Medically Important Fungi: A Guide to Identification

Larone, Davise H. PhD

ISBN-13: 9781555816605

Table of Contents
Table of Contents

Preface to the Fifth Edition

Preface to the First Edition

Acknowledgements

How to Use the Guide

Use of Reference Laboratories

Safety Precautions

PART I: DIRECT MICROSCOPIC EXAMINATION OF CLINICAL SPECIMENS

Written with the assistance of Joan Barenfanger, M.D., Ph.D., and Sara B. Peters, Ph.D., M.D.

Introduction

Histological Terminology

Tissue Reactions to Fungal Infection

Stains

Table 1: Stains for direct microscopic examination of fungi and filamentous bacteria in tissue

Guide to Interpretation of Direct Microscopic Examination

Detailed Descriptions

Actinomycosis

Mycetoma, Actinomycotic or Eumycotic

Nocardiosis

Zygomycosis

Aspergillosis

Hyalohyphomycoses

Dermatophytoses

Tinea versicolor

Tinea nigra

Phaeohyphomycosis

Chromoblastomycosis

Sporotrichosis
Histoplasmosis

Penicilliosis marneffei

Blastomycosis

Paracoccidioidomycosis

Candidiasis (Candidosis)

Trichosporonosis

Cryptococcosis

Pneumocystosis

Protothecosis

Coccidioidomycosis

Rhinosporidiosis

Adiaspiromycosis

Special References

PART II: IDENTIFICATION OF FUNGI IN CULTURE

Guide to Identification of Fungi in Culture

Detailed Descriptions

Filamentous Bacteria

Introduction

Table 2: Differentiation of filamentous aerobic actinomycetes encountered in clinical specimens

Nocardia spp.

Table 3: Phenotypic characteristics of most common clinically encountered Nocardia spp.

Streptomyces spp.

Actinomadura spp.

Nocardiopsis dassonvillei

Yeasts and Yeastlike Organisms

Introduction

Candida albicans

Table 4: Characteristics of the genera of clinically encountered yeasts and yeastlike organisms

Candida dubliniensis

Table 5: Characteristics of Candida spp. most commonly encountered in the clinical laboratory

Table 6: Characteristics that assist in differentiating Candida dubliniensis from Candida albicans

Candida tropicalis

Candida parapsilosis complex

Candida lusitaniae
Candida krusei

Table 7: Differentiating characteristics of Blastoschizomyces capitatus versus Candida krusei

Table 8: Differentiating characteristics of Candida krusei, Candida inconspicua, and C. norvegensis

Candida kefyr (formerly Candida pseudotropicalis)

Candida rugosa

Candida guilliermondii complex

Table 9: Differentiating characteristics of Candida guilliermondii versus Candida famata

Candida lipolytica

Candida zeylanoides

Candida glabrata

Cryptococcus neoformans

Table 10: Characteristics of Cryptococcus spp.

Table 11: Characteristics of yeasts and yeastlike organisms other than Candida spp. and Cryptococcus spp.

Cryptococcus gattii

Rhodotorula spp.

Sporobolomyces salmonicolor

Saccharomyces cerevisiae

Wickerhamomyces anomalus (formerly Pichia anomala and Hansenula anomala) (sexual state); Candida pelliculosa (asexual
state)

Malassezia spp.

Malassezia pachydermatis

Ustilago sp.

Prototheca spp.

Trichosporon spp.

Table 12: Key characteristics of clinically encountered Trichosporon spp.

Blastoschizomyces capitatus

Geotrichum candidum

Thermally Dimorphic Fungi

Introduction

Sporothrix schenckii complex

Table 13: Characteristics for differentiating species of the Sporothrix schenckii complex

Histoplasma capsulatum

Blastomyces dermatitidis

Paracoccidioides brasiliensis

Penicillium marneffei

Thermally Monomorphic Moulds

Zygomycetes

Introduction

Table 14: Differential characteristics of similar organisms in the class Zygomycetes

Table 15: Differential characteristics of the clinically encountered Rhizopus spp.

Rhizopus spp.

Mucor spp.

Rhizomucor spp.

Lichtheimia corymbifera complex (formerly Absidia corymbifera)

Apophysomyces elegans

Saksenaea vasiformis

Cokeromyces recurvatus

Cunninghamella bertholletiae

Syncephalastrum racemosum

Basidiobolus sp.

Conidiobolus coronatus

Dematiaceous Fungi

Introduction

Fonsecaea pedrosoi

Fonsecaea compacta

Rhinocladiella spp.

Phialophora verrucosa

Table 16: Characteristics of Phialophora, Pleurostomophora, Phaeoacremonium, Acremonium, Phialemonium, and

Lecythophora

Pleurostomophora richardsiae (formerly Phialophora richardsiae)

Phaeoacremonium parasiticum (formerly Phialophora parasitica)

Phialemonium spp.

Cladosporium spp.

Table 17: Characteristics of Cladosporium and Cladophialophora spp.

Cladophialophora carrionii

Cladophialophora bantiana

Cladophialophora boppii (formerly Taeniolella boppii)

Pseudallescheria boydii (sexual state) / Scedosporium apiospermum (asexual state) complex

Table 18: Differentiating phenotypic characteristics of the clinically encountered members of the P. boydii complex and S.
prolificansa

Scedosporium prolificans (formerly Scedosporium inflatum)

Ochroconis gallopava (formerly Dactylaria constricta var. gallopava)

Table 19: Differentiation of the clinically encountered Ochroconis species

Table 20: Characteristics of some of the "black yeasts"

Exophiala jeanselmei complex

Exophiala dermatitidis (Wangiella dermatitidis)

Hortaea werneckii (Phaeoannellomyces werneckii)

Madurella mycetomatis

Madurella grisea

Piedraia hortae

Aureobasidium pullulans

Table 21: Differential characteristics of Aureobasidium pullulans versus Hormonema dematioides

Hormonema dematioides

Neoscytalidium dimidiatum (formerly Scytalidium dimidiatum)

Botrytis sp.

Stachybotrys chartarum (S. alternans, S. atra)

Graphium eumorphum

Curvularia spp.

Bipolaris spp.

Table 22: Characteristics of Bipolaris, Drechslera, and Exserohilum spp.

Exserohilum spp.

Helminthosporium sp.

Alternaria sp.

Ulocladium sp.

Stemphylium sp.

Pithomyces sp.

Epicoccum sp.

Nigrospora sp.

Chaetomium sp.

Phoma spp.

Dermatophytes

Introduction

Microsporum audouinii

Microsporum canis var. canis

Microsporum canis var. distortum

Microsporum cookei

Microsporum gypseum complex

Microsporum gallinae
Microsporum nanum

Microsporum vanbreuseghemii

Microsporum ferrugineum

Trichophyton mentagrophytes

Table 23: Differentiation of similar conidia-producing Trichophyton spp.

Trichophyton rubrum

Trichophyton tonsurans

Trichophyton terrestre

Trichophyton megninii

Trichophyton soudanense

Table 24: Growth patterns of Trichophyton species on nutritional test media

Trichophyton schoenleini

Trichophyton verrucosum

Trichophyton violaceum

Trichophyton ajelloi

Epidermophyton floccosum

Hyaline Hyphomycetes

Introduction

Coccidioides immitis/posadasii complex

Table 25: Differential characteristics of fungi in which arthroconidia predominate

Malbranchea spp.

Geomyces pannorum

Arthrographis kalrae

Hormographiella aspergillata

Emmonsia spp.

Table 26: Identification of the most common species of Aspergillus

The Genus Aspergillus

Aspergillus fumigatus

Aspergillus niger

Aspergillus flavus

Aspergillus versicolor

Aspergillus calidoustus

Aspergillus nidulans (asexual state); Emericella nidulans (sexual state)

Aspergillus glaucus (asexual state); Eurotium herbariorum (sexual state)

Aspergillus terreus

Aspergillus clavatus
Penicillium spp.

Paecilomyces spp.

Scopulariopsis spp.

Table 27: Differential characteristics of Paecilomyces variottii versus P. lilacinus

Table 28: Differential characteristics of Scopulariopsis brevicaulis versus S. brumptii

Gliocladium sp.

Trichoderma sp.

Beauveria bassiana

Verticillium sp.

Acremonium (formerly Cephalosporium) spp.

Fusarium spp.

Lecythophora spp.

Trichothecium roseum

Chrysosporium spp.

Table 29: Differential characteristics of Chrysosporium versus Sporotrichum

Sporotrichum sp.

Sepedonium sp.

Chrysonilia sitophila (formerly Monilia sitophila)

PART III: BASICS OF MOLECULAR METHODS FOR FUNGAL IDENTIFICATION

Written with Sanchita Das, M.D., Department of Medicine, Division of Infectious Disease, Weill Medical College of Cornell
University, New York, NY

Introduction

Molecular Terminology

Overview of Classic Molecular Identification Methods

Fungal Targets

Amplification and Non-Sequence Identification Methods

PCR (Polymerase Chain Reaction)

Nested PCR

Real-time PCR

Melting curve analysis

Fluorescence resonance energy transfer (FRET)

TaqMan 5?nuclease

Molecular beacons

Microarray

Repetitive-element PCR (rep-PCR)

Sequence-Based Identification Methods

Sanger sequencing

Pyrosequencing

DNA barcoding

Applications of DNA Sequencing

Accurate method identification

Phylogenetic analysis

Organism typing

Commercial Platforms and Recently Developed Techniques

AccuProbe test

PNA FISH

Luminex xMAP

MALDI-TOF

Selected References for Further Information

PART IV: LABORATORY TECHNIQUE

Laboratory Procedures

Collection and Preparation of Specimens

Methods for Direct Microscopic Examination of Specimens

Primary Isolation

Table 30: Media for primary isolation of fungi

Table 31: Inhibitory mold agar versus. Sabouraud dextrose agar as a primary medium for isolation of fungi

Macroscopic Examination of Cultures

Microscopic Examination of Growth

Procedure for Identification of Yeasts

Direct Identification of Yeasts from Blood Culture (by PNA FISH)

Isolation of Yeast When Mixed with Bacteria

Germ Tube Test for the Presumptive Identification of Candida albicans

Rapid Enzyme Tests for the Presumptive Identification of Candida albicans

Caffeic Acid Disk Test

Olive Oil Disks for Culturing Malassezia species

Conversion of Thermally Dimorphic Fungi in Culture

Method of Inducing Sporulation of Apophysomyces elegans and Saksenaea vasiformis

In Vitro Hair Perforation Test (for Differentiation of Trichophyton mentagrophytes and Trichophyton rubrum)

Germ Tube Test for Differentiation of Some Dematiaceous Fungi

Temperature Tolerance Testing

Maintenance of Stock Fungal Cultures

Controlling Mites

Staining Methods

Acid-Fast Modified Kinyoun Stain for Nocardia spp.

Acid-Fast Stain for Ascospores

Ascospore Stain

Calcofluor White Stain

Giemsa Stain

Gomori Methenamine Silver (GMS) Stain

Gram Stain (Hucker Modification)

Lactophenol Cotton Blue

Lactophenol Cotton Blue with Polyvinyl Alcohol (Huber's Mounting Medium, Modified)

Rehydration of Paraffin-Embedded Tissue (Deparaffination)

Media

Introduction

Acetamide Agar

Arylsulfatase Broth

Ascospore Media

Assimilation Media (for Yeasts)

Birdseed Agar (Niger Seed Agar; Staib Agar)

Brain Heart Infusion (BHI) Agar

Buffered Charcoal Yeast Extract (BCYE) Agar

Canavanine Glycine Bromothymol Blue (CGB) Agat

Casein Agar

CHROMagar Candida Medium

ChromID Candida Medium (formerly Candida ID 2)

Citrate Agar

Cornmeal Agar

Dermatophyte Test Medium (DTM)

Dixon Agar (Modified)

Esculin Agar

Fermentation Broths for Yeasts

Gelatin Medium

Inhibitory Mould Agar (IMA)

Leeming-Notman Agar (Modified)

Loeffler Medium

Lysozyme Medium

Middlebrook Agar Opacity Test for Nocardia farcinica

Mycosel Agar

Nitrate Broth

Polished Rice, or Rice Grain, Medium

Potato Dextrose Agar and Potato Flake Agar

Rapid Assimilation of Trehalose (RAT) Broth

Rapid Sporulation Medium (RSM)

SABHI Agar

Sabouraud Dextrose Agar (SDA)

Sabouraud Dextrose Agar with 15% NaCl

Sabouraud Dextrose Broth

Starch Hydrolysis Agar

Trichophyton Agars

Tyrosine, Xanthine, or Hypoxanthine Agar

Urea Agar

Water Agar

Yeast Extract-Phosphate Agar with Ammonia

COLOR PLATES

GLOSSARY

BIBLIOGRAPHY

WEBSITES