Visualizing microbiology : a healthy perspective

Cover Title Page Copyright Preface About the Authors Brief Contents Contents 1 Microbial World 1.1 The Microbes • A Brief Survey of the Microbial World • The Dominant Form of Life on Earth 1.2 The Conflicts • Growth and Control of Microbes • The Role of the Immune System What a Microbiologist Sees: Wrestling and the Spread of Skin Pathogens • Pathogenesis • Antimicrobial Drugs 1.3 Infectious Disease • Epidemiology and Healthy Practices • Host Defenses and Microbial Pathogenesis Strategies The Microbiologist’s Toolbox: MALDI TOF Mass Spectrometry • Infectious Disease Statistics Case Study: Vaccination: A Casualty of War 1.4 Microbial Ecology and Commercial Applications • The Importance of Environmental Microbes • The Industrial Use of Microorganisms Clinical Application: Pasteurization 2 The Biochemistry of Macromolecules 2.1 Proteins • The Four Levels of Protein Structure • Protein Diversity and Function What a Microbiologist Sees: The Effect of Modified Tertiary Binding on Protein Structure 2.2 Enzymes • Enzyme Action • Factors Influencing the Rate of Enzyme Activity 2.3 Carbohydrates • Simple and Complex Carbohydrates • The Functional Diversity of Carbohydrates Clinical Application: Rapid Glycogen Breakdown in a Diabetic Patient in Shock 2.4 Lipids • The Structural Classes of Lipids Case Study: Acne—A Bacterial Interaction with Skin Oils • Lipid Functions The Microbiologist’s Toolbox: Ziehl-Neelsen Acid-Fast Staining of Mycolic Acid Cell Walls 2.5 Nucleic Acids • The Structures of DNA and RNA • Nucleic Acid Functions 3 Microscopy 3.1 Principles of Microscopy • Magnification • Resolution 3.2 Microscopy Used for Clinical Diagnosis • Bright-field Microscopy • Dark-field Microscopy • Fluorescence Microscopy The Microbiologist’s Toolbox: The Direct Fluorescent Antibody Assay 3.3 Microscopy Used for Research Investigations • Light Microscopy What a Microbiologist Sees: Differential Interference Contrast Microscopy • Electron Microscopy • Nanoprobe-based Microscopy 3.4 Specimen Preparation and Staining • Basic Staining Procedures Case Study: Diagnosing Gonorrhea Using Gram Staining Clinical Application: Diagnosing Tuberculosis Using Acid-fast Staining • Special Staining Procedures 4 Prokaryotic Organisms 4.1 The Prokaryote’s Place in the Living World • Sustaining Life What a Microbiologist Sees: Prokaryotes—The Dominant Form of Life on Earth • Symbiotic Relationships 4.2 Bacterial Cell Shapes and Arrangements • Bacterial Shapes • Bacterial Arrangements 4.3 The Bacterial Cell Wall • Cell Wall Structure • Gram-Positive and Gram-Negative Cell Walls • Atypical Cell Walls Case Study: A Walking Pneumonia Outbreak at a University 4.4 External Structures of Bacterial Cells • The Glycocalyx • Fimbriae and Pili • Flagella The Microbiologist’s Toolbox: The Flagella Stain 4.5 Internal Structures of Bacterial Cells • The Plasma Membrane • The Nucleoid • Ribosomes • Plasmids, Inclusion Bodies, and Membranous Structures • Endospores Clinical Application: Endospore-forming Bacteria 4.6 Prokaryotic Evolution and Classification • The Tree of Life • The Clinical Classification of Prokaryotes 5 Eukaryotic Organisms 5.1 The Eukaryotic Cell • Cell Size • The Eukaryotic Organelles 5.2 The Origins of Eukaryotic Organelles and Organisms • The Autogenous and Endosymbiotic Hypotheses • Eukarya: A Classification Overview 5.3 The Algae • General Characteristics and Unique Features • A Survey of Algae Clinical Application: Agar—The Ideal Solid Medium for Bacterial Culture • Pathogenic Algae 5.4 The Protozoans • General Characteristics and Unique Features • A Survey of Protozoans • Pathogenic Protozoans 5.5 The Fungi • General Characteristics and Unique Features The Microbiologist’s Toolbox: The Growth of Fungal Specimens on Sabouraud Dextrose Agar • A Survey of Fungi • Pathogenic Fungi What a Microbiologist Sees: The Morphological Plasticity of Candida 5.6 The Helminths • General Characteristics and Unique Features • A Survey of Helminths • Pathogenic Helminths Case Study: Cravings 5.7 The Arthropods • A Survey of Arthropods • Pathogenic Arthropods and Arthropod Vectors 6 Viruses and Other Infectious Particles 6.1 Viral Structure and Classification • The Structure of Viruses • The Classification of Viruses 6.2 Viral Replication Cycles • Viruses Replicating in Animal Cells The Microbiologist’s Toolbox: Presumptive Diagnosis of a Viral Infection Using CPE Analysis • Viruses Replicating in Bacterial Cells 6.3 Viruses and Human Health • The Clinical Cultivation of Viruses • The Impact of Viral Infections Case Study: H1N1 in Young Adults • Viruses, Recurrent Infections, and Cancer What a Microbiologist Sees: Connecting Symptoms with the Progression of HIV 6.4 Prevention and Treatment of Viral Infections • The Prevention of Viral Infections Clinical Application: Mandatory Flu Vaccines for Health Care Providers • Antiviral Therapies • Viral Influences on Bacterial Infections 6.5 Viruslike Microbes • Viroids • Satellites • Prions 7 Metabolism 7.1 The Role of Energy in Life • Basic Energy Principles • Energy and Chemical Reactions The Microbiologist’s Toolbox: Identifying Bacteria by Metabolic Differences 7.2 Energy Production Principles • Oxidation-Reduction Reactions • ATP 7.3 Glycolysis and Fermentation • Glycolysis • Fermentation Clinical Application: The Clinical Importance of Alcohol Throughout History 7.4 Aerobic Cellular Respiration • Pyruvate Oxidation and the Citric Acid Cycle • The Electron Transport System • Lipid and Protein Catabolism What a Microbiologist Sees: The Deepwater Horizon Oil Spill–Microbial Bioremediation • Integrated Metabolic Pathways 7.5 Photosynthesis • Reactions of Photosynthesis Case Study: A Metabolic Imbalance in Grand Lake St. Mary’s • Chemosynthesis in Bacteria 8 Microbial Genetics and Genetic Engineering 8.1 DNA as the Genetic Material • DNA Structure and Functions • DNA Replication in Bacteria 8.2 From DNA to Protein • Transcription • Translation 8.3 Sources of Genetic Variation • Mutation • Recombination • Transposition Case Study: The Spread of a Drug-resistance Gene 8.4 Regulation of Gene Expression • Transcriptional Control • Pre- and Posttranscriptional Control 8.5 Recombinant DNA Technology • Recombinant DNA Tools and Gene Cloning The Microbiologist’s Toolbox: Gel Electrophoresis • Applications of Recombinant DNA Technology What a Microbiologist Sees: Manipulating the Bacterial Genome for Agricultural Benefits • Ethical and Safety Concerns 8.6 Genomics • DNA Sequencing • Genomic Analysis • Applications of Genomics Clinical Application: Screening for Genetic Diseases—BRCA1 Mutation 9 Microbial Growth and Control 9.1 Requirements for Microbial Growth • Energy Sources • Physical Requirements Case Study: Foodborne Illness from Home- Prepared Fermented Tofu • Chemical Requirements 9.2 Bacterial Reproduction and Growth • Cell Division • Growth Rate of Bacteria • Phases of Growth • Methods of Quantifying Bacterial Growth The Microbiologist’s Toolbox: Dilution Plating 9.3 Laboratory Growth of Microorganisms • Obtaining a Pure Culture • Growth Media What a Microbiologist Sees: Biofilm Formation on Teeth • Bacteria That Cannot Be Cultured 9.4 Microbial Cultures in Clinical Practice • Specimen Collection • Specimen Analysis 9.5 Controlling Microbial Growth • Physical Methods • Radiation • Chemical Methods Clinical Application: Alcohol-Based Hand Sanitizers in Health Care Settings 10 Innate Immunity 10.1 An Introduction to Immunity • The Benefits and Consequences of the Immune Response • Innate Versus Adaptive Immunity • The Basic Anatomy of the Immune System 10.2 First-Line Defense Mechanisms • Physical Defenses What a Microbiologist Sees: The Benefits of Fever Case Study: No Spicy Food for Me! • Chemical Defenses 10.3 Innate Cellular Defense Mechanisms • Hematopoiesis • Leukocytes The Microbiologist’s Toolbox: The Differential Count • Phagocytosis • Inflammation 10.4 Protein-Mediated Defense Mechanisms • The Complement Pathways • Interferons • Miscellaneous Proteins with Antimicrobial Action 11 Adaptive Immunity 11.1 Introduction to Adaptive Immunity • Hallmarks of Adaptive Immunity • Antigens and Immunogenicity Clinical Application: Conjugate Vaccines • Lymphocyte Maturation and Clonal Selection • The Major Histocompatibility Complex What a Microbiologist Sees: Transplant Rejection 11.2 Cell-mediated Responses • T-cell Categories • Antigen Processing and Presentation • The T-cell Receptor Complex and Associative Recognition 11.3 T-cell Activation • Early Stages of T-cell Activation • Completion of T-cell Activation Case Study: The Mantoux Test 11.4 Antibody-mediated Responses • Basic Antibody Structure The Microbiologist’s Toolbox: The Coagulase Agglutination Assay • Immunoglobulin Classes and Their Specific Functions 11.5 B-cell Activation • B-cell Receptors and Pathogen Binding • Antibody Production and Clonal Expansion • B-cell Effector Mechanisms 12 Vaccination, Immunoassays, and Immune Disorders 12.1 Vaccines and Vaccination • A Brief History of Vaccination • Modern Vaccines • Vaccines and Public Health • Vaccine Safety and Misconceptions 12.2 Immunoassays • Monoclonal Antibodies The Microbiologist’s Toolbox: Human Monoclonal Antibody Therapy for Non-Hodgkin’s Lymphoma • Types of Immunoassays 12.3 Hypersensitivities • Type I Hypersensitivity • Type II Hypersensitivity What a Microbiologist Sees: Fetal Rh Incompatibility • Type III Hypersensitivity • Type IV Hypersensitivity 12.4 Autoimmune Diseases and Immunodeficiencies • Autoimmune Diseases • Immunodeficiencies Clinical Application: Bone Marrow Transplants for Immunodeficient Patients Case Study: Prioritizing Immunizations 13 Microbial Pathogenesis 13.1 Entering and Adhering to the Host • Microbial Reservoirs • Portals of Entry and Exit • Adhering to Host Cells 13.2 Transmission of Microbes • Modes of Transmission Case Study: The Cholera Epidemic in Goma, Zaire • Horizontal and Vertical Transmission 13.3 Bypassing Host Defenses • Evading Immune Attack • Altering Pathogen Antigens • Damaging the Host Immune System 13.4 Damaging Host Tissues • Direct Damage • Enzymes • Endotoxins • Exotoxins Clinical Application: Toxoid-based Vaccines • Immunopathy The Microbiologist’s Toolbox: Analysis of Hemolysis on Blood Agar 13.5 Factors Influencing Disease Outcomes • Host Factors What a Microbiologist Sees: Stress and Infection • Microbial Factors 14 Antimicrobial Agents 14.1 Principles of Antimicrobial Chemotherapy • The Discovery and Development of Antimicrobial Agents • Choosing the Best Antimicrobial Agent The Microbiologist’s Toolbox: The Broth Dilution Test 14.2 Antibacterial Agents • Inhibitors of Cell Wall Synthesis • Inhibitors of Protein Synthesis • Inhibitors of Nucleic Acid Synthesis • Agents That Target the Bacterial Plasma Membrane • Antimycobacterial Agents Clinical Application: The Fight Against Drug-Resistant Tuberculosis 14.3 Antiviral Agents • Inhibitors of Virus Entry • Inhibitors of Viral Nucleic Acid Synthesis • Inhibitors of Viral Protein Synthesis • Inhibitors of Viral Assembly and Release 14.4 Antifungal and Antiparasitic Agents • Antifungal Agents • Antiparasitic Agents Case Study: Problems with Malaria Medication in Mozambique 14.5 Antimicrobial Drug Resistance • Principles of Drug Resistance • Mechanisms of Drug Resistance • Human Factors Contributing to Antimicrobial Resistance What a Microbiologist Sees: Livestock-Associated Drug-Resistant S. aureus 15 Epidemiology and Infection Control 15.1 Epidemiology and Public Health • Early Epidemiological Successes • Significant Accomplishments of Epidemiology 15.2 Epidemiological Surveillance • Prevalence, Incidence Rates, and Mortality Rates What a Microbiologist Sees: Antibiotic-impregnated Bone Cement • Epidemic Curves • Disease Surveillance 15.3 Epidemiological Studies and Clinical Trials • Case-Control and Cohort Studies • Clinical Trials Case Study: A Foodborne Outbreak Among Inmates at a County Jail 15.4 Health Care–associated Infections • Common Health Care-Associated Infections Clinical Application: Reducing the Risk of Bloodstream Infections • Surgical Site Infections • CAUTIs • PICC Line Infections • CLABSIs 15.5 Preventing Pathogen Spread in Health Care Settings • Hand Hygiene • Universal and Standard Precautions and PPE • Screening The Microbiologist’s Toolbox: MRSA Screening Procedures in the Clinical Laboratory • Isolation Procedures 16 Diseases of the Respiratory System 16.1 The Conflicts • Host Defenses • Microbial Pathogenic Strategies • Normal Microbiota 16.2 Bacterial Diseases of the Respiratory System • Diphtheria • Pertussis • Tuberculosis Case Study: Whooping Cough Outbreak 16.3 Viral Diseases of the Respiratory System • The Common Cold • Influenza What a Microbiologist Sees: Unpredictable Behavior 16.4 Diseases of the Respiratory System Caused by Multiple Pathogens • Sinusitis and Otitis Media • Pharyngitis The Microbiologist’s Toolbox: Diagnosis of Strep Throat • Laryngitis, Croup, Tracheitis, and Epiglottitis • Bronchitis and Bronchiolitis 16.5 Pneumonia Clinical Application: Sputum Samples • General Characteristics of Pneumonia • Epidemiology of Pneumonia • Causes of Pneumonia • Emerging Pathogens 17 Diseases of the Skin and Eyes 17.1 The Conflicts • Host Defenses • Microbial Pathogenic Strategies • Normal Microbiota 17.2 Bacterial Diseases of the Skin • Staphylococcal and Streptococcal Skin Diseases The Microbiologist’s Toolbox: Mannitol Salt Agar—A Versatile Selective/Differential Medium • Pseudomonal Skin Diseases • Miscellaneous Bacterial Skin Diseases 17.3 Viral Diseases of the Skin • Pediatric Viral Rashes Clinical Application: Improving Hand-Hygiene Compliance with Technology • Shingles • Warts • Smallpox 17.4 Fungal, Protozoan, and Arthropod Diseases of the Skin • Fungal Skin Diseases What a Microbiologist Sees: Oral Thrush and Immune System Status • Protozoan Skin Diseases • Arthropod Skin Diseases Case Study: Kindergarten Contact 17.5 Diseases of the Eye • Host Defenses and Microbial Pathogenic Strategies • Conjunctivitis • Other Eye Diseases 18 Diseases of the Nervous System 18.1 The Conflicts • Host Defenses • Microbial Pathogenic Strategies 18.2 Bacterial Diseases of the Nervous System • Bacterial Meningitis • Tetanus • Botulism Clinical Application: Clinical Use of Botulism Toxin • Hansen’s Disease (Leprosy) 18.3 Viral Diseases of the Nervous System • Viral Meningitis Case Study: Viral Meningitis in a High School Student • Encephalitis • Polio What a Microbiologist Sees: Polio Eradication • Rabies • Other Viral Diseases of the Nervous System 18.4 Fungal and Protozoan Diseases of the Nervous System • Fungal Meningitis The Microbiologist’s Toolbox: India Ink Staining of CSF for Cryptococcus • Toxoplasmosis 18.5 Prion Diseases of the Nervous System • Animal Spongiform Encephalopathies • Human Prion Diseases 19 Diseases of the Cardiovascular and Lymphatic Systems 19.1 The Conflicts • Host Defenses • Microbial Pathogenic Strategies 19.2 Sepsis and Cardiac Diseases • Sepsis • Cardiac Diseases The Microbiologist’s Toolbox: The Blood Culture 19.3 Bacterial Diseases of the Cardiovascular and Lymphatic Systems • Brucellosis • Anthrax • Lyme Disease • Plague • Other Bacterial Diseases 19.4 Viral Diseases of the Cardiovascular and Lymphatic Systems • Leukocyte-associated Cardiovascular and Lymphatic Diseases What a Microbiologist Sees: The Diagnosis of Mononucleosis • Viral Hemorrhagic Diseases • Hepatitis Clinical Application: HIV Status and the Spread of Hepatitis 19.5 Protozoan and Helminthic Diseases of the Cardiovascular and Lymphatic Systems • Systemic Protozoan Diseases Case Study: The Kissing Bug • Systemic Helminthic Diseases 20 Diseases of the Gastrointestinal System 20.1 The Conflicts • Host Defenses • Microbial Pathogenic Strategies • Normal Microbiota 20.2 Bacterial Diseases of the Mouth and Upper GI Tract • Dental Caries • Gingivitis and Periodontal Disease What a Microbiologist Sees: Oral Hygiene for Patients with Ventilators • Peptic Ulcer Disease • Staphylococcus aureus Food Intoxication 20.3 Bacterial Diseases of the Lower GI Tract • Diseases Caused by Salmonella • Diarrheagenic E. coli Infections • Campylobacteriosis • Shigellosis The Microbiologist’s Toolbox: Preparing and Analyzing a Fecal Culture • Cholera • Opportunistic Diseases 20.4 Viral Diseases of the GI System • Cold Sores • Mumps • Viral Gastroenteritis Case Study: A Norovirus Outbreak Among Nurses • Hepatitis A and Hepatitis E 20.5 Protozoan Diseases of the GI System • Giardiasis • Amoebic Dysentery • Cryptosporidiosis 20.6 Helminthic Diseases of the GI System • Trematode Infections • Cestode Infections • Nematode Infections 21 Diseases of the Urogenital System 21.1 The Conflicts • Host Defenses • Microbial Pathogenic Strategies • Normal Microbiota 21.2 Bacterial Diseases of the Urinary System • Cystitis What a Microbiologist Sees: Cranberry Juice for UTI Prevention • Pyelonephritis Case Study: Pyelonephritis in a Toddler • Leptospirosis 21.3 Bacterial Diseases of the Reproductive Systems • Prostatitis • Chlamydia • Gonorrhea The Microbiologist’s Toolbox: The Challenge of Culturing Neisseria gonorrhoeae • Pelvic Inflammatory Disease • Syphilis 21.4 Viral Diseases of the Reproductive Systems • Genital Warts Clinical Application: Winning the War on Cervical Cancer • Genital Herpes • Molluscum Contagiosum 21.5 HIV and AIDS • An Emerging Infection • HIV Replication and Pathogenicity • HIV Diagnosis, Treatment, and Outlook 21.6 Fungal and Protozoan Diseases of the Reproductive Systems • Vaginal Yeast Infections • Trichomoniasis 22 Environmental and Industrial Microbiology 22.1 Microbial Ecology • The Ecological Hierarchy • Microbes in Earth’s Ecosystems • Biofilms Clinical Application: A Potential New Therapy for Medical Biofilm Elimination 22.2 Biogeochemical Cycles • The Nitrogen Cycle • The Carbon Cycle • The Phosphorus Cycle What a Microbiologist Sees: Habitat for Acidophiles • The Sulfur Cycle 22.3 Bioremediation • Microorganisms Used in Bioremediation • Sewage Treatment • Freshwater Treatment 22.4 Microorganisms Used in Manufacturing • Products of Biotechnology • Food Production Case Study: Bacon Beer 22.5 Safe Product Processing and Packaging • Food Safety Regulations • Chemical and Physical Controls in Food Production • Canning The Microbiologist’s Toolbox: The Autoclave • Microbial Control in Health Care Settings Appendix A: Answers to Self-Tests Appendix B: Physiological Reference Ranges Glossary Index EULA