Human and Animal Relationships (The Mycota, 6)

THE MYCOTA 6A Comprehensive Treatise on Fungi as Experimental Systems Estimates based on sequencing data suggest that there are around 5.1 million species of fungi. Yet only a small number of fungi are harmful to animals, including humans. In addition to host-pathogen interactions, there are also mutualistic interactions between fungi and animals. Diseases caused by pathogenic fungi range from allergic reactions and superficial infections to invasive mycoses, and have a significant impact on human and animal life. Fungi are also cultivated by animals as a food source in highly developed relationships or are even involved in gut mutualism. This 3rd edition of Volume 6 of The Mycota highlights exemplary interactions between fungal pathogens and their host(s). The book is organized in three parts: Part 1 summarizes our current understanding of important pathogenic fungi such as Candida species, Malassezia yeasts, Aspergillus fumigatus and fungi of the order Mucorales. Part 2 addresses the characterization of the host response towards pathogenic fungi. It focuses on RNA as a mediator of host-pathogen interactions, the human gut mycobiome, the role of the innate immune system in fighting infections, pattern recognition receptors involved in fungal infections, and a summary of established infection models for studying host-fungal-pathogen interactions. Part 3 provides insights into the impact transcriptomics and proteomics technologies have on the research of human-pathogenic fungi. The up-to-date reviews by experts in the field provide the reader with a comprehensive overview of the various research topics in the field of human and animal relationships with fungi and will hopefully help researchers to find inspiration for their own research. Series Preface Volume Preface to the Third Edition Contents Editors and Contributors About the Series Editors About the Volume Editors Contributors Part I: Pathogens 1: Trinity of Environment, Animals, and Humans: A Résumé in the Case of the Fungal Order Mucorales 1.1 Introduction 1.2 History, Etiological Agents, and Taxonomy: Mucorales 1.2.1 History 1.2.2 Etiological Agents and Taxonomy 1.3 Environmental Presence of Mucorales (Geographic Distribution and Ecological Conditions) 1.4 Industrial Applications 1.5 Risk Factors for Mucormycosis 1.5.1 Patient Conditions and Genetic Factors 1.5.2 Comorbidities 1.5.2.1 Diabetes and Ketoacidosis 1.5.2.2 Organ and Stem Cell Transplant Recipients 1.5.2.3 Other Factors 1.5.3 COVID-19-Associated Mucormycosis (CAM) 1.6 Mucormycosis in Humans 1.6.1 Epidemiology 1.6.2 Virulence Factors and Pathophysiology 1.6.3 Immunology 1.6.3.1 The Innate Immune Response to Mucorales Epithelial Cells Macrophages Neutrophils Dendritic Cells Monocytes Natural Killer Cells 1.6.3.2 The Adaptive Immune Response to Mucorales 1.6.4 Clinical Presentations 1.6.4.1 Rhino-Orbital-Cerebral Mucormycosis (ROCM) 1.6.4.2 Pulmonary Mucormycosis 1.6.4.3 Cutaneous Mucormycosis 1.6.4.4 Gastrointestinal Mucormycosis 1.6.4.5 Disseminated Mucormycosis 1.6.4.6 Uncommon Forms of Mucormycosis 1.6.5 Diagnostic Methods 1.6.6 Basics of Treatment 1.7 Mucormycosis in Animals 1.8 Future Perspectives References 2: Pathogenicity Strategies of Candida Species During Interactions with Epithelial Cells 2.1 Introduction 2.2 Pathogenicity Strategies of Candida Species 2.2.1 Candida albicans 2.2.2 C. tropicalis 2.2.3 C. glabrata (Nakaseomyces glabratus) 2.2.4 C. parapsilosis 2.3 Commensalism Versus Infection at the Epithelial Barriers 2.3.1 Stages of Candida-Epithelia Interaction: Adhesion, Invasion, Damage 2.3.2 Mucosal Candida Infections 2.3.2.1 Oral Cavity 2.3.2.2 Vaginal Mucosa 2.3.2.3 Intestinal Tract 2.4 Conclusion References 3: Malassezia Yeasts in Animals in the Next-Generation Sequencing Era 3.1 Introduction 3.2 Current Perspective of the Genus Malassezia 3.3 Main Characteristics of Malassezia Yeasts 3.3.1 Reproduction 3.3.2 Lipid Dependency 3.3.3 Genome 3.4 Epidemiology and Ecology of Malassezia Yeasts 3.4.1 Malassezia in Animals 3.5 Malassezia-Related Diseases in Animals 3.5.1 Dermatitis 3.5.2 Otitis Externa 3.6 Laboratory Diagnosis and Detection Techniques for Malassezia Yeasts 3.6.1 Cytology 3.6.2 Real-Time PCR 3.6.3 Metagenomics 3.7 Identification Methods for Malassezia Yeasts 3.7.1 DNA Sequencing 3.7.2 Genome Sequencing 3.7.3 Other Molecular Methods 3.8 Treatment of Malassezia Diseases 3.9 Antifungal Resistance in M. pachydermatis 3.9.1 Susceptibility Testing 3.9.2 Mechanisms of Resistance 3.9.2.1 Alterations of the ERG11 Gene 3.9.2.2 Efflux Pumps 3.10 Conclusion References 4: Extracellular Proteins and Their Roles in Aspergillus fumigatus Pathogenesis 4.1 Introduction 4.2 Prediction and Identification of A. fumigatus Extracellular Proteins 4.3 Extracellular Proteins and Their Roles in Pathogenicity of A. fumigatus 4.3.1 Roles of Hydrophobins and DHN-Melanin in Masking PAMPs 4.3.2 Surface Proteins as Adhesins 4.3.3 Surface Proteins Interfering with Phagocytosis 4.3.3.1 Induction of Phagocytosis of Conidia by Epithelial Cells 4.3.3.2 Resistance of A. fumigatus Against Phagosomal Killing 4.3.3.3 Interaction of A. fumigatus with Phagocytes 4.3.4 Surface Proteins and Secreted Proteins Disarm the Complement System 4.3.4.1 Surface Proteins Recruit Complement Regulators 4.3.4.2 Secreted Proteases Cleave Complement Components 4.3.5 A. fumigatus Proteins as Allergens 4.3.5.1 Identification of A. fumigatus Extracellular Allergens 4.3.5.2 Epithelial Cell Barrier Damage Leads to Th2 Cell Sensitization 4.3.5.3 Extracellular Proteins Detected by Th2 and Th17 Cells 4.4 Conclusions and Perspectives References Part II: Host-Pathogen Interaction 5: RNA as a Mediator of Host-Fungal Pathogenesis 5.1 Introduction 5.2 RNA Regulation in Fungal Pathogens 5.2.1 RNA in Gene Regulation: Transcription and Translation 5.2.2 RNA Structure and Non-coding RNA 5.2.3 RNAi and Small RNAs: Regulation of Resistance and Genome Defense 5.2.4 Extracellular RNA and Extracellular Vesicles 5.2.5 Other Examples of RNA Regulation in Fungi 5.3 Host RNA Responses 5.3.1 RNA Recognition by Toll-Like Receptors in Fungal Immunity 5.3.2 RIG-I-Like Receptors and the Antifungal Response 5.3.3 Transcriptomic and Non-coding RNA Responses to Fungal Infections 5.3.4 Interkingdom Communication 5.4 Conclusions: Exploiting RNA Biology for Therapy References 6: The Human Gut Mycobiome and Its Potential as a Regulator of the Host’s Metabolic Health 6.1 Introduction 6.2 The Composition of the Human Gut Mycobiome 6.3 Methodological Developments in Characterizing the Human Gut Mycobiome 6.3.1 Culture-Dependent Methods 6.3.2 High-Throughput Sequencing Methods 6.3.2.1 Sample Processing 6.3.2.2 DNA Extraction 6.3.2.3 Amplicon Sequencing 6.3.2.4 Data Analysis 6.3.3 Emerging Methods in Mycobiome Analysis 6.3.3.1 Quantification 6.3.3.2 Arrays and Microarrays 6.3.3.3 Metagenomic Shotgun Sequencing 6.3.3.4 Fungal Strain Identification 6.4 Impact of the Gut Mycobiome on the Host’s Metabolic Health 6.5 Gut Mycobiome Metabolic Products as Regulators of Host Metabolism 6.6 Future Perspectives References 7: The Host’s Innate Immune Response to Pathogenic Candida albicans and Other Fungal Pathogens 7.1 Introduction 7.2 Host Immune Defense with a Focus on Complement 7.3 Fungal Complement Inhibition and Immune Evasion 7.4 Fungal Complement and Immune Evasion 7.4.1 Candida and Complement 7.4.2 Interaction Between Candida and Human Plasma Proteins 7.4.3 Candida Surface Ligands Gpm1, Pra1, Gpd2, and Hgt1 Bind to Human Factor H 7.4.4 Candida albicans Surface Ligands that Bind Plasminogen 7.5 Candida Proteases Mediating Complement and Immune Escape 7.6 Proteomics Approaches to Identifying Proteins Expressed by C. albicans 7.6.1 Proteins on the Surface of C. albicans Yeast Cells and Hyphae 7.6.2 The Immune Proteasome: Immune “Shaving” 7.7 Vesicles: As a New Fungal Pathogen Interface 7.8 Other Candida Genes Relevant to Immune Evasion 7.9 Summary Immune Escape Proteins as Potential Vaccination Targets References 8: Mammalian Pattern Recognition Receptors (PRRs) Involved in Recognition of Fungi 8.1 Introduction 8.2 C-Type Lectin Receptors 8.2.1 Dectin-1 8.2.2 Dectin-2 8.2.3 MCL (CLECSF8 or Dectin-3) 8.2.4 Mincle 8.2.5 Mannose Receptor 8.2.6 DC-SIGN 8.2.7 MelLec 8.2.8 Langerin 8.2.9 CD23 8.2.10 Collectins 8.2.11 Mannose-Binding Lectin 8.2.12 SP-D and SP-A 8.3 Toll-Like Receptors 8.3.1 TLR2 8.3.2 TLR3 8.3.3 TLR4 8.3.4 TLR7 8.3.5 TLR9 8.4 Other Receptors Involved in Fungal Recognition 8.4.1 Scavenger Receptors 8.4.2 Integrins 8.4.3 Galectins 8.4.4 EphA2 8.4.5 Natural Cytotoxicity Receptors 8.4.6 Pentraxins 8.5 Conclusion References 9: Infection Models for Human Pathogenic Fungi 9.1 Introduction 9.2 Model Complexity 9.3 Ethical Considerations 9.4 Available Molecular and Genetic Tools, and Other Practical Considerations 9.5 Cell Culture Models 9.5.1 Cell Lines 9.5.2 Primary Cells 9.5.3 Complex Cell Culture Models 9.6 Invertebrate Models 9.6.1 Caenorhabditis elegans 9.6.2 Drosophila melanogaster 9.6.3 Galleria mellonella 9.7 Mammalian Models 9.7.1 Systemic (Disseminated) Infection 9.7.2 Pulmonary Infection 9.7.3 Mucosal and Skin Infection References Part III: Techniques 10: Transcriptomic Analyses of Host Colonisation in Fungal Pathogens of Humans 10.1 The Host-Adapting Aspergillus fumigatus Transcriptome 10.2 The Host-Adapting Candida Transcriptome 10.3 The Host-Adapting Cryptococcus Transcriptome 10.4 Take Home Points and Perspectives References 11: Proteomics and Its Application to the Human Pathogenic Fungus Aspergillus fumigatus 11.1 Introduction 11.2 Methods of Proteome Analysis 11.2.1 Emergence and Challenges 11.2.2 Sample Preparation 11.2.3 Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) 11.2.4 Quantification Techniques 11.2.5 Single Cell Proteomics (SCP) 11.2.6 Database Search and Data Curation 11.3 Proteomics Studies of the Human Pathogenic Fungus A. fumigatus 11.3.1 Secondary Metabolism 11.3.2 Proteomic Changes During Development 11.3.3 Signaling 11.3.4 Drug-Induced Changes 11.3.5 Biofilm Formation 11.3.6 Proteomics of the Cell Wall, the Cell Surface, and the Cellular Membrane 11.3.7 Secretome 11.3.8 Stress Responses 11.3.9 Regulation and Virulence 11.3.10 Immunoproteomics 11.3.11 Host–Pathogen Interaction 11.4 Conclusion References Index