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CONTENTS Preface xv To the Student xxv PART I Introduction to Microbiology 1 The History and Scope of Microbiology 1 1.1 The Discovery of Microorganisms 2 1.2 The Conflict over Spontaneous Generation 2 1.3 The Role of Microorganisms in Disease 7 Recognition of the Relationship between Microorganisms and Disease 7 The Development of Techniques for Studying Microbial Pathogens 8 Immunological Studies 9 1.4 Industrial Microbiology and Microbial Ecology 10 1.5 Members of the Microbial World 11 1.6 The Scope and Relevance of Microbiology 11 1.7 The Future of Microbiology 13 2 The Study of Microbial Structure: Microscopy and Specimen Preparation 17 2.1 Lenses and the Bending of Light 18 2.2 The Light Microscope 19 The Bright-Field Microscope 19 Microscope Resolution 20 The Dark-Field Microscope 21 The Phase-Contrast Microscope 22 The Differential Interference Contrast Microscope 25 The Fluorescence Microscope 25 2.3 Preparation and Staining of Specimens 27 Fixation 27 Dyes and Simple Staining 27 Differential Staining 28 Staining Specific Structures 28 2.4 Electron Microscopy 30 The Transmission Electron Microscope 30 Specimen Preparation 32 The Scanning Electron Microscope 34 2.5 Newer Techniques in Microscopy 36 Confocal Microscopy 36 Scanning Probe Microscopy 38 3 Procaryotic Cell Structure and Function 41 3.1 An Overview of Procaryotic Cell Structure 42 Size, Shape, and Arrangement 42 Procaryotic Cell Organization 45 3.2 Procaryotic Cell Membranes 46 The Plasma Membrane 46 Internal Membrane Systems 48 3.3 The Cytoplasmic Matrix 49 Inclusion Bodies 49 Ribosomes 52 3.4 The Nucleoid 54 3.5 The Procaryotic Cell Wall 55 Peptidoglycan Structure 56 Gram-Positive Cell Walls 56 Gram-Negative Cell Walls 58 The Mechanism of Gram Staining 60 The Cell Wall and Osmotic Protection 61 3.6 Components External to the Cell Wall 61 Capsules, Slime Layers, and S-Layers 61 Pili and Fimbriae 62 Flagella and Motility 63 3.7 Chemotaxis 66 3.8 The Bacterial Endospore 68 4 Eucaryotic Cell Structure and Function 74 4.1 An Overview of Eucaryotic Cell Structure 76 4.2 The Cytoplasmic Matrix, Microfilaments, Intermediate Filaments, and Microtubules 76 4.3 The Endoplasmic Reticulum 79 4.4 The Golgi Apparatus 80 4.5 Lysosomes and Endocytosis 80 4.6 Eucaryotic Ribosomes 82 4.7 Mitochondria 83 4.8 Chloroplasts 85 4.9 The Nucleus and Cell Division 86 Nuclear Structure 86 The Nucleolus 87 Mitosis and Meiosis 87 4.10 External Cell Coverings 88 4.11 Cilia and Flagella 89 4.12 Comparison of Procaryotic and Eucaryotic Cells 91 PART II Microbial Nutrition, Growth, and Control 5 Microbial Nutrition 95 5.1 The Common Nutrient Requirements 96 5.2 Requirements for Carbon, Hydrogen, and Oxygen 96 5.3 Nutritional Types of Microorganisms 97 5.4 Requirements for Nitrogen, Phosphorus, and Sulfur 98 5.5 Growth Factors 98 5.6 Uptake of Nutrients by the Cell 100 Facilitated Diffusion 100 Active Transport 101 Group Translocation 103 Iron Uptake 104 5.7 Culture Media 104 Synthetic or Defined Media 104 Complex Media 105 Types of Media 105 5.8 Isolation of Pure Cultures 106 The Spread Plate and Streak Plate 106 The Pour Plate 107 Colony Morphology and Growth 108 6 Microbial Growth 112 6.1 The Growth Curve 113 Lag Phase 113 Exponential Phase 114 Stationary Phase 114 Death Phase 115 The Mathematics of Growth 115 6.2 Measurement of Microbial Growth 117 Measurement of Cell Numbers 117 Measurement of Cell Mass 119 6.3 The Continuous Culture of Microorganisms 120 The Chemostat 120 The Turbidostat 121 6.4 The Influence of Environmental Factors on Growth 121 Solutes and Water Activity 121 pH 123 Temperature 125 Oxygen Concentration 127 Pressure 129 Radiation 130 6.5 Microbial Growth in Natural Environments 131 Growth Limitation by Environmental Factors 131 Counting Viable But Nonculturable Vegetative Procaryotes 132 Quorum Sensing and Microbial Populations 132 7 Control of Microorganisms by Physical and Chemical Agents 136 7.1 Definition of Frequently Used Terms 137 7.2 The Pattern of Microbial Death 138 7.3 Conditions Influencing the Effectiveness of Antimicrobial Agent Activity 139 7.4 The Use of Physical Methods in Control 139 Heat 139 Low Temperatures 142 Filtration 142 Radiation 144 7.5 The Use of Chemical Agents in Control 145 Phenolics 145 Alcohols 147 Halogens 147 Heavy Metals 148 Quaternary Ammonium Compounds 148 Aldehydes 148 Sterilizing Gases 148 7.6 Evaluation of Antimicrobial Agent Effectiveness 149 PART III Microbial Metabolism 8 Metabolism: Energy, Enzymes, and Regulation 153 8.1 Energy and Work 154 8.2 The Laws of Thermodynamics 155 8.3 Free Energy and Reactions 156 8.4 The Role of ATP in Metabolism 157 8.5 Oxidation-Reduction Reactions and Electron Carriers 157 8.6 Enzymes 161 Structure and Classification of Enzymes 161 The Mechanism of Enzyme Reactions 161 The Effect of Environment on Enzyme Activity 162 Enzyme Inhibition 164 8.7 The Nature and Significance of Metabolic Regulation 164 8.8 Metabolic Channeling 165 8.9 Control of Enzyme Activity 165 Allosteric Regulation 165 Covalent Modification of Enzymes 167 Feedback Inhibition 169 9 Metabolism: Energy Release and Conservation 172 9.1 An Overview of Metabolism 173 9.2 The Breakdown of Glucose to Pyruvate 176 The Glycolytic Pathway 176 The Pentose Phosphate Pathway 177 The Entner-Doudoroff Pathway 179 9.3 Fermentations 179 9.4 The Tricarboxylic Acid Cycle 183 9.5 Electron Transport and Oxidative Phosphorylation 184 The Electron Transport Chain 184 Oxidative Phosphorylation 187 The Yield of ATP in Glycolysis and Aerobic Respiration 189 9.6 Anaerobic Respiration 190 9.7 Catabolism of Carbohydrates and Intracellular Reserve Polymers 191 Carbohydrates 191 Reserve Polymers 192 9.8 Lipid Catabolism 192 9.9 Protein and Amino Acid Catabolism 192 9.10 Oxidation of Inorganic Molecules 193 9.11 Photosynthesis 195 The Light Reaction in Eucaryotes and Cyanobacteria 196 The Light Reaction in Green and Purple Bacteria 199 10 Metabolism: The Use of Energy in Biosynthesis 204 10.1 Principles Governing Biosynthesis 205 10.2 The Photosynthetic Fixation of CO2 207 The Carboxylation Phase 208 The Reduction Phase 208 The Regeneration Phase 208 10.3 Synthesis of Sugars and Polysaccharides 209 10.4 The Assimilation of Inorganic Phosphorus, Sulfur, and Nitrogen 210 Phosphorus Assimilation 210 Sulfur Assimilation 210 Nitrogen Assimilation 210 Nitrogen Fixation 212 10.5 The Synthesis of Amino Acids 214 10.6 Anaplerotic Reactions 215 10.7 The Synthesis of Purines, Pyrimidines, and Nucleotides 216 Purine Biosynthesis 217 Pyrimidine Biosynthesis 218 10.8 Lipid Synthesis 218 10.9 Peptidoglycan Synthesis 221 10.10 Patterns of Cell Wall Formation 222 Part IV Microbial Molecular Biology and Genetics 11 Genes: Structure, Replication, and Mutation 227 11.1 DNA as Genetic Material 228 11.2 Nucleic Acid Structure 230 DNA Structure 231 RNA Structure 233 The Organization of DNA in Cells 234 11.3 DNA Replication 235 Patterns of DNA Synthesis 235 Mechanism of DNA Replication 236 11.4 The Genetic Code 240 Establishment of the Genetic Code 240 Organization of the Code 240 11.5 Gene Structure 241 Genes That Code for Proteins 242 Genes That Code for tRNA and rRNA 244 11.6 Mutations and Their Chemical Basis 244 Mutations and Mutagenesis 244 Spontaneous Mutations 246 Induced Mutations 246 The Expression of Mutations 248 11.7 Detection and Isolation of Mutants 251 Mutant Detection 251 Mutant Selection 252 Carcinogenicity Testing 253 11.8 DNA Repair 254 Excision Repair 254 Removal of Lesions 254 Postreplication Repair 254 Recombination Repair 255 12 Genes: Expression and Regulation 260 12.1 DNA Transcription or RNA Synthesis 261 Transcription in Procaryotes 261 Transcription in Eucaryotes 263 12.2 Protein Synthesis 265 Transfer RNA and Amino Acid Activation 266 The Ribosome 267 Initiation of Protein Synthesis 268 Elongation of the Polypeptide Chain 270 Termination of Protein Synthesis 270 Protein Folding and Molecular Chaperones 272 Protein Splicing 275 12.3 Regulation of mRNA Synthesis 275 Induction and Repression 275 Negative Control 276 Positive Control 278 12.4 Attenuation 279 12.5 Global Regulatory Systems 281 Catabolite Repression 281 Regulation by Sigma Factors and Control of Sporulation 282 Antisense RNA and the Control of Porin Proteins 282 12.6 Two-Component Phosphorelay Systems 283 12.7 Control of the Cell Cycle 285 13 Microbial Recombination and Plasmids 291 13.1 -Bacterial Recombination: General Principles 292 13.2 Bacterial Plasmids 294 Fertility Factors 295 Resistance Factors 297 Col Plasmids 297 Other Types of Plasmids 297 13.3 Transposable Elements 298 13.4 Bacterial Conjugation 302 F1 3 F2 Mating 302 Hfr Conjugation 303 F? Conjugation 303 13.5 DNA Transformation 305 13.6 Transduction 307 Generalized Transduction 308 Specialized Transduction 309 13.7 Mapping the Genome 312 13.8 -Recombination and Genome Mapping in Viruses 314 PART V DNA Technology and Genomics 14 Recombinant DNA Technology 319 14.1 Historical Perspectives 320 14.2 Synthetic DNA 323 14.3 The Polymerase Chain Reaction 326 14.4 Preparation of Recombinant DNA 327 Isolating and Cloning Fragments 327 Gene Probes 331 Isolating and Purifying Cloned DNA 333 14.5 Cloning Vectors 333 Plasmids 334 Phage Vectors 335 Cosmids 335 Artificial Chromosomes 335 14.6 Inserting Genes into Eucaryotic Cells 335 14.7 Expression of Foreign Genes in Bacteria 336 14.8 Applications of Genetic Engineering 337 Medical Applications 337 Industrial Applications 339 Agricultural Applications 339 14.9 Social Impact of Recombinant DNA Technology 341 15 Microbial Genomics 344 15.1 Introduction 345 15.2 Determining DNA Sequences 345 15.3 Whole-Genome Shotgun Sequencing 345 15.4 Bioinformatics 348 15.5 General Characteristics of Microbial Genomes 348 15.6 Functional Genomics 353 Genome Annotation 353 Evaluation of RNA-Level Gene Expression 354 Evaluation of Protein-Level Gene Expression 356 15.7 The Future of Genomics 356 Part VI The Viruses 16 The Viruses: Introduction and General Characteristics 361 16.1 Early Development of Virology 362 16.2 General Properties of Viruses 363 16.3 The Cultivation of Viruses 364 16.4 Virus Purification and Assays 366 Virus Purification 366 Virus Assays 367 16.5 The Structure of Viruses 368 Virion Size 369 General Structural Properties 369 Helical Capsids 370 Icosahedral Capsids 370 Nucleic Acids 372 Viral Envelopes and Enzymes 374 Viruses with Capsids of Complex Symmetry 376 16.6 Principles of Virus Taxonomy 377 17 The Viruses: Bacteriophages 381 17.1 Classification of Bacteriophages 382 17.2 Reproduction of Double-Stranded DNA Phages: The Lytic Cycle 382 The One-Step Growth Experiment 383 Adsorption to the Host Cell and Penetration 384 Synthesis of Phage Nucleic Acids and Proteins 385 The Assembly of Phage Particles 387 Release of Phage Particles 388 17.3 Reproduction of Single-Stranded DNA Phages 388 17.4 Reproduction of RNA Phages 389 17.5 Temperate Bacteriophages and Lysogeny 390 18 The Viruses: Viruses of Eucaryotes 398 18.1 Classification of Animal Viruses 399 18.2 Reproduction of Animal Viruses 399 Adsorption of Virions 399 Penetration and Uncoating 403 Replication and Transcription in DNA Viruses 403 Replication and Transcription in RNA Viruses 405 Synthesis and Assembly of Virus Capsids 408 Virion Release 408 18.3 Cytocidal Infections and Cell Damage 410 18.4 Persistent, Latent, and Slow Virus Infections 410 18.5 Viruses and Cancer 411 18.6 Plant Viruses 412 Virion Morphology 412 Plant Virus Taxonomy 412 Plant Virus Reproduction 412 Transmission of Plant Viruses 413 18.7 Viruses of Fungi and Algae 415 18.8 Insect Viruses 415 18.9 Viroids and Prions 416 Part VII The Diversity of the Microbial World 421 19 Microbial Taxonomy 421 19.1 General Introduction and Overview 422 19.2 Microbial Evolution and Diversity 423 19.3 Taxonomic Ranks 425 19.4 Classification Systems 426 Phenetic Classification 426 Numerical Taxonomy 426 Phylogenetic Classification 428 19.5 Major Characteristics Used in Taxonomy 428 Classical Characteristics 428 Molecular Characteristics 429 19.6 Assessing Microbial Phylogeny 432 Molecular Chronometers 432 Phylogenetic Trees 433 rRNA, DNA, and Proteins as Indicators of Phylogeny 433 Polyphasic Taxonomy 435 19.7 The Major Divisions of Life 435 Domains 435 Kingdoms 438 19.8 Bergey's Manual of Systematic Bacteriology 440 The First Edition of Bergey's Manual of Systematic Bacteriology 440 The Second Edition of Bergey's Manual of Systematic Bacteriology 441 19.9 A Survey of Procaryotic Phylogeny and Diversity 443 20 The Archaea 450 20.1 Introduction to the Archaea 451 Archaeal Cell Walls 451 Archaeal Lipids and Membranes 452 Genetics and Molecular Biology 453 Metabolism 453 Archaeal Taxonomy 455 20.2 Phylum Crenarchaeota 456 20.3 Phylum Euryarchaeota 458 The Methanogens 458 The Halobacteria 461 The Thermoplasms 463 Extremely Thermophilic S0-Metabolizers 463 Sulfate-Reducing Archaea 463 21 Bacteria: The Deinococci and Nonproteobacteria Gram Negatives 466 21.1 Aquificae and Thermotogae 467 21.2 Deinococcus-Thermus 468 21.3 Photosynthetic Bacteria 468 Phylum Chloroflexi 470 Phylum Chlorobi 470 Phylum Cyanobacteria 471 21.4 Phylum Planctomycetes 477 21.5 Phylum Chlamydiae 477 21.6 Phylum Spirochaetes 479 21.7 Phylum Bacteroidetes 481 22 Bacteria: The Proteobacteria 486 22.1 Class Alphaproteobacteria 487 The Purple Nonsulfur Bacteria 487 Rickettsia and Coxiella 488 The Caulobacteraceae and Hyphomicrobiaceae 490 Family Rhizobiaceae 492 Nitrifying Bacteria 493 22.2 Class Betaproteobacteria 495 Order Neisseriales 495 Order Burkholderiales 495 Order Nitrosomonadales 496 Order Hydrogenophilales 496 22.3 Class Gammaproteobacteria 498 The Purple Sulfur Bacteria 498 Order Thiotrichales 501 Order Methylococcales 502 Order Pseudomonadales 503 Order Vibrionales 504 Order Enterobacteriales 505 Order Pasteurellales 507 22.4 Class Deltaproteobacteria 507 Orders Desulfovibrionales, Desulfobacterales, and Desulfuromonadales 507 Order Bdellovibrionales 510 Order Myxococcales 512 22.5 Class Epsilonproteobacteria 514 23 Bacteria: The Low G 1 C Gram Positives 517 23.1 Class Mollicutes (the Mycoplasmas) 518 23.2 Low G 1 C Gram-Positive Bacteria in Bergey's Manual 521 23.3 Class Clostridia 523 23.4 Class Bacilli 525 Order Bacillales 525 Order Lactobacillales 529 24 Bacteria: The High G 1 C Gram Positives 536 24.1 General Properties of the Actinomycetes 537 24.2 High G 1 C Gram-Positive Bacteria in Bergey's Manual 539 24.3 Suborder Actinomycineae 542 24.4 Suborder Micrococcineae 542 24.5 Suborder Corynebacterineae 543 24.6 Suborder Micromonosporineae 544 24.7 Suborder Propionibacterineae 546 24.8 Suborder Streptomycineae 546 24.9 Suborder Streptosporangineae 548 24.10 Suborder Frankineae 548 24.11 Order Bifidobacteriales 549 25 The Fungi (Eumycota), Slime Molds, and Water Molds 552 25.1 Distribution 554 25.2 Importance 554 25.3 Structure 554 25.4 Nutrition and Metabolism 557 25.5 Reproduction 557 25.6 Characteristics of the Fungal Divisions 559 Division Zygomycota 560 Division Ascomycota 560 Division Basidiomycota 561 Division Deuteromycota 564 Division Chytridiomycota 564 25.7 Slime Molds and Water Molds 564 Division Myxomycota (Acellular Slime Molds) 564 Division Acrasiomycota (Cellular Slime Molds) 565 Division Oomycota 565 26 The Algae 570 26.1 Distribution of Algae 571 26.2 Classification of Algae 571 26.3 Ultrastructure of the Algal Cell 572 26.4 Algal Nutrition 573 26.5 Structure of the Algal Thallus (Vegetative Form) 573 26.6 Algal Reproduction 573 26.7 Characteristics of the Algal Divisions 574 Chlorophyta (Green Algae) 574 Charophyta (Stoneworts/Brittleworts) 576 Euglenophyta (Euglenoids) 576 Chrysophyta (Golden-Brown and Yellow-Green Algae; Diatoms) 577 Phaeophyta (Brown Algae) 578 Rhodophyta (Red Algae) 578 Pyrrhophyta (Dinoflagellates) 579 27 The Protozoa 583 27.1 Distribution 584 27.2 Importance 584 27.3 Morphology 585 27.4 Nutrition 586 27.5 Encystment and Excystment 586 27.6 Locomotory Organelles 586 27.7 Reproduction 586 27.8 Classification 587 27.9 Representative Types 588 Phylum Sarcomastigophora 588 Phylum Labyrinthomorpha 590 Phylum Apicomplexa 591 Phylum Microspora 591 Phylum Ascetospora 591 Phylum Myxozoa 591 Phylum Ciliophora 592 PART VIII Ecology and Symbiosis 595 28 Microorganism Interactions and Microbial Ecology 595 28.1 Foundations of Microbial Ecology 596 28.2 Microbial Interactions 596 Mutualism 598 Protocooperation 604 Commensalism 606 Predation 607 Parasitism 609 Amensalism 609 Competition 609 Symbioses in Complex Systems 610 28.3 Nutrient Cycling Interactions 611 Carbon Cycle 611 Sulfur Cycle 614 Nitrogen Cycle 615 Iron Cycle 616 Manganese Cycle 617 Other Cycles and Cycle Links 617 Microorganisms and Metal Toxicity 618 28.4 The Physical Environment 619 The Microenvironment and Niche 619 Biofilms and Microbial Mats 620 Microorganisms and Ecosystems 622 Microorganism Movement between Ecosystems 623 Stress and Ecosystems 624 28.5 Methods in Microbial Ecology 626 29 Microorganisms in Aquatic Environments 633 29.1 Aquatic Environments and Microorganisms 634 Gases and Aquatic Microorganisms 635 Nutrients in Aquatic Environments 637 Nutrient Cycles in Aquatic Environments 638 29.2 The Microbial Community 639 29.3 Marine Environments 644 29.4 Freshwater Environments 648 Lakes 648 Streams and Rivers 649 Microorganisms in Freshwater Ice 650 29.5 Waters and Disease Transmission 651 Waterborne Pathogens and Water Purification 651 Sanitary Analysis of Waters 653 29.6 Wastewater Treatment 657 Measuring Water Quality 657 Water Treatment Processes 658 29.7 Groundwater Quality and Home Treatment Systems 663 30 Microorganisms in Terrestrial Environments 668 30.1 Soils as an Environment for Microorganisms 669 30.2 Microorganisms in the Soil Environment 670 30.3 Microorganisms and the Formation of Different Soils 672 Tropical and Temperate Region Soils 672 Cold Moist Area Soils 673 Desert Soils 673 Geologically Heated Hyperthermal Soils 674 30.4 Soil Microorganism Associations with Vascular Plants 674 Microorganisms on the Outside of Plants 674 Microorganism Growth within Plants 675 Tripartite and Tetrapartite Associations 685 30.5 Soils, Plants, and Nutrients 686 30.6 Soils, Plants, and the Atmosphere 688 30.7 Microorganisms and Plant Decomposition 690 30.8 The Subsurface Biosphere 691 30.9 Soil Microorganisms and Human Health 693 30.10 Understanding Microbial Diversity in the Soil 693 Part IX Nonspecific Resistance and the Immune Response 31 Normal Microbiota and Nonspecific Host Resistance 697 31.1 Gnotobiotic Animals 698 31.2 Normal Microbiota of the Human Body 699 Distribution of the Normal Microbiota 701 The Relationship between Normal Microbiota and the Host 704 31.3 Overview of Host Resistance 704 31.4 Cells, Tissues, and Organs of the Immune System 705 Cells of the Immune System 705 Organs and Tissues of the Immune System 708 31.5 Physical and Chemical Barriers in Nonspecific Resistance 709 Physical and Mechanical Barriers 709 Chemical Barriers 712 31.6 Inflammation 712 Chronic Inflammation 714 31.7 The Complement System 714 31.8 Phagocytosis 718 31.9 Cytokines 720 Interferons 721 Fever 722 31.10 Natural Killer Cells 723 32 Specific Immunity 728 32.1 Overview of Specific Immunity 729 Types of Acquired Immunity 729 32.2 Antigens 731 Haptens 731 Superantigens 732 Cluster of Differentiation Molecules (CDs) 733 32.3 Antibodies 734 Immunoglobulin Structure 734 Immunoglobulin Function 736 Immunoglobulin Classes 736 Diversity of Antibodies 738 Specificity of Antibodies 741 Sources of Antibodies 741 Hybridomas 743 32.4 T-Cell Biology 745 T-Cell Receptors 745 Major Histocompatibility Complex (MHC) 745 Types of T Cells 748 32.5 B-Cell Biology 751 Antigen-Antibody Binding 752 B-Cell Activation 753 32.6 Action of Antibodies 756 Toxin Neutralization 756 Viral Neutralization 756 Adherence Inhibition 756 IgE and Parasitic Infections 756 Opsonization 756 Immune Complex Formation 756 32.7 The Classical Complement Pathway 758 32.8 Acquired Immune Tolerance 758 32.9 -Summary: The Role of Antibodies and Lymphocytes in Resistance 759 Immunity to Viral Infections 760 Immunity to Bacterial Infections 760 33 Medical Immunology 763 33.1 Vaccines and Immunizations 764 Types of Vaccines and Their Characteristics 766 33.2 Immune Disorders 768 Hypersensitivities 768 Autoimmune Diseases 771 Transplantation (Tissue) Rejection 773 Immunodeficiencies 774 33.3 Antigen-Antibody Interactions In Vitro 774 Agglutination 775 Complement Fixation 778 Enzyme-Linked Immunosorbent Assay 778 Flow Cytometry and Fluorescence 779 Immunoblotting (Western Blot) 779 Immunodiffusion 779 Immunoelectrophoresis 781 Immunofluorescence 781 Immunoprecipitation 781 Liposomes 782 Neutralization 783 Radioimmunoassay 783 Serotyping 784 Part X Microbial Diseases and Their Control 34 Pathogenicity of Microorganisms 787 34.1 Host-Parasite Relationships 788 34.2 Pathogenesis of Viral Diseases 790 Entry, Contact, and Primary Replication 791 Viral Spread and Cell Tropism 791 Cell Injury and Clinical Illness 791 Host Immune Response 791 Recovery from Infection 791 Virus Shedding 791 34.3 Pathogenesis of Bacterial Diseases 791 Maintaining a Reservoir of the Bacterial Pathogen 791 Transport of the Bacterial Pathogen to the Host 792 Attachment and Colonization by the Bacterial Pathogen 792 Invasion of the Bacterial Pathogen 792 Growth and Multiplication of the Bacterial Pathogen 793 Leaving the Host 793 The Clonal Nature of Bacterial Pathogens 793 Regulation of Bacterial Virulence Factors 794 Pathogenicity Islands 794 Toxigenicity 794 34.4 Microbial Mechanisms for Escaping Host Defenses 801 Evasion of Host Defenses by Viruses 801 Evasion of Host Defenses by Bacteria 801 35 Antimicrobial Chemotherapy 805 35.1 The Development of Chemotherapy 806 35.2 General Characteristics of Antimicrobial Drugs 807 35.3 Determining the Level of Antimicrobial Activity 809 Dilution Susceptibility Tests 809 Disk Diffusion Tests 809 Measurement of Drug Concentrations in the Blood 809 35.4 Mechanisms of Action of Antimicrobial Agents 810 35.5 Factors Influencing the Effectiveness of Antimicrobial Drugs 812 35.6 Antibacterial Drugs 812 Sulfonamides or Sulfa Drugs 812 Quinolones 813 Penicillins 813 Cephalosporins 814 The Tetracyclines 815 Aminoglycoside Antibiotics 816 Erythromycin and Other Macrolides 817 Vancomycin and Teicoplanin 817 Chloramphenicol 817 35.7 Drug Resistance 818 Mechanisms of Drug Resistance 818 The Origin and Transmission of Drug Resistance 819 35.8 Antifungal Drugs 820 35.9 Antiviral Drugs 821 36 Clinical Microbiology 826 36.1 Specimens 827 Collection 827 Handling 829 Transport 829 36.2 Identification of Microorganisms from Specimens 831 Microscopy 831 Growth and Biochemical Characteristics 831 Rapid Methods of Identification 840 Immunologic Techniques 842 Bacteriophage Typing 842 Molecular Methods and Analysis of Metabolic Products 842 36.3 Susceptibility Testing 844 36.4 Computers in Clinical Microbiology 844 37 The Epidemiology of Infectious Disease 847 37.1 Epidemiological Terminology 849 37.2 Measuring Frequency: The Epidemiologist's Tools 849 37.3 Infectious Disease Epidemiology 850 37.4 Recognition of an Infectious Disease in a Population 850 Remote Sensing and Geographic Information Systems: Charting Infectious Diseases 850 Correlation with a Single Causative Agent 851 37.5 Recognition of an Epidemic 851 37.6 The Infectious Disease Cycle: Story of a Disease 852 What Pathogen Caused the Disease? 852 What Was the Source and/or Reservoir of the Pathogen? 854 How Was the Pathogen Transmitted? 856 Why Was the Host Susceptible to the Pathogen? 858 How Did the Pathogen Leave the Host? 858 37.7 Virulence and the Mode of Transmission 858 37.8 Emerging and Reemerging Infectious Diseases and Pathogens 859 Reasons for Increases in Emerging and Reemerging Infectious Diseases 860 37.9 Control of Epidemics 862 The Role of the Public Health System: Epidemiological Guardian 862 37.10 The Emerging Threat of Bioterrorism 863 37.11 Global Travel and Health Considerations 863 Space Travel 865 37.12 Nosocomial Infections 866 Source 866 Control, Prevention, and Surveillance 866 The Hospital Epidemiologist 866 38 Human Diseases Caused by Viruses 870 38.1 Airborne Diseases 871 Chickenpox (Varicella) and Shingles (Zoster) 871 Influenza (Flu) 872 Measles (Rubeola) 873 Mumps 875 Respiratory Syndromes and Viral Pneumonia 875 Rubella (German Measles) 875 Smallpox (Variola) 876 38.2 Arthropod-Borne Diseases 877 Colorado Tick Fever 878 Yellow Fever 878 38.3 Direct Contact Diseases 878 Acquired Immune Deficiency Syndrome (AIDS) 878 Cold Sores 884 Common Cold 884 Cytomegalovirus Inclusion Disease 885 Genital Herpes 885 Human Herpesvirus 6 Infections 887 Human Parvovirus B19 Infections 887 Leukemia 887 Mononucleosis (Infectious) 888 Rabies 888 Viral Hepatitides 889 38.4 Food-Borne and Waterborne Diseases 891 Gastroenteritis (Viral) 891 Hepatitis A 892 Hepatitis E 892 Poliomyelitis 892 38.5 Slow Virus and Prion Diseases 893 38.6 Other Diseases 894 Warts 894 39 Human Diseases Caused by Bacteria 899 39.1 Airborne Diseases 900 Diphtheria 900 Legionnaires' Disease and Pontiac Fever 901 Meningitis 902 Mycobacterium avium-M. intracellulare Pneumonia 902 Pertussis 903 Streptococcal Diseases 903 Tuberculosis 906 39.2 Arthropod-Borne Diseases 908 Ehrlichiosis 909 Epidemic (Louse-Borne) Typhus 909 Endemic (Murine) Typhus 909 Lyme Disease 910 Plague 911 Q Fever 912 Rocky Mountain Spotted Fever 913 39.3 Direct Contact Diseases 913 Anthrax 913 Bacterial Vaginosis 914 Cat-Scratch Disease 914 Chancroid 914 Chlamydial Pneumonia 914 Gas Gangrene or Clostridial Myonecrosis 915 Genitourinary Mycoplasmal Diseases 915 Gonorrhea 915 Inclusion Conjunctivitis 916 Leprosy 916 Lymphogranuloma Venereum 917 Mycoplasmal Pneumonia 917 Nongonococcal Urethritis 918 Peptic Ulcer Disease and Gastritis 918 Psittacosis (Ornithosis) 919 Staphylococcal Diseases 919 Syphilis 923 Tetanus 924 Trachoma 925 Tularemia 926 Sexually Transmitted Diseases 926 39.4 Food-Borne and Waterborne Diseases 926 Botulism 929 Campylobacter jejuni Gastroenteritis 929 Cholera 930 Listeriosis 931 Salmonellosis 931 Shigellosis 931 Staphylococcal Food Poisoning 932 Traveler's Diarrhea and Escherichia coli Infections 932 Typhoid Fever 933 39.5 Sepsis and Septic Shock 933 39.6 Dental Infections 933 Dental Plaque 933 Dental Decay (Caries) 936 Periodontal Disease 936 40 Human Diseases Caused by Fungi and Protozoa 941 40.1 Fungal Diseases 942 Superficial Mycoses 942 Cutaneous Mycoses 943 Subcutaneous Mycoses 945 Systemic Mycoses 945 Opportunistic Mycoses 948 40.2 Protozoan Diseases 950 Amebiasis 950 Cryptosporidiosis 952 Freshwater Amoeba Diseases 953 Giardiasis 953 Malaria 954 Hemoflagellate Diseases 956 Toxoplasmosis 957 Trichomoniasis 958 PART XI Food and Industrial Microbiology 41 Microbiology of Food 963 41.1 Microorganism Growth in Foods 964 Intrinsic Factors 964 Extrinsic Factors 965 41.2 Microbial Growth and Food Spoilage 966 41.3 Controlling Food Spoilage 970 Removal of Microorganisms 970 Low Temperature 970 High Temperature 970 Water Availability 971 Chemical-Based Preservation 971 Radiation 972 Microbial Product-Based Inhibition 972 41.4 Food-Borne Diseases 973 Food-Borne Infection 973 Food-Borne Intoxications 975 41.5 Detection of Food-Borne Pathogens 976 41.6 Microbiology of Fermented Foods 978 Fermented Milks 978 Cheese Production 979 Meat and Fish 982 Production of Alcoholic Beverages 982 Production of Breads 984 Other Fermented Foods 985 41.7 Microorganisms as Foods and Food Amendments 986 42 Industrial Microbiology and Biotechnology 991 42.1 Choosing Microorganisms for Industrial Microbiology and Biotechnology 992 Finding Microorganisms in Nature 992 Genetic Manipulation of Microorganisms 993 Preservation of Microorganisms 999 42.2 Microorganism Growth in Controlled Environments 1000 Medium Development 1000 Growth of Microorganisms in an Industrial Setting 1001 42.3 Major Products of Industrial Microbiology 1004 Antibiotics 1004 Amino Acids 1005 Organic Acids 1006 Specialty Compounds for Use in Medicine and Health 1007 Biopolymers 1007 Biosurfactants 1009 Bioconversion Processes 1009 42.4 Microbial Growth in Complex Environments 1009 Biodegradation Using Natural Microbial Communities 1010 Changing Environmental Conditions to Stimulate Biodegradation 1012 Addition of Microorganisms to Complex Microbial Communities 1015 42.5 Biotechnological Applications 1017 Biosensors 1017 Microarrays 1018 Biopesticides 1018 42.6 Impacts of Microbial Biotechnology 1022 Appendix I: A Review of the Chemistry of Biological Molecules A1 Appendix II: Common Metabolic Pathways A12 Appendix III: Classification of Procaryotes According to the First Edition of Bergey's Manual of Systematic Bacteriology A21 Appendix IV: Classification of Procaryotes According to the Second Edition of Bergey's Manual of Systematic Bacteriology A27 Appendix V: Classification of Viruses A35 Glossary GI Credits CI Index II
Library of Congress Subject Headings for this publication: Microbiology