Talaro’s Foundations in Microbiology: Basic Principles, Twelfth Edition
By Berry Chess
Contents:
CHAPTER 1
The Main Themes of Microbiology 2
1.1 The Scope of Microbiology 4
1.2 General Characteristics of
Microorganisms and Their Roles
in the Earth’s Environments 4
The Origins and Dominance of
Microorganisms 4
The Cellular Organization of Microorganisms 7
Noncellular Pathogenic Particles—Viruses and Prions 8
Microbial Dimensions: How Small Is Small? 8
Microbial Involvement in Energy and Nutrient Flow 8
1.3 Human Use of Microorganisms 10
1.4 Microbial Roles in Infectious Diseases 11
The Changing Specter of Infectious Diseases 11
Microbial Roles in Noninfectious Diseases 13
1.5 The Historical Foundations of Microbiology 13
The Development of the Microscope: Seeing Is Believing 13
The Scientific Method and the Search for Knowledge 14
The Development of Medical Microbiology 16
1.6 Taxonomy: Organizing, Classifying, and Naming
Microorganisms 18
The Levels of Classification 19
Assigning Scientific Names 19
1.7 The Origin and Evolution of Microorganisms 21
All Life Is Related and Connected Through Evolution 21
Systems for Presenting a Universal Tree of Life 23
CHAPTER 2
The Chemistry of Biology 30
2.1 Atoms: Fundamental Building Blocks
of All Matter in the Universe 32
Different Types of Atoms: Elements
and Their Properties 33
The Major Elements of Life and Their Primary
Characteristics 33
2.2 Bonds and Molecules 35
Covalent Bonds: Molecules with Shared Electrons 36
Ionic Bonds: Electron Transfer among Atoms 37
Electron Transfer and Oxidation-Reduction
Reactions 38
2.3 Chemical Reactions, Solutions, and pH 39
Formulas, Models, and Equations 39
Solutions: Homogeneous Mixtures of Molecules 40
Acidity, Alkalinity, and the pH Scale 41
2.4 The Chemistry of Carbon and Organic Compounds 43
Functional Groups of Organic Compounds 43
Organic Macromolecules: Superstructures of Life 45
2.5 Molecules of Life: Carbohydrates 45
The Nature of Carbohydrate Bonds 47
The Functions of Carbohydrates in Cells 48
2.6 Molecules of Life: Lipids 49
Membrane Lipids 50
Miscellaneous Lipids 51
2.7 Molecules of Life: Proteins 51
Protein Structure and Diversity 52
2.8 Nucleic Acids: A Program for Genetics 54
The Double Helix of DNA 55
Making New DNA: Passing on the Genetic
Message 55
RNA: Organizers of Protein Synthesis 55
ATP: The Energy Molecule of Cells 56
CHAPTER 3
Tools of the Laboratory:
Methods of Studying
Microorganisms 62
3.1 Methods of Microbial
Investigation 64
3.2 The Microscope: Window on an
Invisible Realm 66
Magnification and Microscope
Design 66
Variations on the Optical Microscope 69
Electron Microscopy 71
3.3 Preparing Specimens for Optical
Microscopes 73
Fresh, Living Preparations 73
Fixed, Stained Smears 73
3.4 Additional Features of the Six “I”s 77
Inoculation, Growth, and Identification
of Cultures 77
Isolation Techniques 77
Identification Techniques 79
3.5 Media: The Foundations of Culturing 80
Types of Media 81
Physical States of Media 81
Chemical Content of Media 82
Media to Suit Every Function 84
CHAPTER 4
A Survey of Prokaryotic Cells
and Microorganisms 92
4.1 Basic Characteristics of
Cells and Life Forms 94
What is Life? 94
4.2 Prokaryotic Profiles: The Bacteria
and Archaea 94
The Structure of a Generalized Bacterial Cell 96
Cell Extensions and Surface Structures 96
Biofilms 100
4.3 The Cell Envelope: The Outer Boundary Layer of
Bacteria 102
Basic Types of Cell Envelopes 102
Structure of Cell Walls 103
The Cell Wall and Infections 104
Mycoplasmas and Other Cell Wall–Deficient Bacteria 105
Cell Membrane Structure 106
4.4 Bacterial Internal Structure 107
Contents of the Cytoplasm 107
Bacterial Endospores: An Extremely Resistant
Life Form 108
4.5 Bacterial Shapes, Arrangements, and Sizes 111
4.6 Classification Systems of Prokaryotic Domains:
Archaea and Bacteria 114
Prokaryotic Taxonomy: A Work in Progress 114
4.7 Survey of Prokaryotic Groups with Unusual
Characteristics 119
Free-Living Nonpathogenic Bacteria 119
Unusual Forms of Medically Significant Bacteria 120
Archaea: The Other Prokaryotes 122
CHAPTER 5
A Survey of Eukaryotic Cells
and Microorganisms 128
5.1 The History of Eukaryotes 130
5.2 Form and Function of the Eukaryotic
Cell: External Structures 131
Locomotor Appendages: Cilia
and Flagella 131
The Glycocalyx 133
Form and Function of the Eukaryotic Cell: Boundary
Structures 133
5.3 Form and Function of the Eukaryotic Cell: Internal
Structures 134
The Nucleus: The Control Center 134
Endoplasmic Reticulum: A Passageway and Production System for
Eukaryotes 135
Golgi Apparatus: A Packaging Machine 136
Mitochondria: Energy Generators of the Cell 137
Chloroplasts: Photosynthesis Machines 138
Ribosomes: Protein Synthesizers 139
The Cytoskeleton: A Support Network 139
5.4 Eukaryotic-Prokaryotic Comparisons and Taxonomy of
Eukaryotes 140
Overview of Taxonomy 140
5.5 The Kingdom Fungi 142
Fungal Nutrition 143
Organization of Microscopic Fungi 144
Reproductive Strategies and Spore Formation 144
Fungal Classification 146
Fungal Identification and Cultivation 147
Fungi in Medicine, Nature, and Industry 147
5.6 Survey of Protists: Algae 149
The Algae: Photosynthetic Protists 150
5.7 Survey of Protists: Protozoa 152
Protozoan Form and Function 152
Protozoan Identification and Cultivation 153
Important Protozoan Pathogens 154
5.8 The Parasitic Helminths 158
General Worm Morphology 158
Life Cycles and Reproduction 158
A Helminth Cycle: The Pinworm 159
Helminth Classification and
Identification 160
Distribution and Importance of Parasitic
Worms 160
CHAPTER 6
An Introduction to Viruses,
Viroids, and Prions 166
6.1 Overview of Viruses 168
Early Searches for the Tiniest
Microbes 168
The Position of Viruses in the
Biological Spectrum 168
6.2 The General Structure of Viruses 168
Size Range 168
Viral Components: Capsids, Nucleic Acids, and Envelopes 170
6.3 How Viruses Are Classified and Named 175
6.4 Modes of Viral Multiplication 175
Multiplication Cycles in Animal Viruses 177
Persistent Viral Infection and Viral Integration 181
6.5 The Multiplication Cycle in Bacteriophages 183
Lysogeny: The Silent Virus Infection 184
6.6 Techniques in Cultivating and Identifying Animal
Viruses 185
Using Cell (Tissue) Culture Techniques 185
Using Bird Embryos 185
Using Live Animal Inoculation 187
6.7 Viral Infection, Detection, and
Treatment 187
6.8 Prions and Other Nonviral Infectious
Particles 187
CHAPTER 7
Microbial Nutrition, Ecology,
and Growth 194
7.1 Microbial Nutrition 196
Chemical Analysis of Cell
Contents 196
Forms, Sources, and Functions
of Essential Nutrients 197
7.2 Classification of Nutritional Types 198
Autotrophs and Their Energy Sources 199
Heterotrophs and Their Energy Sources 201
7.3 Transport: Movement of Substances across the Cell
Membrane 202
Diffusion and Molecular Motion 202
The Diffusion of Water: Osmosis 203
Adaptations to Osmotic Variations in the
Environment 203
The Movement of Solutes across Membranes 204
Active Transport: Bringing in Molecules against
a Gradient 205
Endocytosis: Eating and Drinking by Cells 207
7.4 Environmental Factors that Influence
Microbes 207
Adaptations to Temperature 208
Gas Requirements 210
Effects of pH 212
Osmotic Pressure 213
Miscellaneous Environmental Factors 213
7.5 Ecological Associations among Microorganisms 213
7.6 The Study of Microbial Growth 218
The Basis of Population Growth: Binary Fission and the Bacterial
Cell Cycle 218
The Rate of Population Growth 218
Determinants of Population Growth 219
Other Methods of Analyzing Population
Growth 221
CHAPTER 8
An Introduction to Microbial
Metabolism: The Chemical
Crossroads of Life 228
8.1 An Introduction to Metabolism
and Enzymes 230
Enzymes: Catalyzing the Chemical
Reactions of Life 230
Regulation of Enzymatic Activity and
Metabolic Pathways 237
8.2 The Pursuit and Utilization of Energy 240
Cell Energetics 240
8.3 Pathways of Bioenergetics 243
Catabolism: An Overview of Nutrient Breakdown and Energy
Release 243
Energy Strategies in Microorganisms 243
Aerobic Respiration 245
Pyruvic Acid—A Central Metabolite 247
The Krebs Cycle—A Carbon and Energy Wheel 247
The Respiratory Chain: Electron Transport and Oxidative
Phosphorylation 249
Summary of Aerobic Respiration 252
Anaerobic Respiration 252
8.4 The Importance of Fermentation 253
8.5 Biosynthesis and the Crossing Pathways of
Metabolism 255
The Frugality of the Cell—Waste Not, Want Not 255
Assembly of the Cell 257
8.6 Photosynthesis: The Earth’s Lifeline 258
Light-Dependent Reactions 259
Light-Independent Reactions 260
Other Mechanisms of Photosynthesis 261
CHAPTER 9
An Introduction to
Microbial Genetics 268
9.1 Introduction to Genetics and Genes:
Unlocking the Secrets of
Heredity 270
The Nature of the Genetic
Material 270
The Structure of DNA: A Double Helix with Its Own
Language 272
DNA Replication: Preserving the Code and
Passing It On 273
9.2 Applications of the DNA Code: Transcription and
Translation 277
The Gene-Protein Connection 278
The Major Participants in Transcription and
Translation 278
Transcription: The First Stage of Gene
Expression 279
Translation: The Second Stage of Gene
Expression 281
Eukaryotic Transcription and Translation: Similar yet
Different 284
9.3 Genetic Regulation of Protein Synthesis and
Metabolism 286
The Lactose Operon: A Model for Inducible Gene Regulation in
Bacteria 286
A Repressible Operon 287
RNA and Gene Expression 287
9.4 Mutations: Changes in the Genetic
Code 289
Causes of Mutations 289
Categories of Mutations 290
Repair of Mutations 290
The Ames Test 291
Positive and Negative Effects of Mutations 292
9.5 DNA Recombination Events 293
Transmission of Genetic Material in Bacteria 293
9.6 The Genetics of Animal Viruses 298
Replication Strategies in Animal Viruses 298
CHAPTER 10
Genetic Engineering and
Genetic Analysis 306
10.1 Elements and Applications
of Genetic Engineering 308
Tools and Techniques of DNA
Technology 308
10.2 Recombinant DNA Technology: How to Imitate
Nature 316
Technical Aspects of Recombinant DNA and
Gene Cloning 316
Construction of a Recombinant, Insertion into a Cloning
Host, and Genetic Expression 317
Protein Products of Recombinant DNA
Technology 319
10.3 Genetically Modified Organisms and Other
Applications 320
Recombinant Microbes: Modified Bacteria and
Viruses 320
Recombination in Multicellular Organisms 322
Medical Applications of DNA Technology 325
10.4 Genome Analysis: DNA Profiling and Genetic
Testing 327
DNA Profiling: A Unique Picture of a Genome 327
CHAPTER 11
Physical and Chemical Agents
for Microbial Control 336
11.1 Controlling Microorganisms 338
General Considerations in Microbial
Control 338
Relative Resistance of Microbial
Forms 338
Terminology and Methods of Microbial Control 340
What Is Microbial Death? 341
How Antimicrobial Agents Work: Their Modes of
Action 343
11.2 Physical Methods of Control: Heat 344
Effects of Temperature on Microbial Activities 344
The Effects of Cold and Desiccation 347
11.3 Physical Methods of Control: Radiation and
Filtration 349
Radiation as a Microbial Control Agent 349
Modes of Action of Ionizing Versus Nonionizing
Radiation 349
Ionizing Radiation: Gamma Rays and X-Rays 349
Nonionizing Radiation: Ultraviolet Rays 351
Filtration—A Physical Removal Process 352
11.4 Chemical Agents in Microbial Control 353
Choosing a Microbicidal Chemical 354
Factors that Affect the Germicidal Activities of Chemical
Agents 354
Categories of Chemical Agents 355
CHAPTER 12
Drugs, Microbes, Host—
The Elements of
Chemotherapy 370
12.1 Principles of Antimicrobial
Therapy 372
The Origins of Antimicrobial
Drugs 372
Interactions between Drugs and
Microbes 373
12.2 Survey of Major Antimicrobial Drug Groups 379
Antibacterial Drugs that Act on the Cell Wall 379
Antibiotics that Damage Bacterial Cell Membranes 381
Drugs that Act on DNA or RNA 381
Drugs that Interfere with Protein Synthesis 382
Drugs that Block Metabolic Pathways 383
12.3 Drugs to Treat Fungal, Parasitic, and Viral
Infections 384
Antifungal Drugs 384
Antiparasitic Chemotherapy 385
Antiviral Chemotherapeutic Agents 386
12.4 Interactions between Microbes and Drugs: The Acquisition
of Drug Resistance 389
How Does Drug Resistance Develop? 390
Specific Mechanisms of Drug Resistance 390
Natural Selection and Drug Resistance 393
12.5 Interactions between Drugs and Hosts 395
Toxicity to Organs 395
Allergic Responses to Drugs 396
Suppression and Alteration of the Microbiota
by Antimicrobials 396
12.6 The Process of Selecting an Antimicrobial Drug 397
Identifying the Agent 397
Testing for the Drug Susceptibility of Microorganisms 398
The MIC and the Therapeutic Index 399
Patient Factors in Choosing an Antimicrobial Drug 400
CHAPTER 13
Microbe–Human Interactions:
Infection, Disease, and
Epidemiology 406
13.1 We Are Not Alone 408
Contact, Colonization, Infection,
Disease 408
Resident Microbiota: The Human as a
Habitat 408
Indigenous Microbiota of Specific Regions 412
Colonizers of the Human Skin 413
Microbial Residents of the Gastrointestinal Tract 414
Inhabitants of the Respiratory Tract 415
Microbiota of the Genitourinary Tract 415
13.2 Major Factors in the Development of an Infection 418
Becoming Established: Phase 1—Portals of Entry 419
The Requirement for an Infectious Dose 421
Attaching to the Host: Phase 2 421
Invading the Host and Becoming Established:
Phase 3 423
13.3 The Outcomes of Infection and Disease 426
The Stages of Clinical Infections 426
Patterns of Infection 427
Signs and Symptoms: Warning Signals of
Disease 428
The Portal of Exit: Vacating the Host 429
The Persistence of Microbes and Pathologic
Conditions 430
13.4 Epidemiology: The Study of Disease in
Populations 430
Origins and Transmission Patterns of Infectious
Microbes 431
The Acquisition and Transmission of Infectious
Agents 433
13.5 The Work of Epidemiologists: Investigation and
Surveillance 435
Epidemiological Statistics: Frequency of
Cases 436
Investigative Strategies of the Epidemiologist 438
Hospital Epidemiology and Healthcare-Associated
Infections 438
Standard Blood and Body Fluid
Precautions 441
CHAPTER 14
An Introduction to Host
Defenses and Innate
Immunities 448
14.1 Overview of Host Defense
Mechanisms 450
Barriers at the Portal of Entry: An
Inborn First Line of Defense 450
14.2 Structure and Function of the Organs
of Defense and Immunity 452
How Do White Blood Cells Carry Out Recognition and
Surveillance? 452
Compartments and Connections of the Immune
System 453
14.3 Second-Line Defenses: Inflammation 462
The Inflammatory Response: A Complex Concert of Reactions
to Injury 462
The Stages of Inflammation 463
14.4 Second-Line Defenses: Phagocytosis, Interferon, and
Complement 467
Phagocytosis: Ingestion and Destruction by White Blood
Cells 467
Interferon: Antiviral Cytokines and Immune
Stimulants 469
Complement: A Versatile Backup
System 470
An Outline of Major Host Defenses 472
CHAPTER 15
Adaptive, Specific Immunity,
and Immunization 478
15.1 Specific Immunities:
The Adaptive Line of Defense 480
An Overview of Specific Immune
Responses 480
Development of the Immune Response
System 480
Specific Events in T-Cell Maturation 484
Specific Events in B-Cell Maturation 486
15.2 The Nature of Antigens and Antigenicity 486
Characteristics of Antigens and Immunogens 486
15.3 Immune Reactions to Antigens and the Activities of
T Cells 488
The Role of Antigen Processing and Presentation 488
T-Cell Responses and Cell-Mediated Immunity (CMI) 489
15.4 Immune Activities of B Cells 492
Events in B-Cell Responses 493
Monoclonal Antibodies: Specificity in the Extreme 498
15.5 A Classification Scheme for Specific, Acquired
Immunities 499
Defining Categories by Mode of Acquisition 499
15.6 Immunization: Providing Immune Protection through
Therapy 502
Artificial Passive Immunization 502
Artificial Active Immunity: Vaccination 502
Development of New Vaccines 505
Routes of Administration and Side Effects
of Vaccines 507
To Vaccinate: Why, Whom, and When? 508
Vaccine Protection: Magical but Not Magic 508
CHAPTER 16
Disorders in Immunity 514
16.1 The Immune Response: A Two-
Sided Coin 516
Overreactions to Antigens: Allergy/
Hypersensitivity 516
16.2 Allergic Reactions: Atopy
and Anaphylaxis 517
Modes of Contact with Allergens 517
The Nature of Allergens and Their Portals of Entry 518
Mechanisms of Allergy: Sensitization and
Provocation 519
Cytokines, Target Organs, and Allergic Symptoms 521
Specific Diseases Associated with IgE- and Mast-Cell–Mediated
Allergy 521
Anaphylaxis: A Powerful Systemic Reaction to Allergens 524
Diagnosis of Allergy 524
Treatment and Prevention of Allergy 525
16.3 Type II Hypersensitivities: Reactions that Lyse Foreign
Cells 527
The Basis of Human ABO Antigens and Blood Types 527
Antibodies against A and B Antigens 527
The Rh Factor and Its Clinical Importance 529
16.4 Type III Hypersensitivities: Immune Complex
Reactions 530
Mechanisms of Immune Complex Diseases 531
Types of Immune Complex Disease 531
16.5 Immunopathologies Involving T Cells 532
Type IV Delayed Hypersensitivity 532
T Cells in Relation to Organ Transplantation 532
Practical Examples of Transplantation 535
16.6 Autoimmune Diseases: An Attack on Self 536
Genetic and Gender Correlation in Autoimmune
Disease 536
The Origins of Autoimmune Disease 536
Examples of Autoimmune Disease 537
16.7 Immunodeficiency Diseases and Cancer: Compromised
Immune Responses 539
Primary Immunodeficiency Diseases 539
Secondary Immunodeficiency Diseases 541
The Role of the Immune System in Cancer 542
CHAPTER 17
Procedures for Identifying
Pathogens and Diagnosing
Infections 548
17.1 An Overview of Clinical
Microbiology 550
Phenotypic Methods 550
Genotypic Methods 551
Immunologic Methods 551
On the Track of the Infectious Agent: Specimen
Collection 551
17.2 Phenotypic Methods 553
Immediate Direct Examination of Specimen 553
Cultivation of Specimen 553
17.3 Genotypic Methods 556
DNA Analysis Using Genetic Probes 556
Roles of the Polymerase Chain Reaction and Ribosomal RNA in
Identification 556
17.4 Immunologic Methods 558
General Features of Immune Testing 559
Agglutination and Precipitation Reactions 560
The Western Blot for Detecting Proteins 561
Complement Fixation 562
Point-of-Care and Rapid Diagnostic Tests 563
Miscellaneous Serological Tests 564
Fluorescent Antibody and Immunofluorescent
Testing 565
17.5 Immunoassays: Tests with High Sensitivity 566
Radioimmunoassay (RIA) 566
Enzyme-Linked Immunosorbent Assay (ELISA) 566
17.6 Viruses as a Special Diagnostic Case 566
APPENDIX A Detailed Steps in the Glycolysis Pathway A-1
APPENDIX B Tests and Guidelines B-1
APPENDIX C General Classification Techniques and Taxonomy
of Bacteria C-1
APPENDIX D Answers to End of Chapter Questions D-1
ONLINE APPENDICES An Introduction to Concept Mapping,
Significant Events in Microbiology,
Exponents, and Classification of Major
Microbial Disease Agents by System
Affected, Site of Infection, and Routes of
Transmission
Glossary G-1
Index I-1