DESCRIPTIONS OF MEDICAL FUNGI - Mycology Online

DESCRIPTIONS OF MEDICAL FUNGITHIRD EDITION(revised November 2016)SARAH KIDD1,3, CATRIONA HALLIDAY2,HELEN ALEXIOU1 and DAVID ELLIS1,31National Mycology Reference CentreSA Pathology, Adelaide, SOUTH AUSTRALIA2Clinical Mycology Reference LaboratoryCentre for Infectious Diseases and MicrobiologyLaboratory Services, Pathology West, ICPMR,Westmead Hospital, Westmead, NEW SOUTH WALES3DEPARTMENT OF MOLECULAR & CELLULAR BIOLOGYSCHOOL OF BIOLOGICAL SCIENCESUNIVERSITY OF ADELAIDE, ADELAIDEAUSTRALIA2016We thank Pfizer Australia for an unrestricted educational grant to the Australianand New Zealand Mycology Interest Group to cover the cost of the printing.

Published by the AuthorsContact: Dr. Sarah E. KiddHead, National Mycology Reference CentreMicrobiology & Infectious DiseasesSA PathologyFrome Rd, Adelaide, SA 5000Email: sarah.kidd@sa.gov.auPhone: (08) 8222 3571Fax:(08) 8222 3543www.mycology.adelaide.edu.au Copyright 2016The 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: 579.5Printed in Adelaide byNewstyle Printing41 Manchester StreetMile End, South Australia 5031Front cover: Cryptococcus neoformans, and montages including Syncephalastrum,Scedosporium, Aspergillus, Rhizopus, Microsporum, Purpureocillium, Paecilomycesand Trichophyton. Back cover: the colours of Trichophyton spp.

Descriptions of Medical FungiiiiPREFACEThe first edition of this book entitled Descriptions of Medical QAP Fungi was publishedin 1992 by David Ellis, Steve Davis, Helen Alexiou, Tania Pfeiffer and ZabetaManatakis. The original concept was to provide all laboratories in the Royal College ofPathologists of Australasia (RCPA) Mycology Quality Assurance Program (QAP) witha set of description sheets covering medically important fungi. A second edition entitledDescriptions of Medical Fungi was released in 2007 by David Ellis, Steve Davis, HelenAlexiou, Rosemary Handke and Robyn Bartley. We now provide an updated thirdedition which includes new and revised descriptions. We have endeavoured to reconcilecurrent morphological descriptions with more recent phylogenetic studies, howevernomenclature changes in mycology are ongoing. To search for current acceptedfungal names go to Index Fungorum (www.indexfungorum.org) and Mycobank (www.mycobank.org).Morphological Descriptions: These descriptions have by necessity been kept briefand many have been based on descriptions by other authors. For further informationregarding any of the mycoses or pathogenic fungi mentioned, the reader is referred tothe 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 FungiKingdomFungal PhylaExamplesProtozoaMyxomycotaSlime ndida, Aspergillus, Scedosporium,Fusarium, Paecilomyces, Penicillium,Cladophialophora, Bipolaris, and otherhyphomycetes, including the dimorphicfungi, dermatophytes, and coccus, Trichosporon, omycorrhizal on plantsMicrosporidia170 genera, 1300 speciesZygomycotaApophysomyces, Lichtheimia, Mucor,Saksenaea, Rhizomucor, Rhizopus.Fungi are now classified across three Kingdoms. Descriptions in this book arelimited to the Eumycota and include medically important representatives from theAscomycota, Basidiomycota and Zygomycota.

ivDescriptions of Medical FungiPREFACEKey Morphological CharactersCulture 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 Moulds1. Conidial characteristics: Septation [one-celled, two-celled, multicelled with transverse septa only, or multicelled withboth 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 (youngestconidium 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 ofconidia on a geniculate or zig-zag rachis)4. Type of conidiogenous cell present: Non-specialised Phialide (specialised conidiogenous cells that produces conidia in basipetal successionwithout increasing in length) Annellide (specialised conidiogenous cell producing conidia in basipetal succession by aseries of short percurrent proliferations (annellations). The tip of an annellide increases inlength 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 FungivPREFACEMolecular and/or MALDI-TOF MS Identification: The use of PCR-based assays, DNAsequencing, and other molecular methods, including those incorporating proteomicapproaches such as matrix assisted laser desorption ionization time of flight massspectroscopy (MALDI-TOF MS) have shown promising results to aid in accurate speciesidentification of fungal cultures. These are used mainly to complement conventionalmethods since they require standardisation before widespread implementation can berecommended (Halliday et al. 2015). Molecular-based fungal identification is particularlyhelpful for fungi that lack distinguishing morphological features, e.g. Apophysomyceselegans, 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 formore definitive identifications.Schematic diagram of the fungal rDNA gene cluster (adapted from CLSI MM18-Aand Halliday et al. 2015). The 18S, 5.8S and 28S rDNA genes are separated by thetwo internal transcribed spacers. The 28S and 5S rDNA genes are separated by theintergenic spacer 1 (IGS1). The intergenic spacer 2 (IGS2) separates the rDNA repeatunits from each other.Regardless of the genetic locus selected, accurate sequence-based identification isdependent upon database accuracy and adequate species representation. GenBankis well known to contain numerous errors in sequences and the species namesattributed to the sequences, which are rarely corrected. Therefore caution must beused when interpreting sequencing comparisons against this database, and the use ofmultiple sequence databases is encouraged. Well-curated databases that are helpfulfor 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).

viDescriptions of Medical FungiPREFACEFrequently used molecular targets for species identification are outlined below:Molecular TargetApplicationITSInternal transcribed spacerregions (ITS1-5.8S-ITS2)Species level identification of widerange of fungiD1/D2D1/D2 variable domains ofthe 28S rDNA geneSpecies identification of many of theMucoralesβ-tubulinBeta tubulin IIAccurate species resolution ofAspergillus.CalCalmodulinSpecies discrimination of Alternaria.EF-1αElongation factor alphasubunitSpecies complex identification ofFusarium.RPB1RPB2RNA polymerase I subunitRNA polymerase II seSpecies discrimination of Bipolaris,Curvularia, Verticillium.CHSChitin synthaseSpecies discrimination of SporothrixChi18-5Chitinase 18-5Species discrimination of TrichodermaSpecies complex identification withingenera of Fusarium, Penicillium andTalaromyces.Species discrimination of Aspergillus,Cladosporium, Coniochaeta, Verticillium,Verruconis.Antifungal Susceptibility: For many species, antifungal susceptibility data has alsobeen provided. This has been derived from both the literature and data from Australianclinical isolates generated by using the CLSI M27-A Standard for yeasts and the CLSIM38-A Standard for moulds. This composite data is provided as a guide only. In manycases the clinical relevance of in vitro antifungal susceptibility results remains difficultto interpret, and expert advice from a consulting microbiologist or infectious diseasespecialist may be required.CLSI M27-S4 clinical breakpoints are marked where available (green for susceptible,yellow for susceptible dose dependant or intermediate, red for resistant).Abbreviations: Amphotericin B (AmB), Fluconazole (FLU), Itraconazole (ITRA),Posaconazole (POSA), Voriconazole (VORI), Anidulafungin (ANID), Caspofungin(CAS), Micafungin (MICA), 5-Fluorocytosine (5FC), Terbinafine (TERB).Risk group (RG) recommendations are based on published data and on currentdefinitions in accordance with the Australian/New Zealand Standard AS/NZS2243.3:2010. Safety in laboratories Part 3: Microbiological safety and containment.Note: International biosafety guidelines vary in their RG ratings of fungal species.

Descriptions of Medical FungiviiCONTENTSAcremoniumAcrophialophora fusisporaAlternariaAphanoascus fulvescensApophysomyces complexArthroderma insingulare (formerly Trichophyton terrestre)Arthroderma uncinatum (formerly Trichophyton ajelloi)Arthrographis kalraeAspergillusAspergillus flavus complexAspergillus fumigatus complexAspergillus felisAspergillus fumigatusAspergillus lentulusNeosartorya fischeriAspergillus nidulans complexAspergillus niger complexAspergillus terreus complexAureobasidium pullulansBasidiobolus ranarumBeauveriaBipolarisBlastomyces dermatitidisCandidaCandida albicansCandida catenulataCandida dubliniensisCandida glabrata complexCandida bracarensisCandida glabrataCandida nivariensisCandida haemuloniiCandida inconspicuaCandida parapsilosis complexCandida metapsilosisCandida orthopsilosisCandida parapsilosisLodderomyces elongisporusCandida rugosaCandida tropicalisChaetomiumChrysosporium tropicumCladophialophoraCladophialophora bantianaCladophialophora carrioniiCladosporiumClavispora lusitaniae (formerly Candida lusitaniae)Coccidioides immitis/posadasii 73839404041424344454546474849505152535355575960