Visualizing Microbiology
Visualizing Microbiology
;
John Wiley & Sons Inc
08/2017
768
Loose-leaf
Inglês
9781119443124
1501
Descrição não disponível.
1Microbial World 2 1.1 The Microbes 4 * A Brief Survey of the Microbial World 5 * The Dominant Form of Life on Earth 6 1.2 The Conflicts 8 * Growth and Control of Microbes 8 * The Role of the Immune System 10 What a Microbiologist Sees: Wrestling and the Spread of Skin Pathogens 10 * Pathogenesis 11 * Antimicrobial Drugs 12 1.3 Infectious Disease 13 * Epidemiology and Healthy Practices 13 * Host Defenses and Microbial Pathogenesis Strategies 14 The Microbiologist's Toolbox: MALDI TOF Mass Spectrometry 15 * Infectious Disease Statistics 16 Case Study: Vaccination: A Casualty of War 17 1.4 Microbial Ecology and Commercial Applications 18 * The Importance of Environmental Microbes 18 * The Industrial Use of Microorganisms 19 Clinical Application: Pasteurization 20 2 The Biochemistry of Macromolecules 26 2.1 Proteins 28 * The Four Levels of Protein Structure 28 * Protein Diversity and Function 34 What a Microbiologist Sees: The Effect of Modified Tertiary Binding on Protein Structure 34 2.2 Enzymes 35 * Enzyme Action 36 * Factors Influencing the Rate of Enzyme Activity 37 2.3 Carbohydrates 40 * Simple and Complex Carbohydrates 41 * The Functional Diversity of Carbohydrates 41 Clinical Application: Rapid Glycogen Breakdown in a Diabetic Patient in Shock 42 2.4 Lipids 43 * The Structural Classes of Lipids 43 Case Study: Acne-A Bacterial Interaction with Skin Oils 44 * Lipid Functions 47 The Microbiologist's Toolbox: Ziehl-Neelsen Acid-Fast Staining of Mycolic Acid Cell Walls 48 2.5 Nucleic Acids 49 * The Structures of DNA and RNA 49 * Nucleic Acid Functions 52 3 Microscopy 60 3.1 Principles of Microscopy 62 * Magnification 63 * Resolution 64 3.2 Microscopy Used for Clinical Diagnosis 65 * Bright-field Microscopy 65 * Dark-field Microscopy 66 * Fluorescence Microscopy 67 The Microbiologist's Toolbox: The Direct Fluorescent Antibody Assay 67 3.3 Microscopy Used for Research Investigations 68 * Light Microscopy 68 What a Microbiologist Sees: Differential Interference Contrast Microscopy 70 * Electron Microscopy 70 * Nanoprobe-based Microscopy 72 3.4 Specimen Preparation and Staining 72 * Basic Staining Procedures 72 Case Study: Diagnosing Gonorrhea Using Gram Staining 74 Clinical Application: Diagnosing Tuberculosis Using Acid-fast Staining 75 * Special Staining Procedures 75 4 Prokaryotic Organisms 82 4.1 The Prokaryote's Place in the Living World 84 * Sustaining Life 84 What a Microbiologist Sees: Prokaryotes- The Dominant Form of Life on Earth 85 * Symbiotic Relationships 86 4.2 Bacterial Cell Shapes and Arrangements 87 * Bacterial Shapes 87 * Bacterial Arrangements 87 4.3 The Bacterial Cell Wall 89 * Cell Wall Structure 89 * Gram-Positive and Gram-Negative Cell Walls 91 * Atypical Cell Walls 92 Case Study: A Walking Pneumonia Outbreak at a University 93 4.4 External Structures of Bacterial Cells 94 * The Glycocalyx 94 * Fimbriae and Pili 94 * Flagella 95 The Microbiologist's Toolbox: The Flagella Stain 97 4.5 Internal Structures of Bacterial Cells 97 * The Plasma Membrane 98 * The Nucleoid 99 * Ribosomes 99 * Plasmids, Inclusion Bodies, and Membranous Structures 100 * Endospores 101 Clinical Application: Endospore-forming Bacteria 101 4.6 Prokaryotic Evolution and Classification 103 * The Tree of Life 103 * The Clinical Classification of Prokaryotes 105 5 Eukaryotic Organisms 112 5.1 The Eukaryotic Cell 114 * Cell Size 114 * The Eukaryotic Organelles 114 5.2 The Origins of Eukaryotic Organelles and Organisms 120 * The Autogenous and Endosymbiotic Hypotheses 120 * Eukarya: A Classification Overview 120 5.3 The Algae 122 * General Characteristics and Unique Features 122 * A Survey of Algae 122 Clinical Application: Agar-The Ideal Solid Medium for Bacterial Culture 124 * Pathogenic Algae 124 5.4 The Protozoans 125 * General Characteristics and Unique Features 125 * A Survey of Protozoans 126 * Pathogenic Protozoans 128 5.5 The Fungi 129 * General Characteristics and Unique Features 129 The Microbiologist's Toolbox: The Growth of Fungal Specimens on Sabouraud Dextrose Agar 131 * A Survey of Fungi 131 * Pathogenic Fungi 133 What a Microbiologist Sees: The Morphological Plasticity of Candida 134 5.6 The Helminths 135 * General Characteristics and Unique Features 135 * A Survey of Helminths 135 * Pathogenic Helminths 135 Case Study: Cravings 138 5.7 The Arthropods 139 * A Survey of Arthropods 139 * Pathogenic Arthropods and Arthropod Vectors 139 6 Viruses and Other Infectious Particles 146 6.1 Viral Structure and Classification 148 * The Structure of Viruses 148 * The Classification of Viruses 150 6.2 Viral Replication Cycles 153 * Viruses Replicating in Animal Cells 153 The Microbiologist's Toolbox: Presumptive Diagnosis of a Viral Infection Using CPE Analysis 158 * Viruses Replicating in Bacterial Cells 158 6.3 Viruses and Human Health 160 * The Clinical Cultivation of Viruses 160 * The Impact of Viral Infections 160 Case Study: H1N1 in Young Adults 161 * Viruses, Recurrent Infections, and Cancer 162 What a Microbiologist Sees: Connecting Symptoms with the Progression of HIV 163 6.4 Prevention and Treatment of Viral Infections 164 * The Prevention of Viral Infections 164 Clinical Application: Mandatory Flu Vaccines for Health Care Providers 164 * Antiviral Therapies 165 * Viral Influences on Bacterial Infections 166 6.5 Viruslike Microbes 170 * Viroids 170 * Satellites 170 * Prions 171 7 Metabolism 178 7.1 The Role of Energy in Life 180 * Basic Energy Principles 180 * Energy and Chemical Reactions 180 The Microbiologist's Toolbox: Identifying Bacteria by Metabolic Differences 182 7.2 Energy Production Principles 182 * Oxidation-Reduction Reactions 182 * ATP 183 7.3 Glycolysis and Fermentation 186 * Glycolysis 186 * Fermentation 188 Clinical Application: The Clinical Importance of Alcohol Throughout History 189 7.4 Aerobic Cellular Respiration 190 * Pyruvate Oxidation and the Citric Acid Cycle 190 * The Electron Transport System 192 * Lipid and Protein Catabolism 194 What a Microbiologist Sees: The Deepwater Horizon Oil Spill-Microbial Bioremediation 195 * Integrated Metabolic Pathways 196 7.5 Photosynthesis 196 * Reactions of Photosynthesis 197 Case Study: A Metabolic Imbalance in Grand Lake St. Mary's 202 * Chemosynthesis in Bacteria 202 8 Microbial Genetics and Genetic Engineering 210 8.1 DNA as the Genetic Material 212 * DNA Structure and Functions 212 * DNA Replication in Bacteria 214 8.2 From DNA to Protein 215 * Transcription 215 * Translation 217 8.3 Sources of Genetic Variation 219 * Mutation 219 * Recombination 222 * Transposition 224 Case Study: The Spread of a Drug-resistance Gene 224 8.4 Regulation of Gene Expression 225 * Transcriptional Control 225 * Pre- and Posttranscriptional Control 226 8.5 Recombinant DNA Technology 228 * Recombinant DNA Tools and Gene Cloning 228 The Microbiologist's Toolbox: Gel Electrophoresis 229 * Applications of Recombinant DNA Technology 230 What a Microbiologist Sees: Manipulating the Bacterial Genome for Agricultural Benefits 232 * Ethical and Safety Concerns 233 8.6 Genomics 234 * DNA Sequencing 234 * Genomic Analysis 234 * Applications of Genomics 236 Clinical Application: Screening for Genetic Diseases-BRCA1 Mutation 236 9 Microbial Growth and Control 240 9.1 Requirements for Microbial Growth 244 * Energy Sources 244 * Physical Requirements 244 Case Study: Foodborne Illness from Home- Prepared Fermented Tofu 245 * Chemical Requirements 247 9.2 Bacterial Reproduction and Growth 249 * Cell Division 249 * Growth Rate of Bacteria 250 * Phases of Growth 251 * Methods of Quantifying Bacterial Growth 252 The Microbiologist's Toolbox: Dilution Plating 253 9.3 Laboratory Growth of Microorganisms 254 * Obtaining a Pure Culture 254 * Growth Media 254 What a Microbiologist Sees: Biofilm Formation on Teeth 258 * Bacteria That Cannot Be Cultured 258 9.4 Microbial Cultures in Clinical Practice 260 * Specimen Collection 260 * Specimen Analysis 260 9.5 Controlling Microbial Growth 263 * Physical Methods 263 * Radiation 264 * Chemical Methods 266 Clinical Application: Alcohol-Based Hand Sanitizers in Health Care Settings 267 10 Innate Immunity 274 10.1 An Introduction to Immunity 276 * The Benefits and Consequences of the Immune Response 276 * Innate Versus Adaptive Immunity 276 * The Basic Anatomy of the Immune System 278 10.2 First-Line Defense Mechanisms 282 * Physical Defenses 282 What a Microbiologist Sees: The Benefits of Fever 283 Case Study: No Spicy Food for Me! 284 * Chemical Defenses 285 10.3 Innate Cellular Defense Mechanisms 286 * Hematopoiesis 286 * Leukocytes 287 The Microbiologist's Toolbox: The Differential Count 289 * Phagocytosis 290 * Inflammation 290 10.4 Protein-Mediated Defense Mechanisms 294 * The Complement Pathways 294 * Interferons 294 * Miscellaneous Proteins with Antimicrobial Action 296 11 Adaptive Immunity 304 11.1 Introduction to Adaptive Immunity 306 * Hallmarks of Adaptive Immunity 306 * Antigens and Immunogenicity 306 Clinical Application: Conjugate Vaccines 308 * Lymphocyte Maturation and Clonal Selection 308 * The Major Histocompatibility Complex 311 What a Microbiologist Sees: Transplant Rejection 312 11.2 Cell-mediated Responses 313 * T-cell Categories 313 * Antigen Processing and Presentation 315 * The T-cell Receptor Complex and Associative Recognition 316 11.3 T-cell Activation 317 * Early Stages of T-cell Activation 317 * Completion of T-cell Activation 318 Case Study: The Mantoux Test 318 11.4 Antibody-mediated Responses 320 * Basic Antibody Structure 320 The Microbiologist's Toolbox: The Coagulase Agglutination Assay 321 * Immunoglobulin Classes and Their Specific Functions 322 11.5 B-cell Activation 323 * B-cell Receptors and Pathogen Binding 323 * Antibody Production and Clonal Expansion 325 * B-cell Effector Mechanisms 327 12 Vaccination, Immunoassays, and Immune Disorders 334 12.1 Vaccines and Vaccination 336 * A Brief History of Vaccination 336 * Modern Vaccines 336 * Vaccines and Public Health 339 * Vaccine Safety and Misconceptions 342 12.2 Immunoassays 343 * Monoclonal Antibodies 343 The Microbiologist's Toolbox: Human Monoclonal Antibody Therapy for Non-Hodgkin's Lymphoma 345 * Types of Immunoassays 346 12.3 Hypersensitivities 350 * Type I Hypersensitivity 350 * Type II Hypersensitivity 352 What a Microbiologist Sees: Fetal Rh Incompatibility 353 * Type III Hypersensitivity 354 * Type IV Hypersensitivity 355 12.4 Autoimmune Diseases and Immuno deficiencies 356 * Autoimmune Diseases 356 * Immuno deficiencies 357 Clinical Application: Bone Marrow Transplants for Immunodeficient Patients 358 Case Study: Prioritizing Immunizations 359 13 Microbial Pathogenesis 366 13.1 Entering and Adhering to the Host 368 * Microbial Reservoirs 368 * Portals of Entry and Exit 369 * Adhering to Host Cells 370 13.2 Transmission of Microbes 372 * Modes of Transmission 372 Case Study: The Cholera Epidemic in Goma, Zaire 374 * Horizontal and Vertical Transmission 374 13.3 Bypassing Host Defenses 376 * Evading Immune Attack 376 * Altering Pathogen Antigens 378 * Damaging the Host Immune System 380 13.4 Damaging Host Tissues 381 * Direct Damage 381 * Enzymes 382 * Endotoxins 382 * Exotoxins 384 Clinical Application: Toxoid-based Vaccines 385 * Immunopathy 387 The Microbiologist's Toolbox: Analysis of Hemolysis on Blood Agar 388 13.5 Factors Influencing Disease Outcomes 389 * Host Factors 389 What a Microbiologist Sees: Stress and Infection 390 * Microbial Factors 391 14 Antimicrobial Agents 398 14.1 Principles of Antimicrobial Chemotherapy 400 * The Discovery and Development of Antimicrobial Agents 400 * Choosing the Best Antimicrobial Agent 402 The Microbiologist's Toolbox: The Broth Dilution Test 404 14.2 Antibacterial Agents 406 * Inhibitors of Cell Wall Synthesis 406 * Inhibitors of Protein Synthesis 409 * Inhibitors of Nucleic Acid Synthesis 410 * Agents That Target the Bacterial Plasma Membrane 412 * Antimycobacterial Agents 412 Clinical Application: The Fight Against Drug-Resistant Tuberculosis 412 14.3 Antiviral Agents 415 * Inhibitors of Virus Entry 416 * Inhibitors of Viral Nucleic Acid Synthesis 417 * Inhibitors of Viral Protein Synthesis 418 * Inhibitors of Viral Assembly and Release 418 14.4 Antifungal and Antiparasitic Agents 419 * Antifungal Agents 420 * Antiparasitic Agents 421 Case Study: Problems with Malaria Medication in Mozambique 423 14.5 Antimicrobial Drug Resistance 425 * Principles of Drug Resistance 425 * Mechanisms of Drug Resistance 426 * Human Factors Contributing to Antimicrobial Resistance 427 What a Microbiologist Sees: Livestock- Associated Drug-Resistant S. aureus 428 15 Epidemiology and Infection Control 434 15.1 Epidemiology and Public Health 436 * Early Epidemiological Successes 436 * Significant Accomplishments of Epidemiology 436 15.2 Epidemiological Surveillance 438 * Prevalence, Incidence Rates, and Mortality Rates 438 What a Microbiologist Sees: Antibioticimpregnated Bone Cement 439 * Epidemic Curves 441 * Disease Surveillance 441 15.3 Epidemiological Studies and Clinical Trials 442 * Case-Control and Cohort Studies 442 * Clinical Trials 443 Case Study: A Foodborne Outbreak Among Inmates at a County Jail 444 15.4 Health Care-associated Infections 446 * Common Health Care-Associated Infections 446 Clinical Application: Reducing the Risk of Bloodstream Infections 447 * Surgical Site Infections 447 * CAUTIs 450 * PICC Line Infections 450 * CLABSIs 451 15.5 Preventing Pathogen Spread in Health Care Settings 451 * Hand Hygiene 451 * Universal and Standard Precautions and PPE 453 * Screening 454 The Microbiologist's Toolbox: MRSA Screening Procedures in the Clinical Laboratory 455 * Isolation Procedures 456 16 Diseases of the Respiratory System 462 16.1 The Conflicts 464 * Host Defenses 464 * Microbial Pathogenic Strategies 464 * Normal Microbiota 465 16.2 Bacterial Diseases of the Respiratory System 466 * Diphtheria 466 * Pertussis 467 * Tuberculosis 468 Case Study: Whooping Cough Outbreak 469 16.3 Viral Diseases of the Respiratory System 472 * The Common Cold 472 * Influenza 473 What a Microbiologist Sees: Unpredictable Behavior 476 16.4 Diseases of the Respiratory System Caused by Multiple Pathogens 477 * Sinusitis and Otitis Media 477 * Pharyngitis 479 The Microbiologist's Toolbox: Diagnosis of Strep Throat 481 * Laryngitis, Croup, Tracheitis, and Epiglottitis 482 * Bronchitis and Bronchiolitis 483 16.5 Pneumonia 483 Clinical Application: Sputum Samples 484 * General Characteristics of Pneumonia 484 * Epidemiology of Pneumonia 485 * Causes of Pneumonia 486 * Emerging Pathogens 488 17 Diseases of the Skin and Eyes 496 17.1 The Conflicts 498 * Host Defenses 498 * Microbial Pathogenic Strategies 498 * Normal Microbiota 501 17.2 Bacterial Diseases of the Skin 502 * Staphylococcal and Streptococcal Skin Diseases 502 The Microbiologist's Toolbox: Mannitol Salt Agar-A Versatile Selective/Differential Medium 505 * Pseudomonal Skin Diseases 505 * Miscellaneous Bacterial Skin Diseases 506 17.3 Viral Diseases of the Skin 508 * Pediatric Viral Rashes 508 Clinical Application: Improving Hand-Hygiene Compliance with Technology 509 * Shingles 512 * Warts 513 * Smallpox 514 17.4 Fungal, Protozoan, and Arthropod Diseases of the Skin 516 * Fungal Skin Diseases 516 What a Microbiologist Sees: Oral Thrush and Immune System Status 517 * Protozoan Skin Diseases 517 * Arthropod Skin Diseases 519 Case Study: Kindergarten Contact 520 17.5 Diseases of the Eye 521 * Host Defenses and Microbial Pathogenic Strategies 522 * Conjunctivitis 522 * Other Eye Diseases 523 18 Diseases of the Nervous System 532 18.1 The Conflicts 534 * Host Defenses 534 * Microbial Pathogenic Strategies 534 18.2 Bacterial Diseases of the Nervous System 536 * Bacterial Meningitis 536 * Tetanus 540 * Botulism 540 Clinical Application: Clinical Use of Botulism Toxin 541 * Hansen's Disease (Leprosy) 543 18.3 Viral Diseases of the Nervous System 543 * Viral Meningitis 543 Case Study: Viral Meningitis in a High School Student 544 * Encephalitis 545 * Polio 547 What a Microbiologist Sees: Polio Eradication 547 * Rabies 548 * Other Viral Diseases of the Nervous System 550 18.4 Fungal and Protozoan Diseases of the Nervous System 551 * Fungal Meningitis 551 The Microbiologist's Toolbox: India Ink Staining of CSF for Cryptococcus 552 * Toxoplasmosis 552 18.5 Prion Diseases of the Nervous System 554 * Animal Spongiform Encephalopathies 554 * Human Prion Diseases 554 19 Diseases of the Cardiovascular and Lymphatic Systems 562 19.1 The Conflicts 564 * Host Defenses 564 * Microbial Pathogenic Strategies 564 19.2 Sepsis and Cardiac Diseases 566 * Sepsis 566 * Cardiac Diseases 569 The Microbiologist's Toolbox: The Blood Culture 571 19.3 Bacterial Diseases of the Cardiovascular and Lymphatic Systems 572 * Brucellosis 572 * Anthrax 574 * Lyme Disease 575 * Plague 577 * Other Bacterial Diseases 580 19.4 Viral Diseases of the Cardiovascular and Lymphatic Systems 581 * Leukocyte-associated Cardiovascular and Lymphatic Diseases 581 What a Microbiologist Sees: The Diagnosis of Mononucleosis 582 * Viral Hemorrhagic Diseases 583 * Hepatitis 585 Clinical Application: HIV Status and the Spread of Hepatitis 586 19.5 Protozoan and Helminthic Diseases of the Cardiovascular and Lymphatic Systems 587 * Systemic Protozoan Diseases 587 Case Study: The Kissing Bug 588 * Systemic Helminthic Diseases 590 20 Diseases of the Gastrointestinal System 598 20.1 The Conflicts 600 * Host Defenses 600 * Microbial Pathogenic Strategies 600 * Normal Microbiota 600 20.2 Bacterial Diseases of the Mouth and Upper GI Tract 602 * Dental Caries 602 * Gingivitis and Periodontal Disease 603 What a Microbiologist Sees: Oral Hygiene for Patients with Ventilators 604 * Peptic Ulcer Disease 606 * Staphylococcus aureus Food Intoxication 606 20.3 Bacterial Diseases of the Lower GI Tract 607 * Diseases Caused by Salmonella 607 * Diarrheagenic E. coli Infections 608 * Campylobacteriosis 608 * Shigellosis 608 The Microbiologist's Toolbox: Preparing and Analyzing a Fecal Culture 609 * Cholera 610 * Opportunistic Diseases 612 20.4 Viral Diseases of the GI System 614 * Cold Sores 614 * Mumps 614 * Viral Gastroenteritis 615 Case Study: A Norovirus Outbreak Among Nurses 616 * Hepatitis A and Hepatitis E 617 20.5 Protozoan Diseases of the GI System 618 * Giardiasis 618 * Amoebic Dysentery 618 * Cryptosporidiosis 619 20.6 Helminthic Diseases of the GI System 620 * Trematode Infections 620 * Cestode Infections 621 * Nematode Infections 622 21 Diseases of the Urogenital System 632 21.1 The Conflicts 634 * Host Defenses 634 * Microbial Pathogenic Strategies 634 * Normal Microbiota 636 21.2 Bacterial Diseases of the Urinary System 637 * Cystitis 637 What a Microbiologist Sees: Cranberry Juice for UTI Prevention 639 * Pyelonephritis 640 Case Study: Pyelonephritis in a Toddler 641 * Leptospirosis 641 21.3 Bacterial Diseases of the Reproductive Systems 643 * Prostatitis 643 * Chlamydia 643 * Gonorrhea 645 The Microbiologist's Toolbox: The Challenge of Culturing Neisseria gonorrhoeae 646 * Pelvic Inflammatory Disease 646 * Syphilis 648 21.4 Viral Diseases of the Reproductive Systems 650 * Genital Warts 650 Clinical Application: Winning the War on Cervical Cancer 652 * Genital Herpes 652 * Molluscum Contagiosum 653 21.5 HIV and AIDS 654 * An Emerging Infection 655 * HIV Replication and Pathogenicity 657 * HIV Diagnosis, Treatment, and Outlook 658 21.6 Fungal and Protozoan Diseases of the Reproductive Systems 660 * Vaginal Yeast Infections 660 * Trichomoniasis 662 22 Environmental and Industrial Microbiology 670 22.1 Microbial Ecology 672 * The Ecological Hierarchy 672 * Microbes in Earth's Ecosystems 674 * Biofilms 676 Clinical Application: A Potential New Therapy for Medical Biofilm Elimination 677 22.2 Biogeochemical Cycles 678 * The Nitrogen Cycle 679 * The Carbon Cycle 680 * The Phosphorus Cycle 681 What a Microbiologist Sees: Habitat for Acidophiles 683 * The Sulfur Cycle 683 22.3 Bioremediation 684 * Microorganisms Used in Bioremediation 685 * Sewage Treatment 685 * Freshwater Treatment 687 22.4 Microorganisms Used in Manufacturing 687 * Products of Biotechnology 687 * Food Production 688 Case Study: Bacon Beer 691 22.5 Safe Product Processing and Packaging 692 * Food Safety Regulations 692 * Chemical and Physical Controls in Food Production 693 * Canning 694 The Microbiologist's Toolbox: The Autoclave 696 * Microbial Control in Health Care Settings 696 Appendix A: Answers to Self-Tests 702 Appendix B: Physiological Reference Ranges 705 Glossary 708 Index 726
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visualizing microbiology; microbiology; visualizing series; content; students; multimedia; life; narrative; engagement; platform; videos; combination; visuals; introduction; pedagogy; study; course; requirement; fundamentals
1Microbial World 2 1.1 The Microbes 4 * A Brief Survey of the Microbial World 5 * The Dominant Form of Life on Earth 6 1.2 The Conflicts 8 * Growth and Control of Microbes 8 * The Role of the Immune System 10 What a Microbiologist Sees: Wrestling and the Spread of Skin Pathogens 10 * Pathogenesis 11 * Antimicrobial Drugs 12 1.3 Infectious Disease 13 * Epidemiology and Healthy Practices 13 * Host Defenses and Microbial Pathogenesis Strategies 14 The Microbiologist's Toolbox: MALDI TOF Mass Spectrometry 15 * Infectious Disease Statistics 16 Case Study: Vaccination: A Casualty of War 17 1.4 Microbial Ecology and Commercial Applications 18 * The Importance of Environmental Microbes 18 * The Industrial Use of Microorganisms 19 Clinical Application: Pasteurization 20 2 The Biochemistry of Macromolecules 26 2.1 Proteins 28 * The Four Levels of Protein Structure 28 * Protein Diversity and Function 34 What a Microbiologist Sees: The Effect of Modified Tertiary Binding on Protein Structure 34 2.2 Enzymes 35 * Enzyme Action 36 * Factors Influencing the Rate of Enzyme Activity 37 2.3 Carbohydrates 40 * Simple and Complex Carbohydrates 41 * The Functional Diversity of Carbohydrates 41 Clinical Application: Rapid Glycogen Breakdown in a Diabetic Patient in Shock 42 2.4 Lipids 43 * The Structural Classes of Lipids 43 Case Study: Acne-A Bacterial Interaction with Skin Oils 44 * Lipid Functions 47 The Microbiologist's Toolbox: Ziehl-Neelsen Acid-Fast Staining of Mycolic Acid Cell Walls 48 2.5 Nucleic Acids 49 * The Structures of DNA and RNA 49 * Nucleic Acid Functions 52 3 Microscopy 60 3.1 Principles of Microscopy 62 * Magnification 63 * Resolution 64 3.2 Microscopy Used for Clinical Diagnosis 65 * Bright-field Microscopy 65 * Dark-field Microscopy 66 * Fluorescence Microscopy 67 The Microbiologist's Toolbox: The Direct Fluorescent Antibody Assay 67 3.3 Microscopy Used for Research Investigations 68 * Light Microscopy 68 What a Microbiologist Sees: Differential Interference Contrast Microscopy 70 * Electron Microscopy 70 * Nanoprobe-based Microscopy 72 3.4 Specimen Preparation and Staining 72 * Basic Staining Procedures 72 Case Study: Diagnosing Gonorrhea Using Gram Staining 74 Clinical Application: Diagnosing Tuberculosis Using Acid-fast Staining 75 * Special Staining Procedures 75 4 Prokaryotic Organisms 82 4.1 The Prokaryote's Place in the Living World 84 * Sustaining Life 84 What a Microbiologist Sees: Prokaryotes- The Dominant Form of Life on Earth 85 * Symbiotic Relationships 86 4.2 Bacterial Cell Shapes and Arrangements 87 * Bacterial Shapes 87 * Bacterial Arrangements 87 4.3 The Bacterial Cell Wall 89 * Cell Wall Structure 89 * Gram-Positive and Gram-Negative Cell Walls 91 * Atypical Cell Walls 92 Case Study: A Walking Pneumonia Outbreak at a University 93 4.4 External Structures of Bacterial Cells 94 * The Glycocalyx 94 * Fimbriae and Pili 94 * Flagella 95 The Microbiologist's Toolbox: The Flagella Stain 97 4.5 Internal Structures of Bacterial Cells 97 * The Plasma Membrane 98 * The Nucleoid 99 * Ribosomes 99 * Plasmids, Inclusion Bodies, and Membranous Structures 100 * Endospores 101 Clinical Application: Endospore-forming Bacteria 101 4.6 Prokaryotic Evolution and Classification 103 * The Tree of Life 103 * The Clinical Classification of Prokaryotes 105 5 Eukaryotic Organisms 112 5.1 The Eukaryotic Cell 114 * Cell Size 114 * The Eukaryotic Organelles 114 5.2 The Origins of Eukaryotic Organelles and Organisms 120 * The Autogenous and Endosymbiotic Hypotheses 120 * Eukarya: A Classification Overview 120 5.3 The Algae 122 * General Characteristics and Unique Features 122 * A Survey of Algae 122 Clinical Application: Agar-The Ideal Solid Medium for Bacterial Culture 124 * Pathogenic Algae 124 5.4 The Protozoans 125 * General Characteristics and Unique Features 125 * A Survey of Protozoans 126 * Pathogenic Protozoans 128 5.5 The Fungi 129 * General Characteristics and Unique Features 129 The Microbiologist's Toolbox: The Growth of Fungal Specimens on Sabouraud Dextrose Agar 131 * A Survey of Fungi 131 * Pathogenic Fungi 133 What a Microbiologist Sees: The Morphological Plasticity of Candida 134 5.6 The Helminths 135 * General Characteristics and Unique Features 135 * A Survey of Helminths 135 * Pathogenic Helminths 135 Case Study: Cravings 138 5.7 The Arthropods 139 * A Survey of Arthropods 139 * Pathogenic Arthropods and Arthropod Vectors 139 6 Viruses and Other Infectious Particles 146 6.1 Viral Structure and Classification 148 * The Structure of Viruses 148 * The Classification of Viruses 150 6.2 Viral Replication Cycles 153 * Viruses Replicating in Animal Cells 153 The Microbiologist's Toolbox: Presumptive Diagnosis of a Viral Infection Using CPE Analysis 158 * Viruses Replicating in Bacterial Cells 158 6.3 Viruses and Human Health 160 * The Clinical Cultivation of Viruses 160 * The Impact of Viral Infections 160 Case Study: H1N1 in Young Adults 161 * Viruses, Recurrent Infections, and Cancer 162 What a Microbiologist Sees: Connecting Symptoms with the Progression of HIV 163 6.4 Prevention and Treatment of Viral Infections 164 * The Prevention of Viral Infections 164 Clinical Application: Mandatory Flu Vaccines for Health Care Providers 164 * Antiviral Therapies 165 * Viral Influences on Bacterial Infections 166 6.5 Viruslike Microbes 170 * Viroids 170 * Satellites 170 * Prions 171 7 Metabolism 178 7.1 The Role of Energy in Life 180 * Basic Energy Principles 180 * Energy and Chemical Reactions 180 The Microbiologist's Toolbox: Identifying Bacteria by Metabolic Differences 182 7.2 Energy Production Principles 182 * Oxidation-Reduction Reactions 182 * ATP 183 7.3 Glycolysis and Fermentation 186 * Glycolysis 186 * Fermentation 188 Clinical Application: The Clinical Importance of Alcohol Throughout History 189 7.4 Aerobic Cellular Respiration 190 * Pyruvate Oxidation and the Citric Acid Cycle 190 * The Electron Transport System 192 * Lipid and Protein Catabolism 194 What a Microbiologist Sees: The Deepwater Horizon Oil Spill-Microbial Bioremediation 195 * Integrated Metabolic Pathways 196 7.5 Photosynthesis 196 * Reactions of Photosynthesis 197 Case Study: A Metabolic Imbalance in Grand Lake St. Mary's 202 * Chemosynthesis in Bacteria 202 8 Microbial Genetics and Genetic Engineering 210 8.1 DNA as the Genetic Material 212 * DNA Structure and Functions 212 * DNA Replication in Bacteria 214 8.2 From DNA to Protein 215 * Transcription 215 * Translation 217 8.3 Sources of Genetic Variation 219 * Mutation 219 * Recombination 222 * Transposition 224 Case Study: The Spread of a Drug-resistance Gene 224 8.4 Regulation of Gene Expression 225 * Transcriptional Control 225 * Pre- and Posttranscriptional Control 226 8.5 Recombinant DNA Technology 228 * Recombinant DNA Tools and Gene Cloning 228 The Microbiologist's Toolbox: Gel Electrophoresis 229 * Applications of Recombinant DNA Technology 230 What a Microbiologist Sees: Manipulating the Bacterial Genome for Agricultural Benefits 232 * Ethical and Safety Concerns 233 8.6 Genomics 234 * DNA Sequencing 234 * Genomic Analysis 234 * Applications of Genomics 236 Clinical Application: Screening for Genetic Diseases-BRCA1 Mutation 236 9 Microbial Growth and Control 240 9.1 Requirements for Microbial Growth 244 * Energy Sources 244 * Physical Requirements 244 Case Study: Foodborne Illness from Home- Prepared Fermented Tofu 245 * Chemical Requirements 247 9.2 Bacterial Reproduction and Growth 249 * Cell Division 249 * Growth Rate of Bacteria 250 * Phases of Growth 251 * Methods of Quantifying Bacterial Growth 252 The Microbiologist's Toolbox: Dilution Plating 253 9.3 Laboratory Growth of Microorganisms 254 * Obtaining a Pure Culture 254 * Growth Media 254 What a Microbiologist Sees: Biofilm Formation on Teeth 258 * Bacteria That Cannot Be Cultured 258 9.4 Microbial Cultures in Clinical Practice 260 * Specimen Collection 260 * Specimen Analysis 260 9.5 Controlling Microbial Growth 263 * Physical Methods 263 * Radiation 264 * Chemical Methods 266 Clinical Application: Alcohol-Based Hand Sanitizers in Health Care Settings 267 10 Innate Immunity 274 10.1 An Introduction to Immunity 276 * The Benefits and Consequences of the Immune Response 276 * Innate Versus Adaptive Immunity 276 * The Basic Anatomy of the Immune System 278 10.2 First-Line Defense Mechanisms 282 * Physical Defenses 282 What a Microbiologist Sees: The Benefits of Fever 283 Case Study: No Spicy Food for Me! 284 * Chemical Defenses 285 10.3 Innate Cellular Defense Mechanisms 286 * Hematopoiesis 286 * Leukocytes 287 The Microbiologist's Toolbox: The Differential Count 289 * Phagocytosis 290 * Inflammation 290 10.4 Protein-Mediated Defense Mechanisms 294 * The Complement Pathways 294 * Interferons 294 * Miscellaneous Proteins with Antimicrobial Action 296 11 Adaptive Immunity 304 11.1 Introduction to Adaptive Immunity 306 * Hallmarks of Adaptive Immunity 306 * Antigens and Immunogenicity 306 Clinical Application: Conjugate Vaccines 308 * Lymphocyte Maturation and Clonal Selection 308 * The Major Histocompatibility Complex 311 What a Microbiologist Sees: Transplant Rejection 312 11.2 Cell-mediated Responses 313 * T-cell Categories 313 * Antigen Processing and Presentation 315 * The T-cell Receptor Complex and Associative Recognition 316 11.3 T-cell Activation 317 * Early Stages of T-cell Activation 317 * Completion of T-cell Activation 318 Case Study: The Mantoux Test 318 11.4 Antibody-mediated Responses 320 * Basic Antibody Structure 320 The Microbiologist's Toolbox: The Coagulase Agglutination Assay 321 * Immunoglobulin Classes and Their Specific Functions 322 11.5 B-cell Activation 323 * B-cell Receptors and Pathogen Binding 323 * Antibody Production and Clonal Expansion 325 * B-cell Effector Mechanisms 327 12 Vaccination, Immunoassays, and Immune Disorders 334 12.1 Vaccines and Vaccination 336 * A Brief History of Vaccination 336 * Modern Vaccines 336 * Vaccines and Public Health 339 * Vaccine Safety and Misconceptions 342 12.2 Immunoassays 343 * Monoclonal Antibodies 343 The Microbiologist's Toolbox: Human Monoclonal Antibody Therapy for Non-Hodgkin's Lymphoma 345 * Types of Immunoassays 346 12.3 Hypersensitivities 350 * Type I Hypersensitivity 350 * Type II Hypersensitivity 352 What a Microbiologist Sees: Fetal Rh Incompatibility 353 * Type III Hypersensitivity 354 * Type IV Hypersensitivity 355 12.4 Autoimmune Diseases and Immuno deficiencies 356 * Autoimmune Diseases 356 * Immuno deficiencies 357 Clinical Application: Bone Marrow Transplants for Immunodeficient Patients 358 Case Study: Prioritizing Immunizations 359 13 Microbial Pathogenesis 366 13.1 Entering and Adhering to the Host 368 * Microbial Reservoirs 368 * Portals of Entry and Exit 369 * Adhering to Host Cells 370 13.2 Transmission of Microbes 372 * Modes of Transmission 372 Case Study: The Cholera Epidemic in Goma, Zaire 374 * Horizontal and Vertical Transmission 374 13.3 Bypassing Host Defenses 376 * Evading Immune Attack 376 * Altering Pathogen Antigens 378 * Damaging the Host Immune System 380 13.4 Damaging Host Tissues 381 * Direct Damage 381 * Enzymes 382 * Endotoxins 382 * Exotoxins 384 Clinical Application: Toxoid-based Vaccines 385 * Immunopathy 387 The Microbiologist's Toolbox: Analysis of Hemolysis on Blood Agar 388 13.5 Factors Influencing Disease Outcomes 389 * Host Factors 389 What a Microbiologist Sees: Stress and Infection 390 * Microbial Factors 391 14 Antimicrobial Agents 398 14.1 Principles of Antimicrobial Chemotherapy 400 * The Discovery and Development of Antimicrobial Agents 400 * Choosing the Best Antimicrobial Agent 402 The Microbiologist's Toolbox: The Broth Dilution Test 404 14.2 Antibacterial Agents 406 * Inhibitors of Cell Wall Synthesis 406 * Inhibitors of Protein Synthesis 409 * Inhibitors of Nucleic Acid Synthesis 410 * Agents That Target the Bacterial Plasma Membrane 412 * Antimycobacterial Agents 412 Clinical Application: The Fight Against Drug-Resistant Tuberculosis 412 14.3 Antiviral Agents 415 * Inhibitors of Virus Entry 416 * Inhibitors of Viral Nucleic Acid Synthesis 417 * Inhibitors of Viral Protein Synthesis 418 * Inhibitors of Viral Assembly and Release 418 14.4 Antifungal and Antiparasitic Agents 419 * Antifungal Agents 420 * Antiparasitic Agents 421 Case Study: Problems with Malaria Medication in Mozambique 423 14.5 Antimicrobial Drug Resistance 425 * Principles of Drug Resistance 425 * Mechanisms of Drug Resistance 426 * Human Factors Contributing to Antimicrobial Resistance 427 What a Microbiologist Sees: Livestock- Associated Drug-Resistant S. aureus 428 15 Epidemiology and Infection Control 434 15.1 Epidemiology and Public Health 436 * Early Epidemiological Successes 436 * Significant Accomplishments of Epidemiology 436 15.2 Epidemiological Surveillance 438 * Prevalence, Incidence Rates, and Mortality Rates 438 What a Microbiologist Sees: Antibioticimpregnated Bone Cement 439 * Epidemic Curves 441 * Disease Surveillance 441 15.3 Epidemiological Studies and Clinical Trials 442 * Case-Control and Cohort Studies 442 * Clinical Trials 443 Case Study: A Foodborne Outbreak Among Inmates at a County Jail 444 15.4 Health Care-associated Infections 446 * Common Health Care-Associated Infections 446 Clinical Application: Reducing the Risk of Bloodstream Infections 447 * Surgical Site Infections 447 * CAUTIs 450 * PICC Line Infections 450 * CLABSIs 451 15.5 Preventing Pathogen Spread in Health Care Settings 451 * Hand Hygiene 451 * Universal and Standard Precautions and PPE 453 * Screening 454 The Microbiologist's Toolbox: MRSA Screening Procedures in the Clinical Laboratory 455 * Isolation Procedures 456 16 Diseases of the Respiratory System 462 16.1 The Conflicts 464 * Host Defenses 464 * Microbial Pathogenic Strategies 464 * Normal Microbiota 465 16.2 Bacterial Diseases of the Respiratory System 466 * Diphtheria 466 * Pertussis 467 * Tuberculosis 468 Case Study: Whooping Cough Outbreak 469 16.3 Viral Diseases of the Respiratory System 472 * The Common Cold 472 * Influenza 473 What a Microbiologist Sees: Unpredictable Behavior 476 16.4 Diseases of the Respiratory System Caused by Multiple Pathogens 477 * Sinusitis and Otitis Media 477 * Pharyngitis 479 The Microbiologist's Toolbox: Diagnosis of Strep Throat 481 * Laryngitis, Croup, Tracheitis, and Epiglottitis 482 * Bronchitis and Bronchiolitis 483 16.5 Pneumonia 483 Clinical Application: Sputum Samples 484 * General Characteristics of Pneumonia 484 * Epidemiology of Pneumonia 485 * Causes of Pneumonia 486 * Emerging Pathogens 488 17 Diseases of the Skin and Eyes 496 17.1 The Conflicts 498 * Host Defenses 498 * Microbial Pathogenic Strategies 498 * Normal Microbiota 501 17.2 Bacterial Diseases of the Skin 502 * Staphylococcal and Streptococcal Skin Diseases 502 The Microbiologist's Toolbox: Mannitol Salt Agar-A Versatile Selective/Differential Medium 505 * Pseudomonal Skin Diseases 505 * Miscellaneous Bacterial Skin Diseases 506 17.3 Viral Diseases of the Skin 508 * Pediatric Viral Rashes 508 Clinical Application: Improving Hand-Hygiene Compliance with Technology 509 * Shingles 512 * Warts 513 * Smallpox 514 17.4 Fungal, Protozoan, and Arthropod Diseases of the Skin 516 * Fungal Skin Diseases 516 What a Microbiologist Sees: Oral Thrush and Immune System Status 517 * Protozoan Skin Diseases 517 * Arthropod Skin Diseases 519 Case Study: Kindergarten Contact 520 17.5 Diseases of the Eye 521 * Host Defenses and Microbial Pathogenic Strategies 522 * Conjunctivitis 522 * Other Eye Diseases 523 18 Diseases of the Nervous System 532 18.1 The Conflicts 534 * Host Defenses 534 * Microbial Pathogenic Strategies 534 18.2 Bacterial Diseases of the Nervous System 536 * Bacterial Meningitis 536 * Tetanus 540 * Botulism 540 Clinical Application: Clinical Use of Botulism Toxin 541 * Hansen's Disease (Leprosy) 543 18.3 Viral Diseases of the Nervous System 543 * Viral Meningitis 543 Case Study: Viral Meningitis in a High School Student 544 * Encephalitis 545 * Polio 547 What a Microbiologist Sees: Polio Eradication 547 * Rabies 548 * Other Viral Diseases of the Nervous System 550 18.4 Fungal and Protozoan Diseases of the Nervous System 551 * Fungal Meningitis 551 The Microbiologist's Toolbox: India Ink Staining of CSF for Cryptococcus 552 * Toxoplasmosis 552 18.5 Prion Diseases of the Nervous System 554 * Animal Spongiform Encephalopathies 554 * Human Prion Diseases 554 19 Diseases of the Cardiovascular and Lymphatic Systems 562 19.1 The Conflicts 564 * Host Defenses 564 * Microbial Pathogenic Strategies 564 19.2 Sepsis and Cardiac Diseases 566 * Sepsis 566 * Cardiac Diseases 569 The Microbiologist's Toolbox: The Blood Culture 571 19.3 Bacterial Diseases of the Cardiovascular and Lymphatic Systems 572 * Brucellosis 572 * Anthrax 574 * Lyme Disease 575 * Plague 577 * Other Bacterial Diseases 580 19.4 Viral Diseases of the Cardiovascular and Lymphatic Systems 581 * Leukocyte-associated Cardiovascular and Lymphatic Diseases 581 What a Microbiologist Sees: The Diagnosis of Mononucleosis 582 * Viral Hemorrhagic Diseases 583 * Hepatitis 585 Clinical Application: HIV Status and the Spread of Hepatitis 586 19.5 Protozoan and Helminthic Diseases of the Cardiovascular and Lymphatic Systems 587 * Systemic Protozoan Diseases 587 Case Study: The Kissing Bug 588 * Systemic Helminthic Diseases 590 20 Diseases of the Gastrointestinal System 598 20.1 The Conflicts 600 * Host Defenses 600 * Microbial Pathogenic Strategies 600 * Normal Microbiota 600 20.2 Bacterial Diseases of the Mouth and Upper GI Tract 602 * Dental Caries 602 * Gingivitis and Periodontal Disease 603 What a Microbiologist Sees: Oral Hygiene for Patients with Ventilators 604 * Peptic Ulcer Disease 606 * Staphylococcus aureus Food Intoxication 606 20.3 Bacterial Diseases of the Lower GI Tract 607 * Diseases Caused by Salmonella 607 * Diarrheagenic E. coli Infections 608 * Campylobacteriosis 608 * Shigellosis 608 The Microbiologist's Toolbox: Preparing and Analyzing a Fecal Culture 609 * Cholera 610 * Opportunistic Diseases 612 20.4 Viral Diseases of the GI System 614 * Cold Sores 614 * Mumps 614 * Viral Gastroenteritis 615 Case Study: A Norovirus Outbreak Among Nurses 616 * Hepatitis A and Hepatitis E 617 20.5 Protozoan Diseases of the GI System 618 * Giardiasis 618 * Amoebic Dysentery 618 * Cryptosporidiosis 619 20.6 Helminthic Diseases of the GI System 620 * Trematode Infections 620 * Cestode Infections 621 * Nematode Infections 622 21 Diseases of the Urogenital System 632 21.1 The Conflicts 634 * Host Defenses 634 * Microbial Pathogenic Strategies 634 * Normal Microbiota 636 21.2 Bacterial Diseases of the Urinary System 637 * Cystitis 637 What a Microbiologist Sees: Cranberry Juice for UTI Prevention 639 * Pyelonephritis 640 Case Study: Pyelonephritis in a Toddler 641 * Leptospirosis 641 21.3 Bacterial Diseases of the Reproductive Systems 643 * Prostatitis 643 * Chlamydia 643 * Gonorrhea 645 The Microbiologist's Toolbox: The Challenge of Culturing Neisseria gonorrhoeae 646 * Pelvic Inflammatory Disease 646 * Syphilis 648 21.4 Viral Diseases of the Reproductive Systems 650 * Genital Warts 650 Clinical Application: Winning the War on Cervical Cancer 652 * Genital Herpes 652 * Molluscum Contagiosum 653 21.5 HIV and AIDS 654 * An Emerging Infection 655 * HIV Replication and Pathogenicity 657 * HIV Diagnosis, Treatment, and Outlook 658 21.6 Fungal and Protozoan Diseases of the Reproductive Systems 660 * Vaginal Yeast Infections 660 * Trichomoniasis 662 22 Environmental and Industrial Microbiology 670 22.1 Microbial Ecology 672 * The Ecological Hierarchy 672 * Microbes in Earth's Ecosystems 674 * Biofilms 676 Clinical Application: A Potential New Therapy for Medical Biofilm Elimination 677 22.2 Biogeochemical Cycles 678 * The Nitrogen Cycle 679 * The Carbon Cycle 680 * The Phosphorus Cycle 681 What a Microbiologist Sees: Habitat for Acidophiles 683 * The Sulfur Cycle 683 22.3 Bioremediation 684 * Microorganisms Used in Bioremediation 685 * Sewage Treatment 685 * Freshwater Treatment 687 22.4 Microorganisms Used in Manufacturing 687 * Products of Biotechnology 687 * Food Production 688 Case Study: Bacon Beer 691 22.5 Safe Product Processing and Packaging 692 * Food Safety Regulations 692 * Chemical and Physical Controls in Food Production 693 * Canning 694 The Microbiologist's Toolbox: The Autoclave 696 * Microbial Control in Health Care Settings 696 Appendix A: Answers to Self-Tests 702 Appendix B: Physiological Reference Ranges 705 Glossary 708 Index 726
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