646951294 (paperback). Notes: Includes bibliographical references and index. Subjects: fungi--Indexes. Mycology--Indexes. Other creators/contributors: Halliday, catriona l., author. Alexiou, Helen, author. Ellis, David (David H.), author. Dewey Number: 579.5 Printed in adelaide by Newstyle Printing 41 Manchester Street Mile End, South australia 5031 front cover: Cryptococcus neoformans, and montages including Syncephalastrum, Scedosporium, Aspergillus, Rhizopus, Microsporum, Purpureocillium, Paecilomyces and Trichophyton. back cover: the colours of Trichophyton spp. Descriptions of Medical Fungi iii PREFACE The first edition of this book entitled Descriptions of Medical QaP fungi was published in 1992 by David Ellis, Steve Davis, Helen alexiou, Tania Pfeiffer and Zabeta Manatakis. The original concept was to provide all laboratories in the Royal college of Pathologists of australasia (RcPa) Mycology Quality assurance Program (QaP) with a set of description sheets covering medically important fungi. a second edition entitled Descriptions of Medical fungi was released in 2007 by David Ellis, Steve Davis, Helen alexiou, Rosemary Handke and Robyn bartley. We now provide an updated third edition which includes new and revised descriptions. We have endeavoured to reconcile current morphological descriptions with more recent phylogenetic studies, however nomenclature changes in mycology are ongoing. To search for current accepted fungal names go to Index fungorum (www.indexfungorum.org) and Mycobank (www. mycobank.org). Morphological Descriptions: These descriptions have by necessity been kept brief and many have been based on descriptions by other authors. for further information regarding any of the mycoses or pathogenic fungi mentioned, the reader is referred to the citations provided. for the precise definitions of the mycological terminology used, the reader is referred to ainsworth and bisby’s Dictionary of the fungi (Kirk et al. 2008). Classification of the Fungi Kingdom Fungal Phyla Examples Protozoa Myxomycota Slime moulds chromista Oomycota Pythium Eumycota ascomycota Candida, Aspergillus, Scedosporium, Fusarium, Paecilomyces, Penicillium, Cladophialophora, Bipolaris, and other hyphomycetes, including the dimorphic fungi, dermatophytes, and Pneumocystis (Taphrinomycotina). basidiomycota Cryptococcus, Trichosporon, Malassezia. chytridiomycota chytrids glomeromycota Endomycorrhizal on plants Microsporidia 170 genera, 1300 species Zygomycota Apophysomyces, Lichtheimia, Mucor, Saksenaea, Rhizomucor, Rhizopus. fungi are now classified across three Kingdoms. Descriptions in this book are limited to the Eumycota and include medically important representatives from the ascomycota, basidiomycota and Zygomycota. iv Descriptions of Medical Fungi PREFACE Key Morphological Characters Culture Characteristics: • Surface texture [glabrous, suede-like, powdery, granular, fluffy, downy, cottony] • Surface topography [flat, raised, heaped, folded, domed, radial grooved] • Surface pigmentation [white, cream, yellow, brown, pink, grey, black etc] • Reverse pigmentation [none, yellow, brown, red, black, etc] • Growth rate [colony diameter <5 cm in 14 days or >5 cm in 15 days] • Growth at 37Oc, 40Oc, 45Oc. Zygomycota. Sporangia characteristics: • Arrangement of sporangiospores [multispored, sporangiola, merosporangium] • Arrangement of sporangiophores [unbranched often in groups or frequently branched] • Sporangium shape [pyriform, spherical, flask-shaped etc] • Sporangium size [<100 μm diam. or >100 μm diam.] • Columella [Present or absent] • Apophyses [Present or absent] • Sporangiophore height [<0.8 mm or >1 mm] • Rhizoids [Present or absent] (look in the agar) • Sporangiospore size [<6 μm or >6 μm] Hyphomycetes - Conidial Moulds 1. Conidial characteristics: • Septation [one-celled, two-celled, multicelled with transverse septa only, or multicelled with both transverse and longitudinal septa] • Shape [spherical, sub-spherical, pyriform, clavate, ellipsoidal, etc] • Size [need a graduated eyepiece, length <10 μm or >10 μm] • Colour [hyaline or darkly pigmented] • Wall texture [smooth, rough, verrucose, echinulate] • How many conidial types present? [i.e. micro and macro] 2. Arrangement of conidia as they are borne on the conidiogenous cells: • Solitary [single or in balls] • Catenulate (in chains) [acropetal (youngest conidium at the tip) or basipetal (youngest conidium at the base] 3. Growth of the conidiogenous cell: • Determinant (no growth of the conidiophore after the formation of conidia) • Sympodial (a mode of conidiogenous cell growth which results in the development of conidia on a geniculate or zig-zag rachis) 4. Type of conidiogenous cell present: • Non-specialised • Phialide (specialised conidiogenous cells that produces conidia in basipetal succession without increasing in length) • Annellide (specialised conidiogenous cell producing conidia in basipetal succession by a series of short percurrent proliferations (annellations). The tip of an annellide increases in length and becomes narrower as each subsequent conidium is formed) 5. Any additional features present: • Hyphal structures [clamps, spirals, nodular organs, etc] • Synnemata, Sporodochia, chlamydoconidia, Pycnidia • Confirmatory tests for dermatophytes Descriptions of Medical Fungi v PREFACE Molecular and/or MALDI-TOF MS Identification:The use of PcR-based assays, DNa sequencing, and other molecular methods, including those incorporating proteomic approaches such as matrix assisted laser desorption ionization time of flight mass spectroscopy (MalDI-TOf MS) have shown promising results to aid in accurate species identification of fungal cultures. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended (Halliday et al. 2015). Molecular-based fungal identification is particularly helpful for fungi that lack distinguishing morphological features, e.g. Apophysomyces elegans, or to distinguish between species of the Aspergillus fumigatus complex. comparative sequence analysis is now the ‘gold standard’ for identification of fungi. Methods are referenced where available and in many instances are recommended for more definitive identifications. Schematic diagram of the fungal rDNa gene cluster (adapted from clSI MM18-a and Halliday et al. 2015). The 18S, 5.8S and 28S rDNa genes are separated by the two internal transcribed spacers. The 28S and 5S rDNa genes are separated by the intergenic spacer 1 (IgS1). The intergenic spacer 2 (IgS2) separates the rDNa repeat units from each other. Regardless of the genetic locus selected, accurate sequence-based identification is dependent upon database accuracy and adequate species representation. genbank is well known to contain numerous errors in sequences and the species names attributed to the sequences, which are rarely corrected. Therefore caution must be used when interpreting sequencing comparisons against this database, and the use of multiple sequence databases is encouraged. Well-curated databases that are helpful for species identification include: 1. International Society for Human and animal Mycoses (ISHaM) ITS database (http:// its.mycologylab.org/). 2. CBS-KNaW fungal biodiversity centre database (http://www.cbs.knaw.nl). vi Descriptions of Medical Fungi PREFACE frequently used molecular targets for species identification are outlined below: Molecular Target Application Internal transcribed spacer Species level identification of wide ITS regions (ITS1-5.8S-ITS2) range of fungi D1/D2 variable domains of Species identification of many of the D1/D2 the 28S rDNa gene Mucorales accurate species resolution of β-tubulin beta tubulin II Aspergillus. Cal calmodulin Species discrimination of Alternaria. Elongation factor alpha Species complex identification of EF-1α subunit Fusarium. Species complex identification within RPB1 RNa polymerase I subunit genera of Fusarium, Penicillium and RPB2 RNa polymerase II subunit Talaromyces. Species discrimination of Aspergillus, ACT actin Cladosporium, Coniochaeta, Verticillium, Verruconis. glycerol-3-phosphate Species discrimination of Bipolaris, GPDH dehydrogenase Curvularia, Verticillium. CHS chitin synthase Species discrimination of Sporothrix Chi18-5 chitinase 18-5 Species discrimination of Trichoderma Antifungal Susceptibility: for many