Description
TABLE OF CONTENTS
1Â The Microbial World 1
1.1 The Microbes 2
A Brief Survey of the Microbial World 3
The Dominant Form of Life on Earth 4
1.2 The Conflicts 6
Growth and Control of Microbes 6
The Role of the Immune System 8
What a Microbiologist Sees: Wrestling and the Spread of Skin Pathogens 8
Pathogenesis 9
Antimicrobial Drugs 10
1.3 Infectious Disease 11
Epidemiology and Healthy Practices 11
Host Defenses and Microbial Pathogenesis Strategies 12
Infectious Disease Statistics 12
The Microbiologist’s Toolbox: MALDI-TOF Mass Spectrometry 13
Case Study: Vaccination: A Casualty of War 15
1.4 Microbial Ecology and Commercial Applications 16
The Importance of Environmental Microbes 16
The Industrial Use of Microorganisms 17
Clinical Application: Pasteurization 18
2Â An Introduction to the Chemical Basis of Life 24
2.1 Atoms, Elements, and Molecules 25
Elements and the Periodic Table 25
Basic Atomic Structure 27
Electron Configuration and Bonding 28
Chemical Interactions 30
What a Microbiologist Sees: Microbe Diagnosis Using Colorimetric Chemical Reactions 31
2.2 Water: Life’s Most Essential Molecule 31
Water’s Unique Properties 31
Aqueous Solutions 33
Acids and Bases 34
The Microbiologist’s Toolbox: Diagnosis Using pH-Sensitive Chemical Reactions 36
Case Study: Trading One Infection for Another 37
2.3 Carbon’s Key Role in Biochemistry 38
The Diversity of Carbon Chemistry 38
Isomers 39
Clinical Application: Isomers as a New Antibacterial Mechanism of Action 39
Building Complex Organic Molecules 40
3Â The Biochemistry of Macromolecules 45
3.1 Proteins 46
The Four Levels of Protein Structure 46
Protein Diversity and Function 49
What a Microbiologist Sees: The Effect of Modified Tertiary Binding on Protein Structure 52
3.2 Enzymes 53
Enzyme Action 53
Factors Influencing the Rate of Enzyme Activity 55
3.3 Carbohydrates 57
Simple and Complex Carbohydrates 57
The Functional Diversity of Carbohydrates 59
Clinical Application: Rapid Glycogen Breakdown in a Diabetic Patient in Shock 60
3.4 Lipids 60
The Structural Classes of Lipids 61
Case Study: Acne—A Bacterial Interaction with Skin Oils 62
Lipid Functions 65
The Microbiologist’s Toolbox: Ziehl–Neelsen Acid-Fast Staining of Mycolic Acid Cell Walls 66
3.5 Nucleic Acids 67
The Structures of DNA and RNA 67
Nucleic Acid Functions 68
4Â Microscopy 75
4.1 Principles of Microscopy 76
Magnification 77
Resolution 78
4.2 Microscopy Used for Clinical Diagnosis 79
Bright-field Microscopy 79
Dark-field Microscopy 80
Fluorescence Microscopy 81
The Microbiologist’s Toolbox: The Direct Fluorescent Antibody Assay 81
4.3 Microscopy Used for Research Investigations 82
Light Microscopy 82
What a Microbiologist Sees: Differential Interference Contrast Microscopy 83
Electron Microscopy 84
Nanoprobe-based Microscopy 84
4.4 Specimen Preparation and Staining 86
Basic Staining Procedures 86
Case Study: Diagnosing Gonorrhea Using the Gram Stain 88
Special Staining Procedures 88
Clinical Application: Diagnosing Tuberculosis Using Acid-fast Staining 89
5Â Prokaryotic Organisms 95
5.1 The Prokaryote’s Place in the Living World 96
Sustaining Life 96
What a Microbiologist Sees: Prokaryotes—The Dominant Form of Life on Earth 97
Symbiotic Relationships 98
5.2 Bacterial Cell Shapes and Arrangements 99
Bacterial Shapes 99
Bacterial Arrangements 99
5.3 The Bacterial Cell Wall 101
Cell Wall Structure 102
Gram-positive and Gram-negative Cell Walls 103
Atypical Cell Walls 104
Case Study: A Walking Pneumonia Outbreak at a University 105
5.4 External Structures of Bacterial Cells 106
The Glycocalyx 106
Fimbriae and Pili 106
Flagella 107
The Microbiologist’s Toolbox: The Flagella Stain 108
5.5 Internal Structures of Bacterial Cells 109
The Plasma Membrane 109
The Nucleoid 110
Ribosomes 111
Plasmids, Inclusion Bodies, and Membranous Structures 112
Endospores 113
Clinical Application: Endospore-forming Bacteria 113
5.6 Prokaryotic Evolution and Classification 115
The Tree of Life 115
The Clinical Classification of Prokaryotes 117
6Â The Eukaryotic Cell 122
6.1 An Introduction to Eukaryotic Cells 123
Cell Size 123
Multicellular Organisms 123
6.2 The Plasma Membrane and Cell Wall 124
The Plasma Membrane 124
The Microbiologist’s Toolbox: Fluorescence-Activated Cell Sorting (FACS) 125
The Cell Wall 125
Clinical Application: Agar—The Ideal Solid Medium for Bacterial Culture 126
6.3 Internal Structures 127
The Nucleus and Genetic Material 128
Ribosomes 130
The Endomembrane System 130
Mitochondria and Chloroplasts 131
The Cytoskeleton 132
6.4 External Structures and Other Cellular Forms 134
Cellular Junctions 134
Flagella, Cilia, and Pseudopodia 134
Spores 134
Cysts and Sporocysts 136
Case Study: Valley Fever 136
What a Microbiologist Sees: O&P Examination of Stool 137
6.5 Eukaryotic Evolution and Classification 138
The Autogenous and Endosymbiotic Hypotheses 138
The Evolution of Multicellular Organisms 140
Eukarya: A Classification Overview 140
7Â Eukaryotic Organisms 145
7.1 The Algae 146
General Characteristics and Unique Features 146
A Survey of Algae 146
Pathogenic Algae 146
The Microbiologist’s Toolbox: Sabouraud Dextrose Agar 148
7.2 The Protozoans 149
General Characteristics and Unique Features 149
A Survey of Protozoans 149
Pathogenic Protozoans 151
7.3 The Fungi 152
General Characteristics and Unique Features 153
What a Microbiologist Sees: The Morphological Plasticity of Candida 154
A Survey of Fungi 155
Pathogenic Fungi 157
Clinical Application:Â Candida auris:Â An Emerging Fungal Pathogen 157
7.4 The Helminths 159
General Characteristics and Unique Features 159
A Survey of the Helminths 159
Pathogenic Helminths 161
Case Study: Cravings 162
7.5 The Arthropods 163
A Survey of the Arthropods 163
Pathogenic Arthropods and Arthropod Vectors 163
8Â Viruses and Infectious Particles 169
8.1 Viral Structure and Classification 170
The Structure of Viruses 170
The Classification of Viruses 172
8.2 Viral Replication Cycles 175
Viruses Replicating in Animal Cells 175
The Microbiologist’s Toolbox: Presumptive Diagnosis of a Viral Infection Using CPE Analysis 179
Viruses Replicating in Bacterial Cells 179
8.3 Viruses and Human Health 181
The Clinical Cultivation of Viruses 181
The Impact of Viral Infections 181
Case Study: A Bad Case of the Flu 182
Viruses, Recurrent Infections, and Cancer 183
What a Microbiologist Sees: Connecting Symptoms with the Progression of HIV 183
8.4 Prevention and Treatment of Viral Infections 184
The Prevention of Viral Infections 185
Antiviral Therapies 185
Clinical Application: Protecting the Most Vulnerable Patients 185
Viral Influences on Bacterial Infections 187
8.5 Viruslike Infectious Agents 190
Viroids 190
Satellites 191
Prions 191
9Â Metabolism 197
9.1 The Role of Energy in Life 198
Basic Energy Principles 198
Energy and Chemical Reactions 198
The Microbiologist’s Toolbox: Identifying Bacteria by Metabolic Differences 200
9.2 Energy Production Principles 200
Oxidation-Reduction Reactions 200
ATP 201
9.3 Glycolysis and Fermentation 203
Glycolysis 204
Fermentation 204
Clinical Application: The Clinical Importance of Alcohol Throughout History 207
9.4 Aerobic Cellular Respiration 208
Pyruvate Oxidation and the Citric Acid Cycle 208
The Electron Transport System 210
Lipid and Protein Catabolism 211
Integrated Metabolic Pathways 213
What a Microbiologist Sees: Microbial Bioremediation of an Oil Spill 213
9.5 Photosynthesis 214
Reactions of Photosynthesis 214
Chemosynthesis in Bacteria 219
Case Study: A Metabolic Imbalance in Grand Lake St. Mary’s 220
10Â Microbial Genetics and Genetic Engineering 226
10.1 DNA as the Genetic Material 227
DNA Structure and Functions 227
DNA Replication in Bacteria 228
10.2 From DNA to Protein 230
Transcription 230
Translation 232
10.3 Sources of Genetic Variation 234
Mutation 234
Recombination 237
Transposition 237
Case Study: The Spread of a Drug-Resistant Gene 239
10.4 Regulation of Gene Expression 240
Transcriptional Control 240
Pre-and Posttranscriptional Control 240
10.5 Recombinant DNA Technology 242
Recombinant DNA Tools and Gene Cloning 242
The Microbiologist’s Toolbox: Gel Electrophoresis 243
Applications of Recombinant DNA Technology 244
What a Microbiologist Sees: Manipulating the Bacterial Genome for Agricultural Benefits 246
Ethical and Safety Concerns 247
10.6 Genomics 248
DNA Sequencing 248
Genomic Analysis 248
Applications of Genomics 250
Clinical Application: Screening for Genetic Diseases—BRCA1 Mutation 251
11Â Microbial Growth and Control 257
11.1 Requirements for Microbial Growth 258
Energy Sources 258
Physical Requirements 258
Case Study: Foodborne Illness from Home-Prepared Fermented Tofu 259
Chemical Requirements 261
11.2 Bacterial Reproduction and Growth 262
Cell Division 263
Growth Rate of Bacteria 263
Phases of Growth 264
Methods of Quantifying Bacterial Growth 265
The Microbiologist’s Toolbox: Dilution Plating 267
11.3 Laboratory Growth of Microorganisms 268
Obtaining a Pure Culture 268
Growth Media 269
Bacteria That Cannot Be Cultured 272
What a Microbiologist Sees: Biofilm Formation on Teeth 272
11.4 Microbial Cultures in Clinical Practice 273
Specimen Collection 273
Specimen Analysis 275
11.5 Controlling Microbial Growth 277
Physical Methods 277
Radiation 278
Chemical Methods 279
Clinical Application: Alcohol-Based Hand Sanitizers in Health Care Settings 281
12Â Antimicrobial Agents 287
12.1 Principles of Antimicrobial Chemotherapy 288
The Discovery and Development of Antimicrobial Agents 288
Choosing the Best Antimicrobial Agent 289
The Microbiologist’s Toolbox: The Broth Dilution Test 292
12.2 Antibacterial Agents 293
Inhibitors of Cell Wall Synthesis 293
Inhibitors of Protein Synthesis 296
Inhibitors of Nucleic Acid Synthesis 299
Agents That Target the Bacterial Plasma Membrane 300
Clinical Application: The Fight Against Drug-Resistant Tuberculosis 300
Antimycobacterial Agents 301
12.3 Antiviral Agents 303
Inhibitors of HIV 304
Inhibitors of Hepatitis B and C Viruses 306
Inhibitors of Influenza A and B Viruses 307
Inhibitors of Herpes Viruses 307
12.4 Antifungal and Antiparasitic Agents 308
Antifungal Agents 308
Antiparasitic Agents 310
Case Study: Problems with Malaria Medication in Mozambique 312
12.5 Antimicrobial Drug Resistance 313
Principles of Drug Resistance 314
Mechanisms of Drug Resistance 314
Human Factors Contributing to Antimicrobial Resistance 316
What a Microbiologist Sees: Livestock-Associated Drug-Resistant S. aureus 316
13Â Innate Immunity 323
13.1 An Introduction to Immunity 324
The Benefits and Consequences of the Immune Response 324
Innate Versus Adaptive Immunity 324
The Basic Anatomy of the Immune System 326
13.2 First-Line Defense Mechanisms 330
Physical Defenses 330
Chemical Defenses 331
What a Microbiologist Sees: The Benefits of Fever 331
Case Study: No Spicy Food for Me! 332
13.3 Innate Cellular Defense Mechanisms 334
Hematopoiesis 334
Leukocytes 335
The Microbiologist’s Toolbox: The Differential Count 337
Phagocytosis 338
Inflammation 338
13.4 Protein-Mediated Defense Mechanisms 341
The Complement Pathways 341
Interferons 343
Other Protein-Mediated Defense Mechanisms 343
14Â Adaptive Immunity 351
14.1 Introduction to Adaptive Immunity 352
Hallmarks of Adaptive Immunity 352
Antigens and Immunogenicity 352
Lymphocyte Maturation and Clonal Selection 354
Clinical Application: Conjugate Vaccines 354
The Major Histocompatibility Complex 357
What a Microbiologist Sees: Transplant Rejection 357
14.2 Cell-Mediated Responses 358
T-Cell Categories 358
Antigen Processing and Presentation 359
The T-Cell Receptor Complex and Associative Recognition 362
14.3 T-Cell Activation 363
Early Stages of T-Cell Activation 363
Completion of T-Cell Activation 363
Case Study: The Mantoux Test 364
14.4 Antibody-Mediated Responses 365
Basic Antibody Structure 365
The Microbiologist’s Toolbox: The Coagulase Agglutination Assay 366
Immunoglobulin Classes and Their Specific Functions 367
14.5 B-Cell Activation 368
B-Cell Receptors and Pathogen Binding 368
Antibody Production and Clonal Expansion 368
B-Cell Effector Mechanisms 372
15Â Vaccination, Immunoassays, and Immune Disorders 378
15.1 Vaccines and Vaccination 379
A Brief History of Vaccination 379
Modern Vaccines 379
Case Study: Prioritizing Immunizations 381
Vaccines and Public Health 383
Vaccine Safety and Misconceptions 386
15.2 Immunoassays 388
Monoclonal Antibodies 388
Types of Immunoassays 390
The Microbiologist’s Toolbox: Human Monoclonal Antibody Therapy for Non-Hodgkin’s Lymphoma 390
153 Hypersensitivities 394
Type I Hypersensitivity 395
Type II Hypersensitivity 396
Type III Hypersensitivity 397
What a Microbiologist Sees: Fetal Rh Incompatibility 397
Type IV Hypersensitivity 398
15.4 Autoimmune Diseases and Immunodeficiencies 399
Autoimmune Diseases 399
Immunodeficiencies 400
Clinical Application: Bone Marrow Transplants for Immunodeficient Patients 402
16Â Microbial Pathogenesis 408
16.1 Transmission of Microbes 409
Microbial Reservoirs 409
Modes of Transmission 410
Case Study: The Cholera Epidemic in Goma, Zaire 411
Horizontal and Vertical Transmission 412
16.2 Entering and Adhering to the Host 413
Portals of Entry and Exit 413
Adhering to Host Cells 413
16.3 Overcoming Host Defenses 415
Evading Immune Attack 416
Altering Pathogen Antigens 417
Damaging the Host Immune System 418
16.4 Damaging Host Tissues 420
Direct Damage 420
Enzymes 421
Endotoxins 421
Exotoxins 423
Clinical Application: Toxoid-Based Vaccines 424
Immunopathy 426
The Microbiologist’s Toolbox: Analysis of Hemolysis on Blood Agar 426
16.5 Factors Influencing Disease Outcomes 427
Host Factors 428
What a Microbiologist Sees: Stress and Infection 428
Microbial Factors 429
17Â Epidemiology and Infection Control 434
17.1 Epidemiology and Public Health 435
Early Epidemiological Successes 435
Significant Accomplishments of Epidemiology 435
17.2 Epidemiological Surveillance 437
What a Microbiologist Sees: Antibiotic-Impregnated Bone Cement 438
Prevalence, Incidence Rates, and Mortality Rates 438
Epidemic Curves 439
Disease Surveillance 439
17.3 Epidemiological Studies and Clinical Trials 441
Case-Control and Cohort Studies 442
Clinical Trials 442
Case Study: A Foodborne Outbreak among Inmates at a County Jail 443
17.4 Health Care–Associated Infections 445
Common Health Care–Associated Infections 445
Surgical Site Infections 445
Clinical Application: Reducing the Risk of Bloodstream Infections 446
CAUTIs 446
PICC Line Infections 447
CLABSIs 450
17.5 Preventing Pathogen Spread in Health Care Settings 450
Hand Hygiene 450
Universal and Standard Precautions and PPE 450
Screening 452
Isolation Procedures 453
The Microbiologist’s Toolbox: MRSA Screening Procedures in the Clinical Laboratory 454
18Â Diseases of the Respiratory System 460
18.1 The Conflicts 461
Host Defenses 461
Microbial Pathogenic Strategies 461
Normal Microbiota 462
18.2 Bacterial Diseases of the Respiratory System 463
Diphtheria 463
Pertussis 464
Case Study: Whooping Cough Outbreak 465
Tuberculosis 466
18.3 Viral Diseases of the Respiratory System 468
The Common Cold 468
Influenza 470
What a Microbiologist Sees: Unpredictable Behavior 473
18.4 Diseases of the Respiratory System Caused by Multiple Pathogens 474
Sinusitis and Otitis Media 474
Pharyngitis 475
The Microbiologist’s Toolbox: Diagnosis of Strep Throat 478
Laryngitis, Croup, Tracheitis, and Epiglottitis 479
Bronchitis and Bronchiolitis 479
18.5 Pneumonia 480
General Characteristics of Pneumonia 480
Clinical Application: Sputum Samples 481
Epidemiology of Pneumonia 481
Causes of Pneumonia 482
Emerging Pathogens 484
19Â Diseases of the Skin and Eyes 491
19.1 The Conflicts 492
Host Defenses 492
Microbial Pathogenic Strategies 492
Normal Microbiota 493
19.2 Bacterial Diseases of the Skin 495
Staphylococcal and Streptococcal Skin Diseases 495
The Microbiologist’s Toolbox: Mannitol Salt Agar—A Versatile Selective/Differential Medium 498
Pseudomonal Skin Diseases 499
Miscellaneous Bacterial Skin Diseases 499
19.3 Viral Diseases of the Skin 501
Pediatric Viral Rashes 501
Clinical Application: An App to Improve Hand Hygiene 502
Shingles 504
Warts 506
Smallpox 506
19.4 Skin Diseases Caused by Eukaryotic Pathogens 508
Fungal Skin Diseases 508
What a Microbiologist Sees: Oral Thrush and Immune System Status 509
Protozoan Skin Diseases 509
Helminthic Skin Diseases 510
Arthropod Skin Diseases 510
Case Study: Kindergarten Contact 512
19.5 Diseases of the Eye 513
Host Defenses and Microbial Pathogenic Strategies 514
Conjunctivitis 514
Other Eye Diseases 516
20Â Diseases of the Gastrointestinal System 524
20.1 The Conflicts 525
Host Defenses 525
Microbial Pathogenic Strategies 525
Normal Microbiota 525
20.2 Bacterial Diseases of the Mouth and Upper GI Tract 527
Dental Caries 527
Gingivitis and Periodontal Disease 528
What a Microbiologist Sees: Oral Hygiene for Patients with Ventilators 529
Clinical Application: Periodontitis and Alzheimer’s Disease 529
Peptic Ulcer Disease 530
Staphylococcus aureus Food Intoxication 530
20.3 Bacterial Diseases of the Lower GI Tract 531
Diseases Caused by Salmonella 532
Diarrheagenic E. coli Infections 532
Campylobacteriosis 532
The Microbiologist’s Toolbox: Preparing and Analyzing a Fecal Culture 533
Shigellosis 534
Cholera 535
Opportunistic Infections 535
20.4 Viral Diseases of the GI System 538
Cold Sores 538
Mumps 538
Viral Gastroenteritis 539
Hepatitis A 539
Case Study: A Norovirus Outbreak Among Nurses 540
20.5 Protozoan Diseases of the GI System 541
Giardiasis 541
Amoebic Dysentery 542
Cryptosporidiosis 542
20.6 Helminthic Diseases of the GI System 543
Trematode Infections 543
Cestode Infections 544
Nematode Infections 545
21Â Diseases of the Urogenital System 554
21.1 The Conflicts 555
Host Defenses 555
Microbial Pathogenic Strategies 555
Normal Microbiota 555
21.2 Bacterial Diseases of the Urinary System 558
Cystitis 558
Pyelonephritis 559
What a Microbiologist Sees: Cranberry Juice for UTI Prevention 560
Leptospirosis 561
Case Study: Pyelonephritis in a Toddler 561
21.3 Bacterial Diseases of the Reproductive Systems 563
Prostatitis 563
Chlamydia 563
Gonorrhea 565
The Microbiologist’s Toolbox: The Challenge of Culturing Neisseria gonorrhoeae 566
Pelvic Inflammatory Disease 566
Syphilis 568
21.4 Viral Diseases of the Reproductive Systems 570
Genital Warts 570
Clinical Application: Winning the War on Cervical Cancer 571
Genital Herpes 572
Molluscum Contagiosum 573
21.5 HIV Infection and AIDS 574
HIV Origins and Characteristics 574
HIV Replication and Pathogenicity 576
HIV Testing, Treatment, and Outcomes 577
21.6 Fungal and Protozoan Diseases of the Reproductive Systems 579
Vaginal Yeast Infections 579
Trichomoniasis 581
22Â Diseases of the Nervous System 587
22.1 The Conflicts 588
Host Defenses 588
Microbial Pathogenic Strategies 588
22.2 Bacterial Diseases of the Nervous System 590
Bacterial Meningitis 590
Tetanus 593
Botulism 593
Case Study: The High Cost of Forgoing Tetanus Vaccination 594
Clinical Application: Clinical Use of Botulism Toxin 595
Hansen’s Disease (Leprosy) 597
22.3 Viral Diseases of the Nervous System 597
Viral Meningitis 597
Encephalitis 598
Polio 599
What a Microbiologist Sees: Polio Eradication 600
Rabies 601
Other Viral Diseases of the Nervous System 603
22.4 Fungal and Protozoan Diseases of the Nervous System 604
Fungal Meningitis 604
The Microbiologist’s Toolbox: India Ink Staining of CSF for Cryptococcus 604
Toxoplasmosis 605
22.5 Prion Diseases of the Nervous System 606
Animal Spongiform Encephalopathies 606
Human Prion Diseases 606
23Â Diseases of the Cardiovascular and Lymphatic Systems 613
23.1 The Conflicts 614
Host Defenses 614
Microbial Pathogenic Strategies 614
23.2 Sepsis and Cardiac Diseases 616
Sepsis 616
Cardiac Diseases 619
The Microbiologist’s Toolbox: The Blood Culture 620
23.3 Bacterial Diseases of the Cardiovascular and Lymphatic Systems 621
Brucellosis 622
Anthrax 623
Lyme Disease 625
Plague 627
Other Bacterial Diseases 628
23.4 Viral Diseases of the Cardiovascular and Lymphatic Systems 630
Leukocyte-Associated Cardiovascular and Lymphatic Diseases 630
What a Microbiologist Sees: The Diagnosis of Mononucleosis 631
Viral Hemorrhagic Diseases 631
Hepatitis 633
Clinical Application: HIV Status and the Spread of Hepatitis 634
23.5 Fungal, Protozoan, and Helminthic Diseases of the Cardiovascular and Lymphatic Systems 635
Systemic Candida auris Infection 635
Systemic Protozoan Diseases 636
Case Study: The Kissing Bug 637
Systemic Helminthic Diseases 639
24Â Environmental and Industrial Microbiology 646
24.1 Microbial Ecology 647
The Ecological Hierarchy 647
Microbes in Earth’s Ecosystems 647
Biofilms 651
Clinical Application: A Potential New Therapy for Medical Biofilm Elimination 652
24.2 Biogeochemical Cycles 653
The Nitrogen Cycle 653
The Carbon Cycle 654
The Phosphorus Cycle 656
The Sulfur Cycle 657
What a Microbiologist Sees: Habitat for Acidophiles 658
24.3 Bioremediation 659
Principles of Bioremediation 659
Sewage Treatment 660
Water Treatment 661
24.4 Microorganisms Used in Manufacturing 662
Products of Biotechnology 662
Food Production 662
Case Study: Bacon Beer 665
24.5 Safe Product Processing and Packaging 666
Food Safety Regulation 666
Canning 668
Microbial Control in Health Care Settings 669
The Microbiologist’s Toolbox: The Autoclave 669
Appendix A Answers to Self-Tests A-1
Appendix B Physiological Reference Ranges B-5
Glossary G-1
Index I-1
