Oral Microbiology and Immunology

Description

Cover Table of Contents Contributors Preface About the Editors SECTION I. GENERAL PRINCIPLES OF ORAL MICROBIOLOGY AND IMMUNOLOGY 1. General Microbiology Introduction Biological Classification Scheme Bacterial Classification Bacterial Architecture Membranes Cell Wall Peptidoglycan Lipopolysaccharides Lipoteichoic Acids Other Important Components Produced by Bacteria Capsule Fimbriae and Pili Fibrillar Layers Flagella Vesicles Surface Layers Endospores Genetic Organization in Bacteria The Bacterial Chromosome Chromosome Replication in Bacteria Gene Transfer in Bacteria Bacterial Growth and Nutrition Growth Nutrient Acquisition Environmental Sensing Secretion Introduction to Fundamental Concepts in Oral Microbial Ecology Microbial Biofilms Microbial Cooperativity Microbial Antagonism Polymicrobial Communities Ecology of the Oral Microbiota and Development of Oral Diseases KEY POINTS 2. The Immune System and Its Functions Introduction—What Is Immunity? Innate and Adaptive Immunity BOX: Cells of the Immune System Immune Recognition Mechanisms Innate Immune Recognition: Pattern Recognition Receptors Adaptive Immune Recognition: Antigen Receptors Induction and Stages of the Immune Response Tailored Immunity Requires Specialized Subsets of Immune Cells Hallmark Properties of Immunity Properties of Adaptive Immunity Properties of Innate Immunity KEY POINTS FURTHER READING 3. The Oral Environment Introduction Oral Diseases General Features of the Oral Environment Teeth The Oral Soft Tissues (Periodontium, Oral Mucosa, and Tongue) Physical and Host Parameters Affecting Oral Microbial Colonization Temperature pH Oxygen Mechanical Abrasive Forces Fluid Flow Host Age The Oral Microbiota Tooth (Dental) Plaque: Early Determinants of Plaque Formation Calculus The Mucosal Microbiota Recent Concepts of Dental Biofilm Formation Saliva and the Salivary Proteome Saliva-Microbe Interactions Clearance of Bacteria from the Oral Cavity: Agglutinins Pellicle Adhesion Receptors Antimicrobial Components in Saliva Antiviral Components in Saliva Saliva as a Source of Bacterial Nutrition Gingival Crevicular Fluid KEY POINTS FURTHER READING 4. Isolation, Classification, and Identification of Oral Bacteria Introduction Diversity of the Oral Microbiota The Ribosomal 16S rRNA Gene and Bacterial Identification and Classification 16S rRNA Genes and Phylogeny Sampling Oral Bacteria and Recovery of Bacterial DNA from Samples Identifying Oral Bacteria Using Molecular Techniques PCR Detection Quantitative PCR DNA Hybridization Assays Ribosomal 16S rRNA Gene Cloning and Sequence Analysis Next-Generation Sequencing of 16S rRNA Genes Metagenomic Sequence Analysis Species and Strains of Oral Bacteria Naming of Bacteria and Molecular Analysis Direct Observation of Oral Bacteria Cultivation of Oral Bacteria Oxygen Requirements Culture Media Innovations in Bacterial Cultivation Single-Cell Genomics Classification of Cultured Bacteria Antibiotic Susceptibility Other Oral Microorganisms KEY POINTS FURTHER READING 5. Oral Microbial Ecology Introduction Acquisition of Oral Bacteria Colonization by Oral Bacteria Surface Structures and Molecules Involved in Adhesion Mechanisms of Adhesion Host Surface-Specific Constraints on Bacterial Adhesion Adhesion and Metabolism Bacterial Communication Quorum Sensing Competence Contact-Dependent Interactions Antagonism Multicomponent Interactions Communication with Host Cells Gene Regulation KEY POINTS FURTHER READING 6. Oral Microbial Physiology Introduction Survey of Metabolic Activities Important to the Oral Bacterial Community Carbohydrate Fermentation Metabolism of Organic Acids Energy Generation Using Lactate Metabolism of Amino Acids The Role of Proteases in Energy Generation Amino Acid Metabolism by the Stickland Reaction Amino Acid Fermentation by Fusobacterium nucleatum Arginine Metabolism by the Arginine Deiminase System Cross Feeding and Cross Respiration Acid-Base Physiology of Oral Microorganisms Acid-Base Cycling in the Mouth The Range of Acid Tolerance among Oral Bacteria Related to Oral Ecology Acid Tolerance Related to Specific Functions Constitutive and Adaptive Acid Tolerance Alkali Production and Tolerance Acid-Base Physiology, Virulence, and Disease Oxygen Metabolism, Oxidative Stress, and Adaptation Sources of Oxygen for Oral Bacteria Oxygen Levels and Oxidation-Reduction Potentials in Dental Plaque Oxygen Metabolism in Oral Bacteria, Reactive Oxygen Species, and Oxidative Damage Repair Systems Physiology of Oral Biofilms Physicochemical Gradients in Oral Biofilms and Concentrative Capacities of Biofilms for Fluoride and Other Antimicrobials Plaque Nutrition Related to Biofilm Physiology KEY POINTS FURTHER READING 7. Genetics and Molecular Biology of Oral Microorganisms Introduction Fundamental Terms in Bacterial Genetics Bacterial DNA Inheritance Vertical Gene Transfer Horizontal Gene Transfer Defense from Foreign DNA Genetic Manipulation and Analysis Cloning and Vectors Mutagenesis Complementation Transposon Mutagenesis Screening Conclusions KEY POINTS FURTHER READING 8. Applied Molecular Biology and the Oral Microbes Introduction Genomics Gene Organization and Regulation Transcriptional Initiation Measurement of Gene Expression Genomic Structure Small Noncoding RNAs CRISPR Tn-Seq Transcriptomics Proteomics Methods for Protein Identification Posttranslational Modifications Protein Expression Levels Metabolomics and Metabonomics Metabolic Fingerprint Metabonomics Multi-Omics KEY POINTS FURTHER READING 9. Population Genetics of Oral Bacteria Introduction Bacterial Species Show Different Patterns of Evolution Localized Sex in Bacteria Differences in Pathogenicity of Strains Specific Host Adaptation of Bacterial Clones Population Sizes of Pathogenic and Commensal Bacteria Oral Bacteria Show Varying Degrees of Genetic Diversity The Oral Microbiome Is a Dynamic Population Undergoing Constant Changes Virulence Differences within Species of Oral Bacteria? Methods of Strain Differentiation and Search for Virulent Clones Population Genetics Structure of Oral Bacteria KEY POINTS FURTHER READING 10. Immunology of the Oral Cavity Introduction Oral Secretory Immunity Overview of Innate Host Defense Factors in Saliva Cationic Antimicrobial Peptides Proteins with Bacterial Agglutination Properties Metal Ion Chelators Protease Inhibitors Enzymes Acting against Bacterial Cell Walls The Peroxidase System Overview of Specific Host Defense Factors in Saliva The Mucosal Immune System and Induction of S-IgA Antibodies in Saliva Biological Activities of S-IgA Antibodies Subgingival Immunity Innate and Adaptive Immune Players below the Gum Line Features of the Subgingival Environment and Their Impact on Host Response Toll-Like Receptors and Coreceptors Neutrophils Complement Gingival Crevicular Epithelium Adaptive Immunity in the Periodontium KEY POINTS FURTHER READING SECTION II. INFECTION-DRIVEN ORAL DISEASES 11. Dental Caries: Etiology and Pathogenesis Introduction Tooth Structure and Development Sites of Carious Lesions Coronal Caries Root Surface Caries Diet and Dental Caries Cariogenic Effect of the Diet Anticariogenic Properties of Food Cariogenic Dental Biofilm Formation Biochemical Composition of the Cariogenic Biofilm Physicochemical Phenomena in Dental Biofilm Caries Prevention Using Fluoride Experimental Caries Models Laboratorial Methods Animal Models In Situ (Intraoral) Models KEY POINTS FURTHER READING 12. Pathogenic Mechanisms in Dental Caries Introduction The Cariogenic Biofilm: Mutans Group Streptococci and Dietary Sugars Exopolysaccharides and Biofilm Matrix Sugar Transport and Acid Production Acid Stress Tolerance and Survival Other Stress Resistance-and Virulence-Related Mechanisms Polymicrobial Interactions and Cariogenicity Commensal-Pathogen Interactions Acidogenic Interactions Alkalinogenic Interactions Bacterial-Fungal interactions Future Directions and Perspectives KEY POINTS FURTHER READING 13. Periodontal Diseases: General Concepts Introduction Current Classification of Periodontal Diseases Epidemiology of Periodontal Diseases Microbial Etiology of Periodontal Diseases Prevention and Control of Periodontal Diseases Periodontal Diseases and General Health Outcomes KEY POINTS FURTHER READING 14. Virulence Factors of Periodontal Bacteria Introduction Colonization Localization in the Gingival Crevice Attachment Invasion Community Development Toxins Leukotoxin Cytolethal Distending Toxin Proteolytic Enzymes Acquisition of Iron Surface-Associated Bioactive Components Lipopolysaccharide Capsule and Exopolysaccharide Toxic Bacterial Components and Enzymes Outer Membrane Vesicles Secretion of Virulence Factors Resistance to Neutrophil Killing KEY POINTS FURTHER READING 15. Immunopathogenic Mechanisms in Periodontal Disease Introduction Immune Players in Periodontal Disease Complement: Microbial Manipulation and Destructive Inflammation Neutrophils: More Than Just Acute Responders Macrophages: Little Known, More To Unearth Osteoimmunology: Linking Inflammation to Bone Loss Adaptive Immunity: More Harm Than Good? T Lymphocytes B-Lineage Cells Aging and the Host Response: Inflamm-Aging of the Periodontium KEY POINTS FURTHER READING 16. Oral Virology Introduction What Is Oral Virology? What Is a Virus? How Is a Virus Transmitted? The Virus How Viruses Change: Viral Evolution The Viral Life Cycle Virus Taxonomy Discovery of New Viruses Oral Virology: The Viruses Viruses That Can Cause Pathologies in the Oral Cavity Picornaviridae Human Herpesviruses Herpes Simplex Viruses 1 and 2 Varicella-Zoster Virus Cytomegalovirus and Epstein-Barr Virus Human Herpesviruses 6, 7, and 8 Human Papillomaviruses Viruses Present in the Oral Cavity Hepatitis B Virus Hepatitis C Virus Human Immunodeficiency Virus Viral Immune Responses Viruses and the Innate Immune System Viruses and the Adaptive Immune System Viral Evasion Strategies Antiviral Vaccines and Therapies History of Viral Vaccines Antiviral Immunoglobulin Preparations and Vaccines Antiviral Compounds and Therapies KEY POINTS FURTHER READING 17. Fungi and Fungal Infections of the Oral Cavity Introduction Biology Morphology Fungal Interactions Replication Pathogenesis Acquisition Virulence Host Defenses against Fungal Infection Nonspecific Defense Mechanisms Specific Defense Mechanisms Antifungal Therapy Growth and Identification of Fungi Principles of Antifungal Chemotherapy Clinical Conditions Candidiasis Aspergillosis Cryptococcosis Histoplasmosis Blastomycosis Paracoccidioidomycosis Mucormycosis KEY POINTS FURTHER READING 18. Endodontic Infections and Therapeutic Approaches Introduction Overall Definitions and Concepts Pathways of Root Canal Infection Microbial Agents of Endodontic Infections Microbes Associated with Primary Apical Periodontitis Microbes Associated with Posttreatment Apical Periodontitis Extraradicular Infection Biofilms and the Endodontic Microenvironment Root Canal Treatment: Challenges and Current Therapeutic Approaches Variations in Bacterial Susceptibility to Disinfection Procedures Chemomechanical Preparation Root Canal Irrigation Intracanal Medication Root Canal Obturation and Coronal Restoration Concluding Remarks and Perspectives KEY POINTS FURTHER READING 19. Systemic Disease and the Oral Microbiota Introduction Routes from Oral to Systemic Compartments Breaches in the Oral Mucosa Transport and Translocation of Microbes The Potential of Commensal Bacteria To Behave as Pathogens Microbial Chameleons: Changing Gene Expression in Response to Environmental Signals Host Defenses Systemic Diseases Associated with Oral Microbes Bacteremia Infective Endocarditis Disseminated Intravascular Coagulation Atherosclerosis Adverse Pregnancy Outcomes Rheumatoid Arthritis Diabetes Obesity Certain Cancers Sequelae of Oral Viral Infections Immunological Aspects of Oral Microbes and Systemic Disease Heat Shock Proteins Autorecognition Induced by Oral Microorganisms Inflammation: A Link Between Local Dental Disease and Systemic Pathology Summary KEY POINTS FURTHER READING SECTION III. CONTROL OF ORAL DISEASES 20. Antibiotics: Mechanisms of Action, Resistance, and Clinical Use in Dentistry Introduction Antibiotics: Types and Mechanisms of Action Cell Wall-Active Agents Antiribosomal Agents Antifolate Agents Topoisomerase Inhibitors Miscellaneous Agents Antibiotic Combinations Antibiotic Adjuvants Measuring the Effects of Antibiotics Nonantibiotic Antimicrobial Agents and Disinfectants Bacterial Resistance to Antibiotics Resistance: Health Effects and Economic Costs Overview of Resistance Mechanisms Intrinsic and Acquired Resistance Biofilm-Associated Drug Tolerance Use of Antibiotics in Dentistry Treatment of Endodontic (Periapical) Infections Treatment of Odontogenic Infections Systemic Antibiotics Commonly Used To Treat Odontogenic Infections Empirical Antibiotics of Choice for Treating Odontogenic Infections Use of Systemic Antibiotics in Periodontal Therapy Use of Antibiotics To Prevent Infection KEY POINTS FURTHER READING 21. Therapeutic Approaches for Biofilm Control and Host Modulation in Oral Diseases Introduction Bacterial Adhesion and Biofilm Formation Antibiofilm Approaches To Control Oral Diseases Oral Surface Modification Control of Bacterial Force-Sensing EPS Inhibition Probiotic Strategies Disruption of Biofilms Antimicrobial Peptides EPS Matrix Degradation Metabolic Strategies Atmospheric-Pressure Nonthermal Plasma (Cold Plasma) Antimicrobial Nanoparticles New Generation of Antibiofilm Nanostructures Host Response Modulation in Oral Diseases Immunization against Dental Caries Rationale and Scope for Host Modulation Therapies in Periodontal Disease Immunization against Periodontal Disease Strategies for Inhibition and Resolution of Periodontal Inflammation Approaches for Direct Inhibition of Periodontal Tissue Destruction Potential Safety Issues KEY POINTS FURTHER READING 22. Infection Prevention and Control in Dentistry Introduction Introduction to Risk Control Quality Assurance Is the Promise of Performance Cross-Infection Control Is Essentially a Set of Management Strategies for Risk Control What Is Risk Management? Cross-Infection Risks in Dentistry Routes of Spread of Infection Management of Recently Identified Infection Control Risks Practical Application of Infection Control Measures in General Dentistry Definition of Terms Problems Posed for Prevention of Cross-Infection in General Dental Practice Standard Precautions Infection Control Checklist Sterilization of Instruments KEY POINTS FURTHER READING Index