Bacterial Pathogenesis

Preface xvii In Memoriam xix About the Authors xxi Chapter 1 The Power of Bacteria 2 Why Are Bacteria So Much in the Public Health Spotlight Nowadays? 3 Bacteria, a Formidable Ancient Life Form 4 Pressing Current Infectious Disease Issues 6 Emerging and Reemerging Infectious Diseases 6 Foodborne and Waterborne Infections 7 Modern Medicine as a Source of New Diseases 8 Postsurgical and Other Wound Infections 9 Bioterrorism 10 A New Respect for Prevention 10 Surveillance: An Early Warning System 11 Making Hospitals Safe for Patients 12 And Now for Some Good News: You’ve Got a Bacterial Infection! 12 The Helicobacter pylori Revolution 12 The Aftermath 13 Microbiota Shift Diseases 13 A Brave New World of Pathogenesis Research 14 The New Age of Genomics 16 Insights into Pathogen Evolution 17 Modeling the Host-Pathogen Interaction in Experimental Animals 17 Correlation Studies 18 Selected Readings 18 Questions 20 Chapter 2 Skin and Mucosa: The First Lines of Defense against Bacterial Infections 22 The Best Defense: Avoid, Reduce, and Prevent Exposure! 23 Barriers: Skin and Mucosal Membranes 24 The Layers of Cells That Protect the Body 24 Normal Microbiota of the Skin and Mucosa 27 Defenses of the Skin 31 Defenses of Mucosal Surfaces 32 Special Defenses of the Gastrointestinal Tract 34 Special Defenses of the Urogenital Tract 36 Special Defenses of the Respiratory Tract 36 Immune Defenses of the Skin and Mucosa 37 Models for Studying Breaches of Barrier Defenses 38 Selected Readings 39 Questions 39 Chapter 3 The Innate Immune System: Always on Guard 40 Triggering Innate Immune Defenses 41 Innate Immune Cells That Defend Blood and Tissue 42 Neutrophils (PMNs) 42 Monocytes, Macrophages, and Dendritic Cells (DCs) 42 Granulocytes: Basophils, Mast Cells, and Eosinophils 47 Transmigration—How Do Phagocytes Know When and Where to Go? 47 Natural Killer (NK) Cells 48 The Lymphatic System 50 How Phagocytes Recognize and Respond to Bacteria 50 How Phagocytes Kill Bacteria 54 Oxidative Burst in Phagolysosomes 54 Autophagy—Another Pathway for the Killing of Intracellular Pathogens 56 The Complement Cascade 57 Complement Proteins 57 Overview of Complement Pathways and Their Function 58 Steps in Complement Activation 60 Controlling Complement Activation 62 Cytokines and Chemokines—Mediators of Immune Responses 63 Roles of Cytokines and Chemokines in Directing Innate Immune Responses 63 Inflammation and Collateral Damage 65 Septic Shock: The Dark Side of the Innate Defenses 66 Other Innate Defenses of the Body—Nutritional Immunity 69 Selected Readings 70 Questions 70 Chapter 4 The Adaptive Defenses: Antibodies and Cytotoxic T Cells 72 The Specialists: Adapting to a Particular Pathogen Challenge 73 B Cells: Producers of Antibodies 74 The Humoral (Antibody) Immune Response 74 Characteristics of Antibodies and Their Diverse Roles in Preventing Infection 74 Serum Antibodies 76 Secretory Antibodies: Antibodies That Protect Mucosal Surfaces 78 Pathogen and Toxin Neutralization by Antibodies 79 Affinity and Avidity 80 Cytotoxic T Cells, Also Known as Cytotoxic T Lymphocytes (CTLs) 81 Cytotoxic T Lymphocytes: Critical Defense against Intracellular Pathogens 81 Antigen Presentation to the Immune System 82 Processing of Protein Antigens by Dendritic Cells 82 Interaction between APCs and T Cells: The T-Cell-Dependent Response 84 Th-(Th1/Th2/Th17)-Cell-Mediated Immunity 86 Production of Antibodies by B Cells 87 Links between the Innate and Adaptive Defense Systems 88 T-Cell-Independent Antibody Responses 89 Mucosal Immunity: IgA/sIgA Antibodies 89 Development of the Adaptive Immune System from Infancy to Adulthood 92 Adaptive Defense Systems in Nonmammals 93 The Dark Side of the Adaptive Defenses: Autoimmune Disease 93 Selected Readings 94 Questions 94 Solving Problems in Bacterial Pathogenesis 95 Chapter 5 The Microbiota of the Human Body: Microbiomes and Beyond 98 Importance of the Normal Resident Microbial Populations (Microbiota) of the Human Body 99 Characterization of the Body’s Microbiota 100 Taking a Microbial Census by Using Microbial rRNA Gene Sequence Analysis 101 Characterizing Microbiomes by Using Metagenomic Analysis 115 Beyond the Metagenome 117 Overview of the Human Microbiota 123 Skin Microbiota 124 Oropharyngeal Microbiota 125 Microbiota of the Small Intestine and Colon 125 Microbiota of the Vaginal Tract 128 The Other Microbiota: The Forgotten Eukaryotes 130 Selected Readings 130 Questions 131 Solving Problems in Bacterial Pathogenesis 133 Chapter 6 Microbes and Disease: Establishing a Connection 134 History and Relevance of Koch’s Postulates 136 Early Germ Theory 136 Koch’s Postulates: A Set of Criteria Used to Establish a Microbe-Disease Connection 137 Challenges to Satisfying Koch’s Postulates 138 Easier Said than Done . . .  138 The First Postulate: Association of the Microbe with Lesions of the Disease 139 The Second Postulate: Isolating the Bacterium in Pure Culture 140 The Third Postulate: Showing that the Isolated Bacterium Causes Disease Experimentally in Humans or Animals 141 The Fourth Postulate: Reisolating the Bacterium from the Intentionally Infected Animal 143 Modern Alternatives to Satisfy Koch’s Postulates 143 Detecting the Presence of the Pathogen Only in Diseased Tissues 143 Eliminate the Pathogen and Prevent or Cure the Disease 144 Comparative Infectious Disease Causation 147 The Microbiota Shift Disease Problem 147 Koch’s Postulates and Pathogenic Microbial Communities 147 Keystone Pathogens and Microbial Shift Diseases 147 Molecular Koch’s Postulates 149 Concepts of Disease 150 Varieties of Human-Microbe Interactions 150 Views of the Human-Microbe Interaction 150 Virulence as a Complex Phenomenon 152 Selected Readings 152 Questions 153 Solving Problems in Bacterial Pathogenesis 153 Chapter 7 Mechanisms of Genetic Modification and Exchange: Role in Pathogen Evolution 156 Adapt or Perish 158 Acquiring New Virulence Traits by Horizontal Gene Transfer 158 Mechanisms of Genetic Change and Diversification 158 Spontaneous Mutation 158 Phase Variation 159 Antigenic Variation 161 Horizontal Gene Transfer: Mobile Genetic Elements 162 Natural Transformation 162 Conjugation: Plasmids and Transposons 165 Phage Transduction 171 Control of Horizontal Gene Transfer 171 Toxin-Antitoxin Systems—Retaining the Goods 171 Restriction-Modification Systems—Bacterial Innate Immunity from Foreign DNA 173 CRISPR-Cas Systems—Bacterial Adaptive Immunity from Foreign DNA 173 Type 6 Secretion Systems—Bacterial Defense Against Conjugation 174 Pathogenicity Islands and Pathogen Evolution 174 Properties of Pathogenicity Islands 174 Pathogen Evolution in Quantum Leaps 177 Selected Readings 178 Questions 179 Solving Problems in Bacterial Pathogenesis 179 Chapter 8 Identification of Virulence Factors: Measuring Infectivity and Virulence 182 How Does One Experimentally Measure Virulence and Satisfy Koch’s Postulates? 183 Animal Models of Infection 184 Human Volunteers 184 Nonhuman Animal Models 186 Measuring Bacterial Infection in Animal Models 188 Ethical Considerations 188 Animal Model Basics 188 Survival Curve Analysis and Biophotonic Imaging 189 ID50 and LD50 Values 190 Competition Assays 191 Tissue Culture and Organ Culture Models 192 Tissue Culture Models 192 Gentamicin Protection Assay for Cell Adhesion and Invasion 193 Plaque Assay for Intracellular Survival and Cell-to-Cell Spread 195 Fluorescence Microscopy Techniques for Assessing Effects of Pathogens on Host Cells 196 Organ Culture Models 196 The Continuing Need for Reliable and Plentiful Information about Disease Pathology 197 Selected Readings 198 Questions 199 Solving Problems in Bacterial Pathogenesis 200 Chapter 9 Identification of Virulence Factors: Molecular Approaches for Bacterial Factors 202 Finding a Needle in a Haystack 204 Biochemical Approaches 204 Isolation and Purification of Toxic Factors 204 Molecular Genetic Approaches 208 Screening Using Recombinant Genes 208 Reporter Fusions 208 Mutagenesis Screening 210 Genome-wide Sequencing Approaches for Identifying Virulence Genes 214 Tn-Seq Technology to Identify In Vivo-Expressed Genes 214 RNA-Seq Technology to Identify In Vivo-Expressed Genes 216 Comparative Genomic Sequence Analysis for Identifying Virulence Genes 217 Proteomics Approaches for Identifying Virulence Factors 218 Protein Microarrays (Proteoarrays) 218 In Vivo-Induced Antigen Technology (IVIAT) 218 The Importance of Understanding Bacterial Physiology 219 Selected Readings 222 Questions 223 Solving Problems in Bacterial Pathogenesis 223 Chapter 10 Identification of Virulence Factors: Molecular Approaches for Host Factors 226 Comparative Approaches to Identify Host Factors Required for Infection 227 Transgenic Animal Models 228 In vivo Imaging of Animals during Infection 231 Systems Genetics: Comparative Genomics of the Host Response 231 Screening Approaches to Identify Host Factors Required for Infection 235 Genome-Wide Screening 235 Host Response Profiling to Identify Host Factors Required for Infection 240 Transcriptomics 240 Proteomics 243 Metabolomics 246 The Promise and the Caution 247 Selected Readings 248 Questions 249 Solving Problems in Bacterial Pathogenesis 249 Chapter 11 Bacterial Strategies for Colonization and Survival in the Host 254 What Does Not Kill You Makes You Stronger—Or, a Better Pathogen 255 Preinfection 258 Survival in the External Environment 258 Biofilms 258 Motility and Chemotaxis 260 Colonization of Host Surfaces 263 Penetrating Intact Skin 263 Penetrating the Mucin Layer 263 Evading the Host’s Innate Immunity 264 Nutrient and Iron Acquisition Mechanisms 265 Adherence 268 Evading the Host Immune Response 275 Avoiding Complement and Phagocytosis 277 Invasion and Uptake by Host Cells 280 Surviving Phagocytosis 281 Cell-to-Cell Spread 286 Tissue Penetration and Dissemination 288 Beyond Virulence Factors 288 Selected Readings 289 Questions 290 Solving Problems in Bacterial Pathogenesis 290 Special Global Perspective Problem: Integrating Concepts in Pathogenesis 291 Chapter 12 Toxins and Other Toxic Virulence Factors 294 Bacterial Toxins 295 Transparent Mechanisms, Exciting Applications, Mysterious Purposes 295 Toxin Characteristics and Nomenclature 300 Nonprotein Toxins 302 Peptide and Protein Exotoxins 304 Toxic Effector Proteins of Specialized Secretion Systems 312 Examples of Toxin-Mediated Diseases 313 Diphtheria Toxin 313 Clostridial Neurotoxins 319 Cholera Toxin 323 Toxin-Based Therapeutics and Research Tools 327 Immunotoxins 327 Selected Readings 329 Questions 330 Solving Problems in Bacterial Pathogenesis 331 Chapter 13 Delivery of Virulence Factors 334 Bacterial Secretion Systems and Virulence 335 Common Secretory Systems 336 The General Secretory (Sec) System 336 The Accessory Secretory (Sec) System 336 The Cotranslational Signal-Recognition Particle (SRP) System 336 The Twin-Arginine Transport (TAT) System 337 Secretion Systems Specific to Gram-Negative Bacteria 338 Sec-Dependent Secretion Systems 338 Sec-Independent Secretion Systems 341 Specialized Secretion Systems Specific to Gram-Positive Bacteria 350 General Secretory Transporter Systems in Gram-Positive Bacteria 350 Cytolysin-Mediated Translocation (CMT) in S. pyogenes (Group A Strep) 351 Type 7 Secretion System (T7SS) 352 Selected Readings 353 Questions 354 Solving Problems in Bacterial Pathogenesis 355 Chapter 14 Virulence Regulation 360 Virulence Gene Regulation 361 Mechanisms of Regulation 361 Operons, Regulons, and Global Regulators 362 Activators and Repressors 362 Two-Component Regulatory Systems 364 Sigma Factors 368 Transcriptional Terminators and Antiterminators 369 Regulation of Translation Initiation 372 Regulatory Small RNAs 372 Bacterial Chromatin 375 Responding to Environmental Signals 376 Phase Variation and Bistable Switches 376 Hypermutability, Intragenomic Recombination, and Positive Selection 377 Coordinate Virulence Regulation 377 Quorum Sensing 378 Chemotaxis 387 Selected Readings 389 Questions 389 Solving Problems in Bacterial Pathogenesis 390 Special Global Perspective Problems: Integrating Concepts in Pathogenesis 395 Chapter 15 Antimicrobial Compounds and Their Targets 400 Antimicrobial Compounds: The Safety Net of Modern Medicine 401 The Importance of Antimicrobial Compounds 401 Avoiding, Reducing, and Preventing Exposure 402 Killing versus Inhibiting Growth 404 Tests Used to Assess Antibiotics 404 Antiseptics and Disinfectants 405 Antibiotics 407 Characteristics of Antibiotics 407 The Process of Antibiotic Discovery 409 The Economics of Antibiotic Discovery 413 Mechanisms of Antibiotic Action 416 Targets of Antibiotic Action 416 Cell Wall Synthesis Inhibitors 417 Protein Synthesis Inhibitors 422 Antibiotics That Target DNA and RNA Synthesis 425 Inhibitors of Tetrahydrofolate Biosynthesis 429 The Newest Antibiotics 429 The Newest Antibiotic Targets 430 Strategies for Enhancing Antibiotic Efficacy 431 The Continuing Challenge 432 Selected Readings 433 Questions 434 Solving Problems in Bacterial Pathogenesis 435 Chapter 16 Antibiotic Resistance 436 The Dawning of Awareness—Uh, We Have a Problem! 437 How Did We Get to Where We Are? 438 And Now the Really Scary Part . . . 440 Emergence and Challenge of Multidrug Resistance (MDR) 440 Multiple Resistance and Genetic Linkage 441 Next-Generation MDR Pathogens: The “Superbugs”! 441 Mechanisms of Antibiotic Resistance 444 Overview of Resistance Mechanisms 444 Resistance to Antiseptics and Disinfectants 444 Limiting Access of the Antibiotic 445 Enzymatic Inactivation of the Antibiotic 446 Modification or Protection of the Antibiotic Target 451 Failure to Activate an Antibiotic 453 Regulation of Resistance Genes 454 Antibiotic Tolerance and Persister Cells 457 Antibiotic Tolerance 457 Persistence 459 Toxin-Antitoxin Systems 459 Horizontal Gene Transfer (HGT) of Resistance Genes 461 Propagating and Maintaining Antibiotic Resistance through Selective Pressure and Changes in Fitness 463 Will We Return to the Pre-Antibiotic Era? 464 Returning to Status Quo or Moving Forward? 464 The Hunt for Alternative Approaches to Antibiotics 466 Selected Readings 468 Questions 469 Solving Problems in Bacterial Pathogenesis 470 Special Global Perspective Problems: Integrating Concepts in Pathogenesis 470 Chapter 17 Vaccination: A Critical Component of the Modern Medical Armamentarium 476 Vaccines: A Major Health Care Bargain 477 What Makes an Ideal Vaccine? 479 Immunization Programs 480 Barriers to Implementation and Success of Immunization Programs 483 The Antivaccination Movement 484 Vaccine Success Stories 485 Subunit Vaccines 485 Conjugate Vaccines 490 Vaccine “Less-than-Success” Stories 492 A New Age of Vaccine Development: Making Vaccines Better 494 Approaches to Enhancing Immunogenicity 494 Adjuvants 494 Programming Adaptive Immunity 496 Targeting Mucosal Immunity 500 Storage of Vaccines—Strategies to Increase Shelf Life 504 Passive Immunization 504 Selected Readings 505 Questions 505 Solving Problems in Bacterial Pathogenesis 508 Special Global Perspective Problems: Integrating Concepts in Pathogenesis 510 Chapter 18 The Gram-Positive Opportunistic Pathogens 514 What Is an Opportunist? 515 Characteristics of Gram-Positive Opportunists 516 Notable Gram-Positive Opportunists 516 Staphylococcus aureus—Commensal Ready for a Fight 516 Staphylococcus epidermidis—Accidental Pathogen 524 Streptococcus pneumoniae—“Captain of All the Men of Death” 527 Clostridium difficile—True Opportunist 534 Other Gram-Positive Opportunists 542 Selected Readings 543 Questions 544 Solving Problems in Bacterial Pathogenesis 544 Chapter 19 The Gram-Negative Opportunistic Pathogens 548 Jumping Over the (Cell) Wall: Gram-Negative Bacteria Can Be Opportunistic Pathogens Too! 549 Common Traits of Gram-Negative Opportunists 549 The Dark Side of Some Residents of the Human Body 550 The Ever-Changing Face of E. coli 550 Klebsiella pneumoniae Nosocomial Infections 554 Bacteroides fragilis—The Bad Sheep of the Family 555 Porphyromonas gingivalis—A Keystone Pathogen 557 Environmental Inhabitants Weigh in as Opportunists 558 Pseudomonas aeruginosa—A Versatile Opportunist of the Highest Order 558 Burkholderia cepacia Complex—P. aeruginosa’s Evil Twin 565 Acinetobacter baumannii—A Deadly Threat Emerges from the Iraq War 565 Don’t Forget the Arthropods! 567 Ehrlichia spp. 567 Selected Readings 568 Questions 569 Solving Problems in Bacterial Pathogenesis 569 Special Global Perspective Problems: Integrating Concepts in Pathogenesis 570 Chapter 20 The Changing Roles of Microbiologists in an Age of Bioterrorism and Emerging Diseases 574 When Microbiologists Are Called to the Front Line 575 Tracking Down a Bioterrorist 576 Unintentional or Deliberate? 577 Timing 579 Tracing the Source 579 Lessons Learned 579 The “Top Four” Bioterror Agents 582 Bacillus anthracis Spores 582 Smallpox 583 Yersinia pestis 583 Botulinum Neurotoxin 584 What If Bioterrorists Hit Us with Something Completely New? 585 Biosecurity in a Complex, Dynamic, and Ever-Changing World 585 Food Safety and Biosecurity 586 The Case for Food Irradiation 587 The Future of Biosecurity 589 Selected Readings 589 Questions 590 Solving Problems in Bacterial Pathogenesis 591 Glossary 593 Index 661