Visualizing Microbiology

by Anderson, Rodney P.; Young, Linda

• ISBN13: 9781119443124
• ISBN10: 1119443121
• Edition: 1st
• Format: Loose-leaf
• Copyright: 2017-08-14
• Publisher: Wiley

Summary

Visualizing Microbiology, 1st Edition provides an introduction to microbiology for students who require the basic fundamentals of microbiology as a requirement for their major or course of study. The unique visual pedagogy of the Visualizing series provides a powerful combination of content, visuals, multimedia and videos ideal for microbiology. A dynamic learning platform encouraging engagement with real clinical content, Visualizing Microbiology also brings the narrative to life with integrated multimedia helping students see and understand the unseen in the world of microbiology.

Author Biography

Rodney P. Anderson received his Ph.D. in Biological Sciences from the University of Iowa in 1989. His doctoral work centered on protein synthesis mechanisms in E. coli. After graduate school, he began his academic career at Ohio Northern University where he continues to teach and conduct research with undergraduates in the Department of Biological and Allied Health Sciences. He teaches microbiology for majors and allied health students as well as courses in genetics. He has also introduced non-majors to microbiology through interdisciplinary seminars in Disease and Society.
Dr. Anderson has been actively involved in microbiology education. He has been a past President of ASM's Conference on Undergraduate Education which developed the core curriculum for undergraduate microbiology courses and has organized and spoke at a number of education division symposia at ASM’s General Meeting. Outreach activities have included Microbial Discovery Workshops for High School science instructors and doing discovery science activities at local elementary schools. He is an author of two books published by ASM press: Outbreak and The Invisible ABCs.

Linda M. Young, since earning her Ph.D. in botany at The Ohio State University in 1988, has been teaching freshman and advanced-level biology courses at Ohio Northern University, a student-centered institution which emphasizes effective instruction as a faculty member's principle responsibility. Throughout her tenure, Dr. Young has regularly directed student-based research projects and periodically collaborated with investigators at OSU. She served seven years as the Assistant Dean of the Getty College of Arts and Sciences which allowed the opportunity to implement several programs to assist students in academic difficulty, ease freshman transition into college, and support the endeavors of high-achieving students. Although initially educated as a plant/cell physiologist, changing departmental needs led to her retraining. Consequently, Dr. Young now also teaches Microbiology for Allied Health Sciences (nursing) and Introduction to Microbiology (majors). Her research has also changed and now targets infection control issues and antibiosis. Dr. Young serves locally as a member of the Allen County MRSA Task Force and has previously authored the laboratory manual used for General Botany at ONU.

Table of Contents

1Microbial World 2

1.1 The Microbes 4

• A Brief Survey of the Microbial World 5

• The Dominant Form of Life on Earth 6

1.2 The Conflicts 8

• Growth and Control of Microbes 8

• The Role of the Immune System 10

What a Microbiologist Sees: Wrestling and the Spread of Skin Pathogens 10

• Pathogenesis 11

• Antimicrobial Drugs 12

1.3 Infectious Disease 13

• Epidemiology and Healthy Practices 13

• Host Defenses and Microbial Pathogenesis Strategies 14

 The Microbiologist’s Toolbox: MALDI TOF Mass Spectrometry 15

• Infectious Disease Statistics 16

Case Study: Vaccination: A Casualty of War 17

1.4 Microbial Ecology and Commercial Applications 18

• The Importance of Environmental Microbes 18

• The Industrial Use of Microorganisms 19

Clinical Application: Pasteurization 20

2 The Biochemistry of Macromolecules 26

2.1 Proteins 28

• The Four Levels of Protein Structure 28

• Protein Diversity and Function 34

What a Microbiologist Sees: The Effect of Modified Tertiary Binding on Protein Structure 34

2.2 Enzymes 35

• Enzyme Action 36

• Factors Influencing the Rate of Enzyme Activity 37

2.3 Carbohydrates 40

• Simple and Complex Carbohydrates 41

• The Functional Diversity of Carbohydrates 41

Clinical Application: Rapid Glycogen Breakdown in a Diabetic Patient in Shock 42

2.4 Lipids 43

• The Structural Classes of Lipids 43

Case Study: Acne—A Bacterial Interaction with Skin Oils 44

• Lipid Functions 47

The Microbiologist’s Toolbox: Ziehl-Neelsen Acid-Fast Staining of Mycolic Acid Cell Walls 48

2.5 Nucleic Acids 49

• The Structures of DNA and RNA 49

• Nucleic Acid Functions 52

3 Microscopy 60

3.1 Principles of Microscopy 62

• Magnification 63

• Resolution 64

3.2 Microscopy Used for Clinical Diagnosis 65

• Bright-field Microscopy 65

• Dark-field Microscopy 66

• Fluorescence Microscopy 67

The Microbiologist’s Toolbox: The Direct Fluorescent Antibody Assay 67

3.3 Microscopy Used for Research Investigations 68

• Light Microscopy 68

What a Microbiologist Sees: Differential Interference Contrast Microscopy 70

• Electron Microscopy 70

• Nanoprobe-based Microscopy 72

3.4 Specimen Preparation and Staining 72

• Basic Staining Procedures 72

Case Study: Diagnosing Gonorrhea Using Gram Staining 74

Clinical Application: Diagnosing Tuberculosis Using Acid-fast Staining 75

• Special Staining Procedures 75

4 Prokaryotic Organisms 82

4.1 The Prokaryote’s Place in the Living World 84

• Sustaining Life 84

What a Microbiologist Sees: Prokaryotes— The Dominant Form of Life on Earth 85

• Symbiotic Relationships 86

4.2 Bacterial Cell Shapes and Arrangements 87

• Bacterial Shapes 87

• Bacterial Arrangements 87

4.3 The Bacterial Cell Wall 89

• Cell Wall Structure 89

• Gram-Positive and Gram-Negative Cell Walls 91

• Atypical Cell Walls 92

Case Study: A Walking Pneumonia Outbreak at a University 93

4.4 External Structures of Bacterial Cells 94

• The Glycocalyx 94

• Fimbriae and Pili 94

• Flagella 95

The Microbiologist’s Toolbox: The Flagella Stain 97

4.5 Internal Structures of Bacterial Cells 97

• The Plasma Membrane 98

• The Nucleoid 99

• Ribosomes 99

• Plasmids, Inclusion Bodies, and Membranous Structures 100

• Endospores 101

Clinical Application: Endospore-forming Bacteria 101

4.6 Prokaryotic Evolution and Classification 103

• The Tree of Life 103

• The Clinical Classification of Prokaryotes 105

5 Eukaryotic Organisms 112

5.1 The Eukaryotic Cell 114

• Cell Size 114

• The Eukaryotic Organelles 114

5.2 The Origins of Eukaryotic Organelles and Organisms 120

• The Autogenous and Endosymbiotic Hypotheses 120

• Eukarya: A Classification Overview 120

5.3 The Algae 122

• General Characteristics and Unique Features 122

• A Survey of Algae 122

Clinical Application: Agar—The Ideal Solid Medium for Bacterial Culture 124

• Pathogenic Algae 124

5.4 The Protozoans 125

• General Characteristics and Unique Features 125

• A Survey of Protozoans 126

• Pathogenic Protozoans 128

5.5 The Fungi 129

• General Characteristics and Unique Features 129

The Microbiologist’s Toolbox: The Growth of Fungal Specimens on Sabouraud Dextrose Agar 131

• A Survey of Fungi 131

• Pathogenic Fungi 133

What a Microbiologist Sees: The Morphological Plasticity of Candida 134

5.6 The Helminths 135

• General Characteristics and Unique Features 135

• A Survey of Helminths 135

• Pathogenic Helminths 135

Case Study: Cravings 138

5.7 The Arthropods 139

• A Survey of Arthropods 139

• Pathogenic Arthropods and Arthropod Vectors 139

6 Viruses and Other Infectious Particles 146

6.1 Viral Structure and Classification 148

• The Structure of Viruses 148

• The Classification of Viruses 150

6.2 Viral Replication Cycles 153

• Viruses Replicating in Animal Cells 153

The Microbiologist’s Toolbox: Presumptive Diagnosis of a Viral Infection Using CPE

Analysis 158

• Viruses Replicating in Bacterial Cells 158

6.3 Viruses and Human Health 160

• The Clinical Cultivation of Viruses 160

• The Impact of Viral Infections 160

Case Study: H1N1 in Young Adults 161

• Viruses, Recurrent Infections, and Cancer 162

What a Microbiologist Sees: Connecting Symptoms with the Progression of HIV 163

6.4 Prevention and Treatment of Viral Infections 164

• The Prevention of Viral Infections 164

Clinical Application: Mandatory Flu Vaccines for Health Care Providers 164

• Antiviral Therapies 165

• Viral Influences on Bacterial Infections 166

6.5 Viruslike Microbes 170

• Viroids 170

• Satellites 170

• Prions 171

7 Metabolism 178

7.1 The Role of Energy in Life 180

• Basic Energy Principles 180

• Energy and Chemical Reactions 180

The Microbiologist’s Toolbox: Identifying Bacteria by Metabolic Differences 182

7.2 Energy Production Principles 182

• Oxidation-Reduction Reactions 182

• ATP 183

7.3 Glycolysis and Fermentation 186

• Glycolysis 186

• Fermentation 188

Clinical Application: The Clinical Importance of Alcohol Throughout History 189

7.4 Aerobic Cellular Respiration 190

• Pyruvate Oxidation and the Citric Acid Cycle 190

• The Electron Transport System 192

• Lipid and Protein Catabolism 194

What a Microbiologist Sees: The Deepwater Horizon Oil Spill–Microbial Bioremediation 195

• Integrated Metabolic Pathways 196

7.5 Photosynthesis 196

• Reactions of Photosynthesis 197

Case Study: A Metabolic Imbalance in Grand Lake St. Mary’s 202

• Chemosynthesis in Bacteria 202

8 Microbial Genetics and Genetic Engineering 210

8.1 DNA as the Genetic Material 212

• DNA Structure and Functions 212

• DNA Replication in Bacteria 214

8.2 From DNA to Protein 215

• Transcription 215

• Translation 217

8.3 Sources of Genetic Variation 219

• Mutation 219

• Recombination 222

• Transposition 224

Case Study: The Spread of a Drug-resistance Gene 224

8.4 Regulation of Gene Expression 225

• Transcriptional Control 225

• Pre- and Posttranscriptional Control 226

8.5 Recombinant DNA Technology 228

• Recombinant DNA Tools and Gene Cloning 228

The Microbiologist’s Toolbox: Gel Electrophoresis 229

• Applications of Recombinant DNA Technology 230

What a Microbiologist Sees: Manipulating the Bacterial Genome for Agricultural Benefits 232

• Ethical and Safety Concerns 233

8.6 Genomics 234

• DNA Sequencing 234

• Genomic Analysis 234

• Applications of Genomics 236

Clinical Application: Screening for Genetic Diseases—BRCA1 Mutation 236

9 Microbial Growth and Control 240

9.1 Requirements for Microbial Growth 244

• Energy Sources 244

• Physical Requirements 244

Case Study: Foodborne Illness from Home- Prepared Fermented Tofu 245

• Chemical Requirements 247

9.2 Bacterial Reproduction and Growth 249

• Cell Division 249

• Growth Rate of Bacteria 250

• Phases of Growth 251

• Methods of Quantifying Bacterial Growth 252

The Microbiologist’s Toolbox: Dilution Plating 253

9.3 Laboratory Growth of Microorganisms 254

• Obtaining a Pure Culture 254

• Growth Media 254

What a Microbiologist Sees: Biofilm Formation on Teeth 258

• Bacteria That Cannot Be Cultured 258

9.4 Microbial Cultures in Clinical Practice 260

• Specimen Collection 260

• Specimen Analysis 260

9.5 Controlling Microbial Growth 263

• Physical Methods 263

• Radiation 264

• Chemical Methods 266

Clinical Application: Alcohol-Based Hand Sanitizers in Health Care Settings 267

10 Innate Immunity 274

10.1 An Introduction to Immunity 276

• The Benefits and Consequences of the Immune Response 276

• Innate Versus Adaptive Immunity 276

• The Basic Anatomy of the Immune System 278

10.2 First-Line Defense Mechanisms 282

• Physical Defenses 282

What a Microbiologist Sees: The Benefits of Fever 283

Case Study: No Spicy Food for Me! 284

• Chemical Defenses 285

10.3 Innate Cellular Defense Mechanisms 286

• Hematopoiesis 286

• Leukocytes 287

The Microbiologist’s Toolbox: The Differential Count 289

• Phagocytosis 290

• Inflammation 290

10.4 Protein-Mediated Defense Mechanisms 294

• The Complement Pathways 294

• Interferons 294

• Miscellaneous Proteins with Antimicrobial Action 296

11 Adaptive Immunity 304

11.1 Introduction to Adaptive Immunity 306

• Hallmarks of Adaptive Immunity 306

• Antigens and Immunogenicity 306

Clinical Application: Conjugate Vaccines 308

• Lymphocyte Maturation and Clonal Selection 308

• The Major Histocompatibility Complex 311

What a Microbiologist Sees: Transplant Rejection 312

11.2 Cell-mediated Responses 313

• T-cell Categories 313

• Antigen Processing and Presentation 315

• The T-cell Receptor Complex and Associative Recognition 316

11.3 T-cell Activation 317

• Early Stages of T-cell Activation 317

• Completion of T-cell Activation 318

Case Study: The Mantoux Test 318

11.4 Antibody-mediated Responses 320

• Basic Antibody Structure 320

The Microbiologist’s Toolbox: The Coagulase Agglutination Assay 321

• Immunoglobulin Classes and Their Specific Functions 322

11.5 B-cell Activation 323

• B-cell Receptors and Pathogen Binding 323

• Antibody Production and Clonal Expansion 325

• B-cell Effector Mechanisms 327

12 Vaccination, Immunoassays, and Immune Disorders 334

12.1 Vaccines and Vaccination 336

• A Brief History of Vaccination 336

• Modern Vaccines 336

• Vaccines and Public Health 339

• Vaccine Safety and Misconceptions 342

12.2 Immunoassays 343

• Monoclonal Antibodies 343

The Microbiologist’s Toolbox: Human Monoclonal Antibody Therapy for Non-Hodgkin’s Lymphoma 345

• Types of Immunoassays 346

12.3 Hypersensitivities 350

• Type I Hypersensitivity 350

• Type II Hypersensitivity 352

What a Microbiologist Sees: Fetal Rh Incompatibility 353

• Type III Hypersensitivity 354

• Type IV Hypersensitivity 355

12.4 Autoimmune Diseases and Immuno deficiencies 356

• Autoimmune Diseases 356

• Immuno deficiencies 357

Clinical Application: Bone Marrow Transplants for Immunodeficient Patients 358

Case Study: Prioritizing Immunizations 359

13 Microbial Pathogenesis 366

13.1 Entering and Adhering to the Host 368

• Microbial Reservoirs 368

• Portals of Entry and Exit 369

• Adhering to Host Cells 370

13.2 Transmission of Microbes 372

• Modes of Transmission 372

Case Study: The Cholera Epidemic in Goma, Zaire 374

• Horizontal and Vertical Transmission 374

13.3 Bypassing Host Defenses 376

• Evading Immune Attack 376

• Altering Pathogen Antigens 378

• Damaging the Host Immune System 380

13.4 Damaging Host Tissues 381

• Direct Damage 381

• Enzymes 382

• Endotoxins 382

• Exotoxins 384

Clinical Application: Toxoid-based Vaccines 385

• Immunopathy 387

The Microbiologist’s Toolbox: Analysis of Hemolysis on Blood Agar 388

13.5 Factors Influencing Disease Outcomes 389

• Host Factors 389

What a Microbiologist Sees: Stress and Infection 390

• Microbial Factors 391

14 Antimicrobial Agents 398

14.1 Principles of Antimicrobial Chemotherapy 400

• The Discovery and Development of Antimicrobial Agents 400

• Choosing the Best Antimicrobial Agent 402

The Microbiologist’s Toolbox: The Broth Dilution Test 404

14.2 Antibacterial Agents 406

• Inhibitors of Cell Wall Synthesis 406

• Inhibitors of Protein Synthesis 409

• Inhibitors of Nucleic Acid Synthesis 410

• Agents That Target the Bacterial Plasma Membrane 412

• Antimycobacterial Agents 412

Clinical Application: The Fight Against Drug-Resistant Tuberculosis 412

14.3 Antiviral Agents 415

• Inhibitors of Virus Entry 416

• Inhibitors of Viral Nucleic Acid Synthesis 417

• Inhibitors of Viral Protein Synthesis 418

• Inhibitors of Viral Assembly and Release 418

14.4 Antifungal and Antiparasitic Agents 419

• Antifungal Agents 420

• Antiparasitic Agents 421

Case Study: Problems with Malaria Medication in Mozambique 423

14.5 Antimicrobial Drug Resistance 425

• Principles of Drug Resistance 425

• Mechanisms of Drug Resistance 426

• Human Factors Contributing to Antimicrobial Resistance 427

What a Microbiologist Sees: Livestock- Associated Drug-Resistant S. aureus 428

15 Epidemiology and Infection Control 434

15.1 Epidemiology and Public Health 436

• Early Epidemiological Successes 436

• Significant Accomplishments of Epidemiology 436

15.2 Epidemiological Surveillance 438

• Prevalence, Incidence Rates, and Mortality Rates 438

What a Microbiologist Sees: Antibioticimpregnated Bone Cement 439

• Epidemic Curves 441

• Disease Surveillance 441

15.3 Epidemiological Studies and Clinical Trials 442

• Case-Control and Cohort Studies 442

• Clinical Trials 443

Case Study: A Foodborne Outbreak Among Inmates at a County Jail 444

15.4 Health Care–associated Infections 446

• Common Health Care-Associated Infections 446

Clinical Application: Reducing the Risk of Bloodstream Infections 447

• Surgical Site Infections 447

• CAUTIs 450

• PICC Line Infections 450

• CLABSIs 451

15.5 Preventing Pathogen Spread in Health Care Settings 451

• Hand Hygiene 451

• Universal and Standard Precautions and PPE 453

• Screening 454

The Microbiologist’s Toolbox: MRSA Screening Procedures in the Clinical Laboratory 455

• Isolation Procedures 456

16 Diseases of the Respiratory System 462

16.1 The Conflicts 464

• Host Defenses 464

• Microbial Pathogenic Strategies 464

• Normal Microbiota 465

16.2 Bacterial Diseases of the Respiratory System 466

• Diphtheria 466

• Pertussis 467

• Tuberculosis 468

Case Study: Whooping Cough Outbreak 469

16.3 Viral Diseases of the Respiratory System 472

• The Common Cold 472

• Influenza 473

What a Microbiologist Sees: Unpredictable Behavior 476

16.4 Diseases of the Respiratory System Caused by Multiple Pathogens 477

• Sinusitis and Otitis Media 477

• Pharyngitis 479

The Microbiologist’s Toolbox: Diagnosis of Strep Throat 481

• Laryngitis, Croup, Tracheitis, and Epiglottitis 482

• Bronchitis and Bronchiolitis 483

16.5 Pneumonia 483

Clinical Application: Sputum Samples 484

• General Characteristics of Pneumonia 484

• Epidemiology of Pneumonia 485

• Causes of Pneumonia 486

• Emerging Pathogens 488

17 Diseases of the Skin and Eyes 496

17.1 The Conflicts 498

• Host Defenses 498

• Microbial Pathogenic Strategies 498

• Normal Microbiota 501

17.2 Bacterial Diseases of the Skin 502

• Staphylococcal and Streptococcal Skin Diseases 502

The Microbiologist’s Toolbox: Mannitol Salt Agar—A Versatile Selective/Differential Medium 505

• Pseudomonal Skin Diseases 505

• Miscellaneous Bacterial Skin Diseases 506

17.3 Viral Diseases of the Skin 508

• Pediatric Viral Rashes 508

Clinical Application: Improving Hand-Hygiene Compliance with Technology 509

• Shingles 512

• Warts 513

• Smallpox 514

17.4 Fungal, Protozoan, and Arthropod Diseases of the Skin 516

• Fungal Skin Diseases 516

What a Microbiologist Sees: Oral Thrush and Immune System Status 517

• Protozoan Skin Diseases 517

• Arthropod Skin Diseases 519

Case Study: Kindergarten Contact 520

17.5 Diseases of the Eye 521

• Host Defenses and Microbial Pathogenic Strategies 522

• Conjunctivitis 522

• Other Eye Diseases 523

18 Diseases of the Nervous System 532

18.1 The Conflicts 534

• Host Defenses 534

• Microbial Pathogenic Strategies 534

18.2 Bacterial Diseases of the Nervous System 536

• Bacterial Meningitis 536

• Tetanus 540

• Botulism 540

Clinical Application: Clinical Use of Botulism Toxin 541

• Hansen’s Disease (Leprosy) 543

18.3 Viral Diseases of the Nervous System 543

• Viral Meningitis 543

Case Study: Viral Meningitis in a High School Student 544

• Encephalitis 545

• Polio 547

What a Microbiologist Sees: Polio Eradication 547

• Rabies 548

• Other Viral Diseases of the Nervous System 550

18.4 Fungal and Protozoan Diseases of the Nervous System 551

• Fungal Meningitis 551

The Microbiologist’s Toolbox: India Ink Staining of CSF for Cryptococcus 552

• Toxoplasmosis 552

18.5 Prion Diseases of the Nervous System 554

• Animal Spongiform Encephalopathies 554

• Human Prion Diseases 554

19 Diseases of the Cardiovascular and Lymphatic Systems 562

19.1 The Conflicts 564

• Host Defenses 564

• Microbial Pathogenic Strategies 564

19.2 Sepsis and Cardiac Diseases 566

• Sepsis 566

• Cardiac Diseases 569

The Microbiologist’s Toolbox: The Blood Culture 571

19.3 Bacterial Diseases of the Cardiovascular and Lymphatic Systems 572

• Brucellosis 572

• Anthrax 574

• Lyme Disease 575

• Plague 577

• Other Bacterial Diseases 580

19.4 Viral Diseases of the Cardiovascular and Lymphatic Systems 581

• Leukocyte-associated Cardiovascular and Lymphatic Diseases 581

What a Microbiologist Sees: The Diagnosis of Mononucleosis 582

• Viral Hemorrhagic Diseases 583

• Hepatitis 585

Clinical Application: HIV Status and the Spread of Hepatitis 586

19.5 Protozoan and Helminthic Diseases of the Cardiovascular and Lymphatic Systems 587

• Systemic Protozoan Diseases 587

Case Study: The Kissing Bug 588

• Systemic Helminthic Diseases 590

20 Diseases of the Gastrointestinal System 598

20.1 The Conflicts 600

• Host Defenses 600

• Microbial Pathogenic Strategies 600

• Normal Microbiota 600

20.2 Bacterial Diseases of the Mouth and Upper GI Tract 602

• Dental Caries 602

• Gingivitis and Periodontal Disease 603

What a Microbiologist Sees: Oral Hygiene for Patients with Ventilators 604

• Peptic Ulcer Disease 606

• Staphylococcus aureus Food Intoxication 606

20.3 Bacterial Diseases of the Lower GI Tract 607

• Diseases Caused by Salmonella 607

• Diarrheagenic E. coli Infections 608

• Campylobacteriosis 608

• Shigellosis 608

The Microbiologist’s Toolbox: Preparing and Analyzing a Fecal Culture 609

• Cholera 610

• Opportunistic Diseases 612

20.4 Viral Diseases of the GI System 614

• Cold Sores 614

• Mumps 614

• Viral Gastroenteritis 615

Case Study: A Norovirus Outbreak Among Nurses 616

• Hepatitis A and Hepatitis E 617

20.5 Protozoan Diseases of the GI System 618

• Giardiasis 618

• Amoebic Dysentery 618

• Cryptosporidiosis 619

20.6 Helminthic Diseases of the GI System 620

• Trematode Infections 620

• Cestode Infections 621

• Nematode Infections 622

21 Diseases of the Urogenital System 632

21.1 The Conflicts 634

• Host Defenses 634

• Microbial Pathogenic Strategies 634

• Normal Microbiota 636

21.2 Bacterial Diseases of the Urinary System 637

• Cystitis 637

What a Microbiologist Sees: Cranberry Juice for UTI Prevention 639

• Pyelonephritis 640

Case Study: Pyelonephritis in a Toddler 641

• Leptospirosis 641

21.3 Bacterial Diseases of the Reproductive Systems 643

• Prostatitis 643

• Chlamydia 643

• Gonorrhea 645

The Microbiologist’s Toolbox: The Challenge of Culturing Neisseria gonorrhoeae 646

• Pelvic Inflammatory Disease 646

• Syphilis 648

21.4 Viral Diseases of the Reproductive Systems 650

• Genital Warts 650

Clinical Application: Winning the War on Cervical Cancer 652

• Genital Herpes 652

• Molluscum Contagiosum 653

21.5 HIV and AIDS 654

• An Emerging Infection 655

• HIV Replication and Pathogenicity 657

• HIV Diagnosis, Treatment, and Outlook 658

21.6 Fungal and Protozoan Diseases of the Reproductive Systems 660

• Vaginal Yeast Infections 660

• Trichomoniasis 662

22 Environmental and Industrial Microbiology 670

22.1 Microbial Ecology 672

• The Ecological Hierarchy 672

• Microbes in Earth’s Ecosystems 674

• Biofilms 676

Clinical Application: A Potential New Therapy for Medical Biofilm Elimination 677

22.2 Biogeochemical Cycles 678

• The Nitrogen Cycle 679

• The Carbon Cycle 680

• The Phosphorus Cycle 681

What a Microbiologist Sees: Habitat for Acidophiles 683

• The Sulfur Cycle 683

22.3 Bioremediation 684

• Microorganisms Used in Bioremediation 685

• Sewage Treatment 685

• Freshwater Treatment 687

22.4 Microorganisms Used in Manufacturing 687

• Products of Biotechnology 687

• Food Production 688

Case Study: Bacon Beer 691

22.5 Safe Product Processing and Packaging 692

• Food Safety Regulations 692

• Chemical and Physical Controls in Food Production 693

• Canning 694

The Microbiologist’s Toolbox: The Autoclave 696

• Microbial Control in Health Care Settings 696

Appendix A: Answers to Self-Tests 702

Appendix B: Physiological Reference Ranges 705

Glossary 708

Index 726