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List of Tables x Preface to the Seventh Edition xx Preface to the First Edition xx Acknowledgments xx About the Authors xx Basics 000 How To Use the Guide 0 Use of Reference Laboratories and Regulations for Transport 00 Safety Precautions 00 Taxonomy and Nomenclature 00 PART I Direct Microscopic Examination of Clinical Specimens 000 Introduction 000 Histological Terminology 000 Tissue Reactions to Fungal Infections 000 Stains 000 TABLE 1.1 Histochemical stains for fungi and/or filamentous bacteria in tissue 000 Guide to Interpretation of Direct Microscopic Examination 000 Detailed Descriptions 000 Actinomycosis 000 Mycetoma (Actinomycotic or Eumycotic) 000 Nocardiosis Mucormycosis (Zygomycosis) 000 Aspergillosis 000 Miscellaneous Hyalohyphomycoses (Other than Aspergillosis) 000 Dermatophytosis (Tinea, Ringworm) 000 Tinea versicolor 000 Tinea nigra 000 Phaeohyphomycosis 000 Chromoblastomycosis 000 Sporotrichosis 000 Histoplasmosis 000 Emergomycosis 000 Talaromycosis (Penicilliosis) 000 Blastomycosis 000 Paracoccidioidomycosis 000 Lobomycosis Candidiasis Trichosporonosis Cryptococcosis Pneumocystosis Protothecosis Coccidioidomycosis 000 Rhinosporidiosis 000 Adiaspiromycosis 000 PART II Identification of Fungi in Culture 000 Guide to Identification of Fungi in Culture 000 Detailed Descriptions 000 Filamentous Bacteria 000 Introduction to Filamentous Bacteria 000 TABLE 2.1 Differentiation of filamentous aerobic actinomycetes encountered in clinical specimens 000 Nocardia spp. 000 Streptomyces spp. 000 Actinomadura spp. 000 Nocardiopsis dassonvillei 000 Yeasts and Yeastlike Organisms 000 Introduction to Yeasts and Yeastlike Organisms 000 Candida albicans 000 TABLE 2.2 Characteristics of the genera of clinically encountered yeasts and yeastlike organisms 000 Candida dubliniensis 000 TABLE 2.3 Characteristics of Candida spp. most commonly encountered in the clinical laboratory 000 TABLE 2.4 Characteristics that assist in differentiating Candida dubliniensis from Candida albicans 000 Candida tropicalis 000 Candida parapsilosis species complex 000 Candida lusitaniae 000 Candida krusei 000 TABLE 2.5 Differentiating characteristics of Geotrichum capitatum (formerly Blastoschizomyces capitatus) versus Candida krusei 000 TABLE 2.6 Differentiating characteristics of Candida krusei, Candida inconspicua, and Candida norvegensis 000 Candida kefyr 000 Candida rugosa species complex 000 Candida guilliermondii species complex 000 Thermally Monomorphic Moulds 000 Mucormycetes 000 Introduction to Mucormycetes 000 TABLE 2.11 Differential characteristics of similar organisms in the class Mucormycetes 000 TABLE 2.12 Differential characteristics of the clinically encountered Rhizopus spp. 000 Rhizopus spp. 000 Mucor spp. 000 Rhizomucor spp. 000 Lichtheimia corymbifera species complex 000 Apophysomyces elegans species complex 000 Saksenaea vasiformis 000 Cokeromyces recurvatus 000 Cunninghamella bertholletiae 000 Syncephalastrum racemosum 000 Basidiobolus spp. 000 Dermatophytes 000 Introduction to Dermatophytes 000 Latin Terms for Dermatophyte Infections 000 Microsporum audouinii 000 Microsporum canis 000 Paraphyton cookei species complex (formerly Microsporum cookei species complex) 000 Nannizzia gypsea species complex (formerly Microsporum gypseum species complex) 000 Lophophyton gallinae (formerly Microsporum gallinae [zoophilic form] and Microsporum vanbreuseghemii [geophilic form]) Nannizzia nana (formerly Microsporum nanum) Microsporum ferrugineum Hyaline Hyphomycetes 000 Introduction to Hyaline Hyphomycetes 000 Fungi in Which Arthroconidia Predominate 000 TABLE 2.21 Differential characteristics of fungi in which arthroconidia predominate Malbranchea spp. 000 Pseudogymnoascus pannorum (formerly Geomyces pannorum) Arthrographis kalrae Hormographiella aspergillata Common Species of Aspergillus 000 The genus Aspergillus Aspergillus fumigatus species complex Aspergillus niger species complex Aspergillus flavus species complex 000 PART III Basics of Molecular Methods for Fungal Identification 000 Introduction 000 Fungal Targets 000 TABLE 3.1 Frequently used fungal gene targets and primers for sequence-based species identification 000 TABLE 3.2 Examples of fungal gene targets and primers for multilocus sequence-based species identification 000 Classic Molecular Identification Methods 000 Polymerase Chain Reaction 000 Non-Sequencing-Based Identification Methods 000 MALDI-TOF 000 Mass Spectrometry 000 Signal Amplification Methods 000 PNA FISH 000 Nucleic Acid Amplification Methods 000 T2 Magnetic Resonance 000 Broad-Panel Molecular Testing and Other Emerging Sample-to-Answer Technologies 000 Sequencing-Based Identification Methods 000 Sanger Sequencing 000 TABLE 3.3 Lane construction for traditional bidirectional Sanger sequencing 000 Massive Parallel or Next-Generation Sequencing 000 Applications of DNA Sequencing 000 Accurate Molecular Identification 000 TABLE 3.4 Commonly used databases for identification of medically-important fungi 000 Phylogenetic Analysis Organism Typing Detection of Genetic Determinants of Resistance PART IV Laboratory Technique 000 Laboratory Procedures 000 Collection and Preparation of Specimens 000 TABLE 4.1 Common clinical sites for laboratory recovery of pathogenic fungi 000 Methods for Direct Microscopic Examination of Specimens 000 Primary Isolation 000 TABLE 4.2 Media for primary isolation of fungi 000 Macroscopic Examination of Cultures 000 Microscopic Examination of Growth 000 Procedure for Identification of Yeasts 000 Isolation of Yeast When Mixed with Bacteria Germ Tube Test for the Presumptive Identification of Candida albicans 000 Rapid Enzyme Tests for the Presumptive Identification of Candida albicans 000 Caffeic Acid Disk Test 000 Olive Oil Disks for Culturing Malassezia spp. 000 Conversion of Thermally Dimorphic Fungi in Culture 000 Sporulation Inducement Method for Apophysomyces and Saksenaea 000 In vitro Hair Perforation Test (for Differentiation of Trichophyton mentagrophytes and Trichophyton rubrum) 000 Temperature Tolerance Testing 000 Maintenance of Stock Fungal Cultures 000 Controlling Mites 000 Staining Methods 000 Acid-Fast 000 Modified Kinyoun Stain for Nocardia spp. Acid-Fast Stain for Ascospores Ascospore Stain 000 Calcofluor White Stain Giemsa Stain 000 Gomori Methenamine Silver (GMS) Stain 000 Gram Stain (Hucker Modification) 000 Lactophenol Cotton Blue 000 Lactophenol Cotton Blue with Polyvinyl Alcohol (PVA) (Hubers PVA Mounting Medium, Modified) 000 Rehydration of Paraffin-Embedded Tissue (Deparaffination) 000 Media 000 Ascospore Media 000 Assimilation Media (for Yeasts) 000 Birdseed Agar (Niger Seed Agar; Staib Agar) 000 Brain Heart Infusion (BHI) Agar 000 Buffered Charcoal-Yeast Extract (BCYE) Agar 000 Canavanine Glycine Bromothymol Blue (CGB) Agar 000 Casein Agar 000 Sabouraud Dextrose Agar with 15% NaCl 000 Sabouraud Dextrose Broth 000 Starch Hydrolysis Agar 000 Trichophyton Agars 000 Tyrosine Agar Urea Agar Water Agar Image Appendix 000 Glossary 000 References Cited 000 Index 000

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