Lars F. Westblade, PhD, D(ABMM) is the Director of the Clinical Microbiology Service at NewYork-Presbyterian/Weill Cornell Medical Center and Associate Professor at Weill Cornell Medicine with a primary appointment in the Department of Pathology and Laboratory Medicine and a secondary appointment in the Division of Infectious Diseases, Department of Medicine. He earned his doctoral degree from the University of Birmingham in the United Kingdom, and completed a fellowship in medical and public health laboratory microbiology at Washington University School of Medicine in St. Louis.

Eileen M. Burd, PhD, D(ABMM) is the Director of the Clinical Microbiology Laboratory at Emory University Hospital and Professor at Emory University School of Medicine with a primary appointment in the Department of Pathology and Laboratory Medicine and a secondary appointment in the Department of Medicine, Division of Infectious Diseases. She earned her doctoral degree from the Medical College of Wisconsin in Milwaukee and was the Division Head of Microbiology at Henry Ford Hospital in Detroit, Michigan prior to joining the faculty at Emory University in 2007.

Shawn R. Lockhart, PhD, D(ABBM) FAAM is the Senior Clinical Laboratory Advisor in the Mycotic Diseases Branch at the Centers for Disease Control and Prevention. He earned his doctoral degree from the University of Kentucky and completed his clinical microbiology fellowship at the University of Iowa Hospitals and Clinics. He directs the CDC training course in mold identification.

Gary W. Procop, MD, MS is the CEO of the American Board of Pathology and Professor of Pathology at the Cleveland Clinic Lerner School of Medicine. He remains a Consulting Staff for the Institute of Pathology and Laboratory Medicine, where he served as Medical Director for the Mycology Laboratory for more than two decades. He earned his doctoral degree from the Marshall University School of Medicine. His residency in anatomic and clinical pathology was completed at Duke University and his medical microbiology fellowship at the Mayo Clinic.

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) (Huber’s 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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