| Preface |
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xvii | |
| In Memoriam |
|
xix | |
| About the Authors |
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xxi | |
| Chapter 1 The Power of Bacteria |
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2 | (20) |
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Why Are Bacteria So Much in the Public Health Spotlight Nowadays? |
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3 | (1) |
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Bacteria, a Formidable Ancient Life Form |
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4 | (2) |
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Pressing Current Infectious Disease Issues |
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6 | (4) |
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Emerging and Reemerging Infectious Diseases |
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6 | (1) |
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Foodborne and Waterborne Infections |
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7 | (1) |
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Modern Medicine as a Source of New Diseases |
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8 | (1) |
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Postsurgical and Other Wound Infections |
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9 | (1) |
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10 | (1) |
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A New Respect for Prevention |
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10 | (2) |
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Surveillance: An Early Warning System |
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11 | (1) |
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Making Hospitals Safe for Patients |
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12 | (1) |
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And Now for Some Good News: You've Got a Bacterial Infection! |
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12 | (2) |
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The Helicobacter pylori Revolution |
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12 | (1) |
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13 | (1) |
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Microbiota Shift Diseases |
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13 | (1) |
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A Brave New World of Pathogenesis Research |
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14 | (4) |
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16 | (1) |
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Insights into Pathogen Evolution |
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17 | (1) |
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Modeling the Host-Pathogen Interaction in Experimental Animals |
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17 | (1) |
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18 | (1) |
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18 | (2) |
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20 | (2) |
| Chapter 2 Skin and Mucosa: The First Lines of Defense against Bacterial Infections |
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22 | (18) |
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The Best Defense: Avoid, Reduce, and Prevent Exposure! |
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23 | (1) |
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Barriers: Skin and Mucosal Membranes |
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24 | (13) |
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The Layers of Cells That Protect the Body |
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24 | (3) |
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Normal Microbiota of the Skin and Mucosa |
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27 | (4) |
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31 | (1) |
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Defenses of Mucosal Surfaces |
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32 | (2) |
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Special Defenses of the Gastrointestinal Tract |
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34 | (2) |
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Special Defenses of the Urogenital Tract |
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36 | (1) |
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Special Defenses of the Respiratory Tract |
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36 | (1) |
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Immune Defenses of the Skin and Mucosa |
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37 | (1) |
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Models for Studying Breaches of Barrier Defenses |
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38 | (1) |
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39 | (1) |
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39 | (1) |
| Chapter 3 The Innate Immune System: Always on Guard |
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40 | (32) |
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Triggering Innate Immune Defenses |
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41 | (1) |
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Innate Immune Cells That Defend Blood and Tissue |
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42 | (8) |
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42 | (1) |
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Monocytes, Macrophages, and Dendritic Cells (DCs) |
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42 | (5) |
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Granulocytes: Basophils, Mast Cells, and Eosinophils |
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47 | (1) |
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Transmigration-How Do Phagocytes Know When and Where to Go? |
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47 | (1) |
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Natural Killer (NK) Cells |
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48 | (2) |
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50 | (1) |
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How Phagocytes Recognize and Respond to Bacteria |
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50 | (4) |
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How Phagocytes Kill Bacteria |
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54 | (3) |
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Oxidative Burst in Phagolysosomes |
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54 | (2) |
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Autophagy-Another Pathway for the Killing of Intracellular Pathogens |
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56 | (1) |
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57 | (6) |
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57 | (1) |
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Overview of Complement Pathways and Their Function |
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58 | (2) |
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Steps in Complement Activation |
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60 | (2) |
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Controlling Complement Activation |
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62 | (1) |
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Cytokines and Chemokines-Mediators of Immune Responses |
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63 | (3) |
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Roles of Cytokines and Chemokines in Directing Innate Immune Responses |
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63 | (2) |
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Inflammation and Collateral Damage |
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65 | (1) |
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Septic Shock: The Dark Side of the Innate Defenses |
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66 | (3) |
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Other Innate Defenses of the Body-Nutritional Immunity |
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69 | (1) |
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70 | (1) |
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70 | (2) |
| Chapter 4 The Adaptive Defenses: Antibodies and Cytotoxic T Cells |
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72 | (26) |
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The Specialists: Adapting to a Particular Pathogen Challenge |
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73 | (1) |
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B Cells: Producers of Antibodies |
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74 | (7) |
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The Humoral (Antibody) Immune Response |
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74 | (1) |
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Characteristics of Antibodies and Their Diverse Roles in Preventing Infection |
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74 | (2) |
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76 | (2) |
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Secretory Antibodies: Antibodies That Protect Mucosal Surfaces |
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78 | (1) |
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Pathogen and Toxin Neutralization by Antibodies |
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79 | (1) |
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80 | (1) |
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Cytotoxic T Cells, Also Known as Cytotoxic T Lymphocytes (CTLs) |
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81 | (1) |
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Cytotoxic T Lymphocytes: Critical Defense against Intracellular Pathogens |
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81 | (1) |
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Antigen Presentation to the Immune System |
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82 | (6) |
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Processing of Protein Antigens by Dendritic Cells |
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82 | (2) |
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Interaction between APCs and T Cells: The T-Cell-Dependent Response |
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84 | (2) |
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Th-(Th1/Th2/Th17)-Cell-Mediated Immunity |
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86 | (1) |
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Production of Antibodies by B Cells |
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87 | (1) |
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Links between the Innate and Adaptive Defense Systems |
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88 | (1) |
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T-Cell-Independent Antibody Responses |
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89 | (1) |
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Mucosal Immunity: IgA/sIgA Antibodies |
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89 | (3) |
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Development of the Adaptive Immune System from Infancy to Adulthood |
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92 | (1) |
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Adaptive Defense Systems in Nonmammals |
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93 | (1) |
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The Dark Side of the Adaptive Defenses: Autoimmune Disease |
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93 | (1) |
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94 | (1) |
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94 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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95 | (3) |
| Chapter 5 The Microbiota of the Human Body: Microbiomes and Beyond |
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98 | (36) |
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Importance of the Normal Resident Microbial Populations (Microbiota) of the Human Body |
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99 | (1) |
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Characterization of the Body's Microbiota |
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100 | (23) |
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Taking a Microbial Census by Using Microbial rRNA Gene Sequence Analysis |
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101 | (14) |
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Characterizing Microbiomes by Using Metagenomic Analysis |
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115 | (2) |
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117 | (6) |
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Overview of the Human Microbiota |
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123 | (7) |
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124 | (1) |
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125 | (1) |
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Microbiota of the Small Intestine and Colon |
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125 | (3) |
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Microbiota of the Vaginal Tract |
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128 | (2) |
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The Other Microbiota: The Forgotten Eukaryotes |
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130 | (1) |
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130 | (1) |
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131 | (2) |
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Solving Problems in Bacterial Pathogenesis |
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133 | (1) |
| Chapter 6 Microbes and Disease: Establishing a Connection |
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134 | (22) |
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History and Relevance of Koch's Postulates |
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136 | (2) |
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136 | (1) |
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Koch's Postulates: A Set of Criteria Used To Establish a Microbe-Disease Connection |
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137 | (1) |
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Challenges to Satisfying Koch's Postulates |
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138 | (5) |
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138 | (1) |
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The First Postulate: Association of the Microbe with Lesions of the Disease |
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139 | (1) |
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The Second Postulate: Isolating the Bacterium in Pure Culture |
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140 | (1) |
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The Third Postulate: Showing that the Isolated Bacterium Causes Disease Experimentally in Humans or Animals |
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141 | (2) |
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The Fourth Postulate: Reisolating the Bacterium from the Intentionally Infected Animal |
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143 | (1) |
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Modern Alternatives To Satisfy Koch's Postulates |
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143 | (4) |
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Detecting the Presence of the Pathogen Only in Diseased Tissues |
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143 | (1) |
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Eliminate the Pathogen and Prevent or Cure the Disease |
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144 | (3) |
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Comparative Infectious Disease Causation |
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147 | (1) |
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The Microbiota Shift Disease Problem |
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147 | (2) |
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Koch's Postulates and Pathogenic Microbial Communities |
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147 | (1) |
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Keystone Pathogens and Microbial Shift Diseases |
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147 | (2) |
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Molecular Koch's Postulates |
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149 | (1) |
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150 | (2) |
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Varieties of Human-Microbe Interactions |
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150 | (1) |
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Views of the Human-Microbe Interaction |
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150 | (2) |
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Virulence as a Complex Phenomenon |
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152 | (1) |
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152 | (1) |
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153 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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153 | (3) |
| Chapter 7 Mechanisms of Genetic Modification and Exchange: Role in Pathogen Evolution |
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156 | (26) |
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158 | (1) |
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Acquiring New Virulence Traits by Horizontal Gene Transfer |
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158 | (1) |
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Mechanisms of Genetic Change and Diversification |
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158 | (4) |
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158 | (1) |
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159 | (2) |
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161 | (1) |
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Horizontal Gene Transfer: Mobile Genetic Elements |
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162 | (9) |
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162 | (3) |
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Conjugation: Plasmids and Transposons |
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165 | (6) |
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171 | (1) |
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Control of Horizontal Gene Transfer |
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171 | (3) |
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Toxin-Antitoxin Systems-Retaining the Goods |
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171 | (2) |
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Restriction-Modification Systems-Bacterial Innate Immunity from Foreign DNA |
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173 | (1) |
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CRISPR-Cas Systems-Bacterial Adaptive Immunity from Foreign DNA |
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173 | (1) |
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Type 6 Secretion Systems-Bacterial Defense Against Conjugation |
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174 | (1) |
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Pathogenicity Islands and Pathogen Evolution |
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174 | (4) |
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Properties of Pathogenicity Islands |
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174 | (3) |
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Pathogen Evolution in Quantum Leaps |
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177 | (1) |
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178 | (1) |
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179 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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179 | (3) |
| Chapter 8 Identification of Virulence Factors: Measuring Infectivity and Virulence |
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182 | (20) |
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How Does One Experimentally Measure Virulence and Satisfy Koch's Postulates? |
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183 | (1) |
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Animal Models of Infection |
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184 | (4) |
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184 | (2) |
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186 | (2) |
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Measuring Bacterial Infection in Animal Models |
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188 | (4) |
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188 | (1) |
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188 | (1) |
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Survival Curve Analysis and Biophotonic Imaging |
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189 | (1) |
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190 | (1) |
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191 | (1) |
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Tissue Culture and Organ Culture Models |
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192 | (5) |
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192 | (1) |
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Gentamicin Protection Assay for Cell Adhesion and Invasion |
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193 | (2) |
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Plaque Assay for Intracellular Survival and Cell-to-Cell Spread |
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195 | (1) |
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Fluorescence Microscopy Techniques for Assessing Effects of Pathogens on Host Cells |
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196 | (1) |
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196 | (1) |
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The Continuing Need for Reliable and Plentiful Information about Disease Pathology |
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197 | (1) |
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198 | (1) |
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199 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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200 | (2) |
| Chapter 9 Identification of Virulence Factors: Molecular Approaches for Bacterial Factors |
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202 | (24) |
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Finding a Needle in a Haystack |
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204 | (1) |
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204 | (4) |
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Isolation and Purification of Toxic Factors |
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204 | (4) |
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Molecular Genetic Approaches |
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208 | (6) |
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Screening Using Recombinant Genes |
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208 | (1) |
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208 | (2) |
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210 | (4) |
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Genome-wide Sequencing Approaches for Identifying Virulence Genes |
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214 | (4) |
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Tn-Seq Technology to Identify In Vivo-Expressed Genes |
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214 | (2) |
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RNA-Seq Technology to Identify In Vivo-Expressed Genes |
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216 | (1) |
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Comparative Genomic Sequence Analysis for Identifying Virulence Genes |
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217 | (1) |
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Proteomics Approaches for Identifying Virulence Factors |
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218 | (1) |
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Protein Microarrays (Proteoarrays) |
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218 | (1) |
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In Vivo-Induced Antigen Technology (IVIAT) |
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218 | (1) |
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The Importance of Understanding Bacterial Physiology |
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219 | (3) |
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222 | (1) |
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223 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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223 | (3) |
| Chapter 10 Identification of Virulence Factors: Molecular Approaches for Host Factors |
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226 | (28) |
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Comparative Approaches to Identify Host Factors Required for Infection |
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227 | (8) |
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228 | (3) |
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In vivo Imaging of Animals during Infection |
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231 | (1) |
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Systems Genetics: Comparative Genomics of the Host Response |
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231 | (4) |
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Screening Approaches to Identify Host Factors Required for Infection |
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235 | (5) |
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235 | (5) |
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Host Response Profiling to Identify Host Factors Required for Infection |
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240 | (7) |
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240 | (3) |
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243 | (3) |
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246 | (1) |
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The Promise and the Caution |
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247 | (1) |
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248 | (1) |
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249 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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249 | (5) |
| Chapter 11 Bacterial Strategies for Colonization and Survival in the Host |
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254 | (40) |
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What Does Not Kill You Makes You Stronger-Or, a Better Pathogen |
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255 | (3) |
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258 | (5) |
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Survival in the External Environment |
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258 | (1) |
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258 | (2) |
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260 | (3) |
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Colonization of Host Surfaces |
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263 | (12) |
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263 | (1) |
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Penetrating the Mucin Layer |
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263 | (1) |
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Evading the Host's Innate Immunity |
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264 | (1) |
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Nutrient and Iron Acquisition Mechanisms |
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265 | (3) |
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268 | (7) |
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Evading the Host Immune Response |
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275 | (14) |
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Avoiding Complement and Phagocytosis |
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277 | (3) |
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Invasion and Uptake by Host Cells |
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280 | (1) |
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281 | (5) |
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286 | (2) |
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Tissue Penetration and Dissemination |
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288 | (1) |
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288 | (1) |
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289 | (1) |
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290 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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290 | (1) |
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Special Global Perspective Problem: Integrating Concepts in Pathogenesis |
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291 | (3) |
| Chapter 12 Toxins and Other Toxic Virulence Factors |
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294 | (40) |
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295 | (18) |
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Transparent Mechanisms, Exciting Applications, Mysterious Purposes |
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295 | (5) |
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Toxin Characteristics and Nomenclature |
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300 | (2) |
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302 | (2) |
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Peptide and Protein Exotoxins |
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304 | (8) |
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Toxic Effector Proteins of Specialized Secretion Systems |
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312 | (1) |
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Examples of Toxin-Mediated Diseases |
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313 | (14) |
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313 | (6) |
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319 | (4) |
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323 | (4) |
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Toxin-Based Therapeutics and Research Tools |
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327 | (2) |
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327 | (2) |
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329 | (1) |
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330 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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331 | (3) |
| Chapter 13 Delivery of Virulence Factors |
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334 | (26) |
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Bacterial Secretion Systems and Virulence |
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335 | (1) |
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336 | (2) |
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The General Secretory (Sec) System |
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336 | (1) |
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The Accessory Secretory (Sec) System |
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336 | (1) |
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The Cotranslational Signal-Recognition Particle (SRP) System |
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336 | (1) |
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The Twin-Arginine Transport (TAT) System |
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337 | (1) |
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Secretion Systems Specific to Gram-Negative Bacteria |
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338 | (12) |
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Sec-Dependent Secretion Systems |
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338 | (3) |
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Sec-Independent Secretion Systems |
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341 | (9) |
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Specialized Secretion Systems Specific to Gram-Positive Bacteria |
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350 | (3) |
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General Secretory Transporter Systems in Gram-Positive Bacteria |
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350 | (1) |
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Cytolysin-Mediated Translocation (CMT) in S. pyogenes (Group A Strep) |
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351 | (1) |
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Type 7 Secretion System (T7SS) |
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352 | (1) |
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353 | (1) |
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354 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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355 | (5) |
| Chapter 14 Virulence Regulation |
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360 | (40) |
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Virulence Gene Regulation |
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361 | (1) |
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361 | (15) |
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Operons, Regulons, and Global Regulators |
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362 | (1) |
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Activators and Repressors |
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362 | (2) |
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Two-Component Regulatory Systems |
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364 | (4) |
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368 | (1) |
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Transcriptional Terminators and Antiterminators |
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369 | (3) |
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Regulation of Translation Initiation |
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372 | (1) |
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372 | (3) |
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375 | (1) |
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Responding to Environmental Signals |
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376 | (13) |
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Phase Variation and Bistable Switches |
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376 | (1) |
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Hypermutability, Intragenomic Recombination, and Positive Selection |
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377 | (1) |
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Coordinate Virulence Regulation |
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377 | (1) |
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378 | (9) |
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387 | (2) |
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389 | (1) |
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389 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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390 | (5) |
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Special Global Perspective Problems: Integrating Concepts in Pathogenesis |
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395 | (5) |
| Chapter 15 Antimicrobial Compounds and Their Targets |
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400 | (36) |
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Antimicrobial Compounds: The Safety Net of Modern Medicine |
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401 | (4) |
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The Importance of Antimicrobial Compounds |
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401 | (1) |
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Avoiding, Reducing, and Preventing Exposure |
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402 | (2) |
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Killing versus Inhibiting Growth |
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404 | (1) |
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Tests Used To Assess Antibiotics |
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404 | (1) |
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Antiseptics and Disinfectants |
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405 | (2) |
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407 | (9) |
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Characteristics of Antibiotics |
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407 | (2) |
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The Process of Antibiotic Discovery |
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409 | (4) |
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The Economics of Antibiotic Discovery |
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413 | (3) |
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Mechanisms of Antibiotic Action |
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416 | (16) |
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Targets of Antibiotic Action |
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416 | (1) |
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Cell Wall Synthesis Inhibitors |
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417 | (5) |
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Protein Synthesis Inhibitors |
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422 | (3) |
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Antibiotics That Target DNA and RNA Synthesis |
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425 | (4) |
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Inhibitors of Tetrahydrofolate Biosynthesis |
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429 | (1) |
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429 | (1) |
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The Newest Antibiotic Targets |
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430 | (1) |
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Strategies for Enhancing Antibiotic Efficacy |
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431 | (1) |
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432 | (1) |
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433 | (1) |
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434 | (1) |
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Solving Problems in Bacterial Pathogenesis |
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435 | (1) |
| Chapter 16 Antibiotic Resistance |
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436 | (40) |
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The Dawning of Awareness-Uh, We Have a Problem! |
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437 | (1) |
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How Did We Get to Where We Are? |
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438 | (2) |
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And Now the Really Scary Part |
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440 | (4) |
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Emergence and Challenge of Multidrug Resistance (MDR) |
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440 | (1) |
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Multiple Resistance and Genetic Linkage |
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441 | (1) |
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Next-Generation MDR Pathogens: The "Superbugs"! |
|
|
441 | (3) |
|
Mechanisms of Antibiotic Resistance |
|
|
444 | (13) |
|
Overview of Resistance Mechanisms |
|
|
444 | (1) |
|
Resistance to Antiseptics and Disinfectants |
|
|
444 | (1) |
|
Limiting Access of the Antibiotic |
|
|
445 | (1) |
|
Enzymatic Inactivation of the Antibiotic |
|
|
446 | (5) |
|
Modification or Protection of the Antibiotic Target |
|
|
451 | (2) |
|
Failure to Activate an Antibiotic |
|
|
453 | (1) |
|
Regulation of Resistance Genes |
|
|
454 | (3) |
|
Antibiotic Tolerance and Persister Cells |
|
|
457 | (4) |
|
|
|
457 | (2) |
|
|
|
459 | (1) |
|
|
|
459 | (2) |
|
Horizontal Gene Transfer (HGT) of Resistance Genes |
|
|
461 | (2) |
|
Propagating and Maintaining Antibiotic Resistance through Selective Pressure and Changes in Fitness |
|
|
463 | (1) |
|
Will We Return to the Pre-Antibiotic Era? |
|
|
464 | (4) |
|
Returning to Status Quo or Moving Forward? |
|
|
464 | (2) |
|
The Hunt for Alternative Approaches to Antibiotics |
|
|
466 | (2) |
|
|
|
468 | (1) |
|
|
|
469 | (1) |
|
Solving Problems in Bacterial Pathogenesis |
|
|
470 | (1) |
|
Special Global Perspective Problems: Integrating Concepts in Pathogenesis |
|
|
470 | (6) |
| Chapter 17 Vaccination: A Critical Component of the Modern Medical Armamentarium |
|
476 | (38) |
|
Vaccines: A Major Health Care Bargain |
|
|
477 | (2) |
|
What Makes an Ideal Vaccine? |
|
|
479 | (1) |
|
|
|
480 | (5) |
|
Barriers to Implementation and Success of Immunization Programs |
|
|
483 | (1) |
|
The Antivaccination Movement |
|
|
484 | (1) |
|
|
|
485 | (7) |
|
|
|
485 | (5) |
|
|
|
490 | (2) |
|
Vaccine "Less-than-Success" Stories |
|
|
492 | (2) |
|
A New Age of Vaccine Development: Making Vaccines Better |
|
|
494 | (10) |
|
Approaches to Enhancing Immunogenicity |
|
|
494 | (1) |
|
|
|
494 | (2) |
|
Programming Adaptive Immunity |
|
|
496 | (4) |
|
Targeting Mucosal Immunity |
|
|
500 | (4) |
|
Storage of Vaccines-Strategies to Increase Shelf Life |
|
|
504 | (1) |
|
|
|
504 | (1) |
|
|
|
505 | (1) |
|
|
|
505 | (3) |
|
Solving Problems in Bacterial Pathogenesis |
|
|
508 | (2) |
|
Special Global Perspective Problems: Integrating Concepts in Pathogenesis |
|
|
510 | (4) |
| Chapter 18 The Gram-Positive Opportunistic Pathogens |
|
514 | (34) |
|
|
|
515 | (1) |
|
Characteristics of Gram-Positive Opportunists |
|
|
516 | (1) |
|
Notable Gram-Positive Opportunists |
|
|
516 | (26) |
|
Staphylococcus aureus-Commensal Ready for a Fight |
|
|
516 | (8) |
|
Staphylococcus epidermidis-Accidental Pathogen |
|
|
524 | (3) |
|
Streptococcus pneumoniae-"Captain of All the Men of Death" |
|
|
527 | (7) |
|
Clostridium difficile-True Opportunist |
|
|
534 | (8) |
|
Other Gram-Positive Opportunists |
|
|
542 | (1) |
|
|
|
543 | (1) |
|
|
|
544 | (1) |
|
Solving Problems in Bacterial Pathogenesis |
|
|
544 | (4) |
| Chapter 19 The Gram-Negative Opportunistic Pathogens |
|
548 | (26) |
|
Jumping Over the (Cell) Wall: Gram-Negative Bacteria Can Be Opportunistic Pathogens Too! |
|
|
549 | (1) |
|
Common Traits of Gram-Negative Opportunists |
|
|
549 | (1) |
|
The Dark Side of Some Residents of the Human Body |
|
|
550 | (8) |
|
The Ever-Changing Face of E. coli |
|
|
550 | (4) |
|
Klebsiella pneumoniae Nosocomial Infections |
|
|
554 | (1) |
|
Bacteroides fragilis-The Bad Sheep of the Family |
|
|
555 | (2) |
|
Porphyromonas gingivalis-A Keystone Pathogen |
|
|
557 | (1) |
|
Environmental Inhabitants Weigh in as Opportunists |
|
|
558 | (9) |
|
Pseudomonas aeruginosa-A Versatile Opportunist of the Highest Order |
|
|
558 | (7) |
|
Burkholderia cepacia Complex-P. aeruginosa's Evil Twin |
|
|
565 | (1) |
|
Acinetobacter baumannii-A Deadly Threat Emerges from the Iraq War |
|
|
565 | (2) |
|
Don't Forget the Arthropods! |
|
|
567 | (1) |
|
|
|
567 | (1) |
|
|
|
568 | (1) |
|
|
|
569 | (1) |
|
Solving Problems in Bacterial Pathogenesis |
|
|
569 | (1) |
|
Special Global Perspective Problems: Integrating Concepts in Pathogenesis |
|
|
570 | (4) |
| Chapter 20 The Changing Roles of Microbiologists in an Age of Bioterrorism and Emerging Diseases |
|
574 | (19) |
|
When Microbiologists Are Called to the Front Line |
|
|
575 | (1) |
|
Tracking Down a Bioterrorist |
|
|
576 | (3) |
|
Unintentional or Deliberate? |
|
|
577 | (2) |
|
|
|
579 | (1) |
|
|
|
579 | (1) |
|
|
|
579 | (3) |
|
The "Top Four" Bioterror Agents |
|
|
582 | (3) |
|
Bacillus anthraces Spores |
|
|
582 | (1) |
|
|
|
583 | (1) |
|
|
|
583 | (1) |
|
|
|
584 | (1) |
|
What If Bioterrorists Hit Us with Something Completely New? |
|
|
585 | (1) |
|
Biosecurity in a Complex, Dynamic, and Ever-Changing World |
|
|
585 | (1) |
|
Food Safety and Biosecurity |
|
|
586 | (3) |
|
The Case for Food Irradiation |
|
|
587 | (2) |
|
The Future of Biosecurity |
|
|
589 | (1) |
|
|
|
589 | (1) |
|
|
|
590 | (1) |
|
Solving Problems in Bacterial Pathogenesis |
|
|
591 | (2) |
| Glossary |
|
593 | (68) |
| Index |
|
661 | |
Lisainfo e-raamatute kohta