Brief Table of Contents

Brief Table of Contents

Part I Introduction to Microbiology

1 The History and Scope of Microbiology 1

2 The Study of Microbial Structure 17

3 Procaryotic Cell Structure and Function 41

4 Eucaryotic Cell Structure and Function 74

Part II Microbial Nutrition, Growth, and Control

5 Microbial Nutrition 95

6 Microbial Growth 112

7 Control of Microorganisms by Physical and Chemical

Agents 136

Part III Microbial Metabolism

8 Metabolism: Energy, Enzymes, and Regulation 153

9 Metabolism: Energy Release and Conservation 172

10 Metabolism: The Use of Energy in Biosynthesis 204

Part IV Microbial Molecular Biology and Genetics

11 Genes: Structure, Replication, and Mutation 227

12 Genes: Expression and Regulation 260

13 Microbial Recombination and Plasmids 291

Part V DNA Technology and Genomics

14 Recombinant DNA Technology 319

15 Microbial Genomics 344

Part VI The Viruses

16 The Viruses: Introduction and General Characteristics 361

17 The Viruses: Bacteriophages 381

18 The Viruses: Viruses of Eucaryotes 398

Part VII The Diversity of the Microbial World

19 Microbial Taxonomy 421

20 The Archaea 450

21 Bacteria: The Deinococci and Nonproteobacteria Gram Negatives 466

22 Bacteria: The Proteobacteria 486

23 Bacteria: The Low G + C Gram Positives 517

24 Bacteria: The High G + C Gram Positives 536

25 The Fungi (Eumycota), Slime Molds, and Water Molds 552

26 The Algae 570

27 The Protozoa 583

Part VIII Ecology and Symbiosis

28 Microorganism Interactions and Microbial Ecology 595

29 Microorganisms in Aquatic Environments 633

30 Microorganisms in Terrestrial Environments 668

Part IX Nonspecific Resistance and the Immune Response

31 Normal Microbiota and Nonspecific Host Resistance 697

32 Specific Immunity 728

33 Medical Immunology 763

Part X Microbial Diseases and Their Control

34 Pathogenicity of Microorganisms 787

35 Antimicrobial Chemotherapy 805

36 Clinical Microbiology 826

37 The Epidemiology of Infectious Disease 847

38 Human Diseases Caused by Viruses 870

39 Human Diseases Caused by Bacteria 899

40 Human Diseases Caused by Fungi and Protozoa 941

Part XI Food and Industrial Microbiology

41 Microbiology of Food 963

42 Industrial Microbiology and Biotechnology 991

Appendices

Appendix I A Review of the Chemistry of Biological Molecules A-1

Appendix II Common Metabolic Pathways A-12

Appendix III Classification of Bacteria According to the First Edition of Bergey?s Manual of Systematic
Bacteriology A-22

Appendix IV Classification of Bacteria According to the Second Edition of Bergey?s Manual of Systematic
Bacteriology A-27

Appendix V Classification of Viruses A-35

Glossary G1

Credits C1

Index I1

Preface  xv

To the Student  xxiii

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:  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 Bacteria According to the First Edition of Bergey’s Manual of Systematic Bacteriology    A21

Glossary GI

Credits CI

Index II