Additional Information
Book Details
Abstract
Known as the #1 bench reference for practicing microbiologists and an excellent text for students in clinical laboratory science programs, Bailey & Scott’s Diagnostic Microbiology, 13th Edition helps you develop and refine the skills you need for effective laboratory testing. In-depth information is useful and easily accessible, with step-by-step instructions for all the procedures. This edition features more than 20 NEW chapters plus updated material on the newest advances and the latest trends in clinical microbiology. Written by expert Dr. Patricia Tille, this classic reference addresses the topics and issues most relevant to you and your success on the job.
- Hands-on procedures include step-by-step instructions, full-color photos, and expected results, helping you achieve more accurate results.
- Case studies give you the opportunity to apply your skills in a variety of diagnostic scenarios and help improve your decision-making and critical thinking skills.
- Genera and Species to be Considered boxes highlight all of the organisms to be discussed in each chapter, including the current name of the species as well as any previous names.
- Student resources on Evolve enhance your learning with review questions and procedures.
- Convenient, easy-to-read tables summarize key information.
- Detailed, full-color illustrations aid comprehension and help you visualize concepts.
- A glossary of terms is found at the back of the book for quick reference.
- NEW! Learning objectives begin each chapter, giving you a measurable outcome to achieve by the completing the material.
- NEW! Review questions on the Evolve companion website are tied to learning objectives, and enhance your understanding and retention of chapter content.
- NEW! Reader-friendly chapters cover groups of related organisms rather than addressing all at once, including the parasitology, mycology, and virology chapters.
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Front cover | cover | ||
| Inside front cover | ifc1 | ||
| Half title page | i | ||
| Evolve page | ii | ||
| Bailey & Scott's Diagnostic Microbiology, 13/e | iii | ||
| Copyright page | iv | ||
| Dedication | v | ||
| Reviewers | vi | ||
| Contributors | viii | ||
| Acknowledgments | ix | ||
| Preface | ix | ||
| Table of Contents | x | ||
| I Basic Medical Microbiology | 1 | ||
| 1 Microbial Taxonomy | 1 | ||
| Objectives | 1 | ||
| Classification | 1 | ||
| Species | 1 | ||
| Genus | 1 | ||
| Family | 2 | ||
| Nomenclature | 2 | ||
| Identification | 2 | ||
| Identification Methods | 2 | ||
| Chapter Review | 3.e1 | ||
| Bibliography | 3 | ||
| 2 Bacterial Genetics, Metabolism, and Structure | 4 | ||
| Objectives | 4 | ||
| Bacterial Genetics | 4 | ||
| Nucleic Acid Structure and Organization | 4 | ||
| Nucleotide Structure and Sequence | 4 | ||
| DNA Molecular Structure | 5 | ||
| Genes and the Genetic Code | 5 | ||
| Chromosomes | 5 | ||
| Nonchromosomal Elements of the Genome | 5 | ||
| Replication and Expression of Genetic Information | 7 | ||
| Replication | 7 | ||
| Expression of Genetic Information | 8 | ||
| Transcription. | 8 | ||
| Translation. | 8 | ||
| Regulation and Control of Gene Expression | 10 | ||
| Genetic Exchange and Diversity | 12 | ||
| Mutation | 12 | ||
| Genetic Recombination | 12 | ||
| Genetic Exchange | 12 | ||
| Transformation. | 12 | ||
| Transduction. | 12 | ||
| Conjugation. | 13 | ||
| Bacterial Metabolism | 14 | ||
| Fueling | 14 | ||
| Acquisition of Nutrients | 14 | ||
| Production of Precursor Metabolites | 15 | ||
| Energy Production | 15 | ||
| Oxidative Phosphorylation. | 17 | ||
| Biosynthesis | 17 | ||
| Polymerization and Assembly | 18 | ||
| Structure and Function of the Bacterial Cell | 18 | ||
| Eukaryotic and Prokaryotic Cells | 18 | ||
| Bacterial Morphology | 18 | ||
| Bacterial Cell Components | 18 | ||
| Cell Envelope | 19 | ||
| Outer Membrane. | 19 | ||
| Cell Wall (Murein Layer). | 19 | ||
| Periplasmic Space. | 20 | ||
| Cytoplasmic (Inner) Membrane. | 20 | ||
| Cellular Appendages. | 20 | ||
| Cell Interior | 21 | ||
| Chapter Review | 21.e1 | ||
| Bibliography | 21 | ||
| 3 Host-Microorganism Interactions | 22 | ||
| Objectives | 22 | ||
| The Encounter Between Host and Microorganism | 22 | ||
| The Human Host’s Perspective | 22 | ||
| Microbial Reservoirs and Transmission | 22 | ||
| Human and Microbe Interactions | 23 | ||
| Animals as Microbial Reservoirs | 23 | ||
| Insects as Vectors | 24 | ||
| The Environment as a Microbial Reservoir | 24 | ||
| The Microorganism’s Perspective | 24 | ||
| Microorganism Colonization of Host Surfaces | 25 | ||
| The Host’s Perspective | 25 | ||
| Skin and Skin Structures | 25 | ||
| Mucous Membranes | 25 | ||
| General Protective Characteristics. | 25 | ||
| Specific Protective Characteristics. | 26 | ||
| The Microorganism’s Perspective | 27 | ||
| Microbial Colonization | 27 | ||
| Microorganism Entry, Invasion, and Dissemination | 28 | ||
| The Host’s Perspective | 28 | ||
| Disruption of Surface Barriers | 28 | ||
| Responses to Microbial Invasion of Deeper Tissues | 28 | ||
| Nonspecific Responses. | 28 | ||
| Phagocytes. | 28 | ||
| Inflammation. | 29 | ||
| Specific Responses—the Immune System | 30 | ||
| Components of the Immune System | 30 | ||
| Two Branches of the Immune System. | 31 | ||
| The Microorganism’s Perspective | 32 | ||
| Colonization and Infection | 32 | ||
| Pathogens and Virulence | 32 | ||
| Microbial Virulence Factors | 33 | ||
| Attachment. | 33 | ||
| Invasion. | 33 | ||
| Survival Against Inflammation. | 33 | ||
| Survival Against the Immune System. | 34 | ||
| Microbial Toxins. | 34 | ||
| Genetics of Virulence: Pathogenicity Islands | 34 | ||
| Biofilm Formation. | 35 | ||
| Outcome and Prevention of Infectious Diseases | 35 | ||
| Outcome of Infectious Diseases | 35 | ||
| Prevention of Infectious Diseases | 36 | ||
| Immunization | 37 | ||
| Epidemiology | 37 | ||
| Chapter Review | 37.e1 | ||
| Bibliography | 38 | ||
| II General Principles in Clinical Microbiology | 39 | ||
| 1 Safety and Specimen Management | 39 | ||
| 4 Laboratory Safety | 39 | ||
| Objectives | 39 | ||
| Sterilization and Disinfection | 39 | ||
| Methods of Sterilization | 39 | ||
| Methods of Disinfection | 40 | ||
| Physical Methods of Disinfection | 40 | ||
| Chemical Methods of Disinfection | 40 | ||
| Chemical Safety | 41 | ||
| Fire Safety | 42 | ||
| Electrical Safety | 43 | ||
| Handling of Compressed Gases | 43 | ||
| Biosafety | 43 | ||
| Exposure Control Plan | 44 | ||
| Employee Education and Orientation | 44 | ||
| Disposal of Hazardous Waste | 44 | ||
| Standard Precautions | 45 | ||
| Engineering Controls | 46 | ||
| Laboratory Environment | 46 | ||
| Biologic Safety Cabinet | 47 | ||
| Personal Protective Equipment | 48 | ||
| Postexposure Control | 49 | ||
| Classification of Biologic Agents Based on Hazard | 49 | ||
| Mailing Biohazardous Materials | 50 | ||
| Chapter Review | 52.e1 | ||
| Bibliography | 52 | ||
| 5 Specimen Management | 53 | ||
| Objectives | 53 | ||
| General Concepts for Specimen Collection and Handling | 53 | ||
| Appropriate Collection Techniques | 53 | ||
| Specimen Transport | 62 | ||
| Specimen Preservation | 62 | ||
| Specimen Storage | 62 | ||
| Specimen Labeling | 62 | ||
| Specimen Requisition | 62 | ||
| Rejection of Unacceptable Specimens | 63 | ||
| Specimen Processing | 63 | ||
| Gross Examination of Specimen | 63 | ||
| Direct Microscopic Examination | 63 | ||
| Selection of Culture Media | 64 | ||
| Specimen Preparation | 65 | ||
| Inoculation on Solid Media | 65 | ||
| Incubation Conditions | 65 | ||
| Specimen Workup | 66 | ||
| Extent of Identification Required | 66 | ||
| Communication of Laboratory Findings | 66 | ||
| Critical (Panic) Values | 66 | ||
| Expediting Results Reporting: Computerization | 67 | ||
| Chapter Review | 67.e1 | ||
| Bibliography | 67 | ||
| 2 Approaches to Diagnosis of Infectious Diseases | 68 | ||
| 6 Role of Microscopy | 68 | ||
| Objectives | 68 | ||
| Bright-Field (Light) Microscopy | 68 | ||
| Principles of Light Microscopy | 68 | ||
| Magnification | 68 | ||
| Resolution | 69 | ||
| Contrast | 70 | ||
| Staining Techniques for Light Microscopy | 70 | ||
| Smear Preparation | 70 | ||
| Gram Stain | 71 | ||
| Procedure Overview. | 71 | ||
| Principle. | 71 | ||
| Gram Stain Examination. | 71 | ||
| Gram Stain of Bacteria Grown in Culture. | 73 | ||
| Acid-Fast Stains | 73 | ||
| Principle. | 73 | ||
| Procedure Overview. | 73 | ||
| Phase Contrast Microscopy | 76 | ||
| Fluorescent Microscopy | 76 | ||
| Principle of Fluorescent Microscopy | 76 | ||
| Staining Techniques for Fluorescent Microscopy | 76 | ||
| Fluorochroming | 77 | ||
| Acridine Orange. | 78 | ||
| Auramine-Rhodamine. | 78 | ||
| Calcofluor White. | 79 | ||
| Immunofluorescence | 79 | ||
| Dark-Field Microscopy | 79 | ||
| Electron Microscopy | 80 | ||
| Chapter Review | 80.e1 | ||
| Bibliography | 80 | ||
| 7 Traditional Cultivation and Identification | 81 | ||
| Objectives | 81 | ||
| Principles of Bacterial Cultivation | 81 | ||
| Nutritional Requirements | 81 | ||
| General Concepts of Culture Media | 81 | ||
| Phases of Growth Media | 81 | ||
| Media Classifications and Functions | 82 | ||
| Summary of Artificial Media for Routine Bacteriology | 83 | ||
| Brain-Heart Infusion. | 86 | ||
| Chocolate Agar. | 86 | ||
| Columbia CNA with Blood. | 86 | ||
| Gram-Negative (GN) Broth. | 86 | ||
| Hektoen Enteric (HE) Agar. | 86 | ||
| MacConkey Agar. | 86 | ||
| Phenylethyl Alcohol (PEA) Agar. | 87 | ||
| Sheep Blood Agar. | 87 | ||
| Modified Thayer-Martin Agar. | 87 | ||
| Thioglycollate Broth. | 87 | ||
| Xylose-Lysine-Desoxycholate (XLD) Agar. | 88 | ||
| Preparation of Artificial Media | 88 | ||
| Media Sterilization. | 89 | ||
| Cell Cultures. | 89 | ||
| Environmental Requirements | 89 | ||
| Oxygen and Carbon Dioxide Availability | 89 | ||
| Temperature | 89 | ||
| pH | 89 | ||
| Moisture | 89 | ||
| Methods for Providing Optimum Incubation Conditions | 90 | ||
| Bacterial Cultivation | 90 | ||
| Isolation of Bacteria From Specimens | 90 | ||
| Evaluation of Colony Morphologies | 90 | ||
| Type of Media Supporting Bacterial Growth. | 90 | ||
| Relative Quantities of Each Colony Type. | 92 | ||
| Colony Characteristics. | 92 | ||
| Gram Stain and Subcultures. | 92 | ||
| Principles of Identification | 93 | ||
| Organism Identification Using Genotypic Criteria | 94 | ||
| Organism Identification Using Phenotypic Criteria | 94 | ||
| Microscopic Morphology and Staining Characteristics | 95 | ||
| Macroscopic (Colony) Morphology | 96 | ||
| Environmental Requirements for Growth | 96 | ||
| Resistance or Susceptibility to Antimicrobial Agents | 96 | ||
| Nutritional Requirements and Metabolic Capabilities | 97 | ||
| Establishing Enzymatic Capabilities. | 97 | ||
| Types of Enzyme-Based Tests. | 97 | ||
| Single Enzyme Tests. | 97 | ||
| Catalase Test. | 97 | ||
| Oxidase Test. | 97 | ||
| Indole Test. | 97 | ||
| Urease Test. | 97 | ||
| PYR Test. | 97 | ||
| Hippurate Hydrolysis. | 97 | ||
| Tests for Presence of Metabolic Pathways. | 98 | ||
| Oxidation and Fermentation Tests. | 98 | ||
| Amino Acid Degradation. | 98 | ||
| Single Substrate Utilization. | 99 | ||
| Establishing Inhibitor Profiles. | 99 | ||
| Principles of Phenotype-Based Identification Schemes | 99 | ||
| Selection and Inoculation of Identification Test Battery | 99 | ||
| Type of Bacteria to Be Identified | 100 | ||
| Clinical Significance of the Bacterial Isolate | 100 | ||
| Availability of Reliable Testing Methods | 100 | ||
| Incubation for Substrate Utilization | 101 | ||
| Conventional Identification | 101 | ||
| Rapid Identification | 101 | ||
| Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF) | 101 | ||
| Detection of Metabolic Activity | 101 | ||
| Colorimetry | 102 | ||
| Fluorescence | 102 | ||
| Turbidity | 102 | ||
| Analysis of Metabolic Profiles | 102 | ||
| Identification Databases | 102 | ||
| Use of the Database to Identify Unknown Isolates | 103 | ||
| Confidence in Identification. | 103 | ||
| Commercial Identification Systems | 104 | ||
| Advantages and Examples of Commercial System Designs | 104 | ||
| Overview of Commercial Systems | 105 | ||
| Chapter Review | 105.e1 | ||
| Bibliography | 105 | ||
| 8 Nucleic Acid–Based Analytic Methods for Microbial Identification and Characterization | 106 | ||
| Objectives | 106 | ||
| Overview of Molecular Methods | 106 | ||
| Specimen Collection and Transport | 106 | ||
| Nucleic Acid Hybridization Methods | 107 | ||
| Hybridization Steps and Components | 108 | ||
| Production and Labeling of Probe Nucleic Acid. | 108 | ||
| Preparation of Target Nucleic Acid. | 108 | ||
| Mixture and Hybridization of Target and Probe. | 109 | ||
| Detection of Hybridization. | 110 | ||
| Hybridization Formats | 110 | ||
| Solution Format. | 110 | ||
| Solid Support Format. | 110 | ||
| In Situ Hybridization. | 111 | ||
| Peptide Nucleic Acid (PNA) Probes. | 112 | ||
| Hybridization with Signal Amplification. | 112 | ||
| Amplification Methods—PCR Based | 112 | ||
| Overview of PCR and Derivations | 113 | ||
| Extraction and Denaturation of Target Nucleic Acid. | 113 | ||
| Primer Annealing. | 114 | ||
| Extension of Primer-Target Duplex. | 114 | ||
| Detection of PCR Products. | 115 | ||
| Derivations of the PCR Method. | 115 | ||
| Real-Time PCR | 117 | ||
| Digital PCR | 121 | ||
| Amplification Methods: Non–PCR-Based | 122 | ||
| Isothermal Amplification | 122 | ||
| Probe Amplification | 123 | ||
| Sequencing and Enzymatic Digestion of Nucleic Acids | 123 | ||
| Nucleic Acid Sequencing | 123 | ||
| POST-AMPLIFICATION AND TRADITIONAL ANALYSIS | 125 | ||
| Nucleic Acid Electrophoresis | 125 | ||
| Pyrosequencing | 125 | ||
| High-Density DNA Probes | 125 | ||
| Low- to Moderate-Density Arrays | 125 | ||
| Enzymatic Digestion and Electrophoresis of Nucleic Acids | 125 | ||
| Applications of Nucleic Acid–based Methods | 127 | ||
| Direct Detection of Microorganisms | 127 | ||
| Advantages and Disadvantages | 128 | ||
| Specificity. | 128 | ||
| Sensitivity. | 128 | ||
| Amplification Techniques Enhance Sensitivity. | 128 | ||
| Applications for Direct Molecular Detection of Microorganisms | 129 | ||
| Identification of Microorganisms Grown in Culture | 129 | ||
| Characterization of Microorganisms Beyond Identification | 129 | ||
| Detection of Antimicrobial Resistance | 129 | ||
| Investigation of Strain Relatedness/Pulsed-Field Gel Electrophoresis | 130 | ||
| Automation and Instrumentation | 132 | ||
| Chapter Review | 132.e1 | ||
| Bibliography | 132 | ||
| 9 Immunochemical Methods Used for Organism Detection | 133 | ||
| Objectives | 133 | ||
| Production of Antibodies for Use in Laboratory Testing | 133 | ||
| Polyclonal Antibodies | 133 | ||
| Monoclonal Antibodies | 133 | ||
| Principles of Immunochemical Methods Used for Organism Detection | 134 | ||
| Precipitation Tests | 134 | ||
| Double Immunodiffusion | 134 | ||
| Particle Agglutination | 135 | ||
| Latex Agglutination | 135 | ||
| Coagglutination | 136 | ||
| Immunofluorescent Assays | 136 | ||
| Enzyme Immunoassays | 137 | ||
| Solid-Phase Immunoassay | 138 | ||
| Membrane-Bound SPIA | 138 | ||
| Other Immunoassays | 141 | ||
| Chapter Review | 141.e1 | ||
| Bibliography | 141 | ||
| 10 Serologic Diagnosis of Infectious Diseases | 142 | ||
| Objectives | 142 | ||
| Features of the Immune Response | 142 | ||
| Characteristics of Antibodies | 142 | ||
| Features of the Humoral Immune Response Useful in Diagnostic Testing | 143 | ||
| Interpretation of Serologic Tests | 144 | ||
| Serodiagnosis of Infectious Diseases | 144 | ||
| Principles of Serologic Test Methods | 145 | ||
| Separating IgM from IgG for Serologic Testing | 145 | ||
| Methods of Antibody Detection | 146 | ||
| Direct Whole Pathogen Agglutination Assays | 146 | ||
| Particle Agglutination Tests | 147 | ||
| Flocculation Tests | 147 | ||
| Immunodiffusion Assays | 148 | ||
| Hemagglutination Inhibition Assays | 148 | ||
| Neutralization Assays | 148 | ||
| Complement Fixation Assays | 148 | ||
| Enzyme-Linked Immunosorbent Assays | 149 | ||
| Indirect Fluorescent Antibody Tests and Other Immunomicroscopic Methods | 150 | ||
| Radioimmunoassays | 150 | ||
| Fluorescent Immunoassays | 150 | ||
| Western Blot Immunoassays | 152 | ||
| Chapter Review | 152.e1 | ||
| 3 Evaluation of Antimicrobial Activity | 153 | ||
| 11 Principles of Antimicrobial Action and Resistance | 153 | ||
| Objectives | 153 | ||
| Antimicrobial Action | 153 | ||
| Principles | 153 | ||
| Mode of Action of Antibacterial Agents | 155 | ||
| Inhibitors of Cell Wall Synthesis | 155 | ||
| β-Lactam (Beta-Lactam) Antimicrobial Agents. | 155 | ||
| Glycopeptides and Lipopeptides. | 157 | ||
| Inhibitors of Cell Membrane Function | 157 | ||
| Inhibitors of Protein Synthesis | 157 | ||
| Aminoglycosides and Aminocyclitols. | 157 | ||
| Macrolide-Lincosamide-Streptogramin (MLS) Group. | 158 | ||
| Ketolides. | 158 | ||
| Oxazolidinones. | 158 | ||
| Chloramphenicol. | 158 | ||
| Tetracyclines. | 159 | ||
| Glycylglycines. | 159 | ||
| Inhibitors of DNA and RNA Synthesis | 159 | ||
| Fluoroquinolones. | 159 | ||
| Metronidazole. | 159 | ||
| Rifamycin. | 159 | ||
| Inhibitors of Other Metabolic Processes | 160 | ||
| Sulfonamides. | 160 | ||
| Trimethoprim. | 160 | ||
| Nitrofurantoin. | 160 | ||
| Mechanisms of Antibiotic Resistance | 160 | ||
| Principles | 160 | ||
| Biologic Versus Clinical Resistance | 160 | ||
| Environmentally Mediated Antimicrobial Resistance | 161 | ||
| Microorganism-Mediated Antimicrobial Resistance | 161 | ||
| Intrinsic Resistance | 162 | ||
| Acquired Resistance | 162 | ||
| Common Pathways for Antimicrobial Resistance | 162 | ||
| Resistance to Beta-Lactam Antibiotics | 163 | ||
| Resistance to Glycopeptides | 165 | ||
| Resistance to Aminoglycosides | 166 | ||
| Resistance to Quinolones | 166 | ||
| Resistance to Other Antimicrobial Agents | 166 | ||
| Emergence and Dissemination of Antimicrobial Resistance | 166 | ||
| Chapter Review | 167.e1 | ||
| Bibliography | 167 | ||
| 12 Laboratory Methods and Strategies for Antimicrobial Susceptibility Testing | 168 | ||
| Objectives | 168 | ||
| Goal and Limitations | 168 | ||
| Standardization | 168 | ||
| Limitations of Standardization | 169 | ||
| Testing Methods | 169 | ||
| Principles | 169 | ||
| Methods That Directly Measure Antimicrobial Activity | 169 | ||
| Conventional Testing Methods: General Considerations | 169 | ||
| Inoculum Preparation. | 169 | ||
| Selection of Antimicrobial Agents for Testing. | 170 | ||
| Conventional Testing Methods: Broth Dilution | 170 | ||
| Procedures. | 171 | ||
| Medium and Antimicrobial Agents. | 171 | ||
| Inoculation and Incubation. | 171 | ||
| Reading and Interpretation of Results. | 172 | ||
| Advantages and Disadvantages. | 172 | ||
| Conventional Testing Methods: Agar Dilution | 173 | ||
| Conventional Testing Methods: Disk Diffusion | 174 | ||
| Procedures. | 175 | ||
| Medium and Antimicrobial Agents. | 175 | ||
| Inoculation and Incubation. | 176 | ||
| Reading and Interpretation of Results. | 176 | ||
| Advantages and Disadvantages. | 177 | ||
| Commercial Susceptibility Testing Systems | 178 | ||
| Broth Microdilution Methods. | 178 | ||
| Agar Dilution Derivations. | 178 | ||
| Diffusion in Agar Derivations. | 178 | ||
| Automated Antimicrobial Susceptibility Test Systems. | 178 | ||
| Alternative Approaches for Enhancing Resistance Detection | 179 | ||
| Supplemental Testing Methods. | 180 | ||
| Predictor Antimicrobial Agents. | 183 | ||
| Methods That Directly Detect Specific Resistance Mechanisms | 183 | ||
| Phenotypic Methods | 183 | ||
| β-Lactamase Detection. | 183 | ||
| Chloramphenicol Acetyltransferase Detection. | 183 | ||
| Genotypic Methods | 184 | ||
| Special Methods for Complex Antimicrobial/Organism Interactions | 184 | ||
| Bactericidal Tests | 184 | ||
| Minimal Bactericidal Concentration. | 185 | ||
| Time-Kill Studies. | 185 | ||
| Serum Bactericidal (Schlichter Test). | 185 | ||
| Tests for Activity of Antimicrobial Combinations | 185 | ||
| Laboratory Strategies for Antimicrobial Susceptibility Testing | 186 | ||
| Relevance | 186 | ||
| When to Perform a Susceptibility Test | 187 | ||
| Determining Clinical Significance | 187 | ||
| Predictability of Antimicrobial Susceptibility | 187 | ||
| Availability of Reliable Susceptibility Testing Methods | 188 | ||
| Selection of Antimicrobial Agents for Testing | 188 | ||
| Accuracy | 188 | ||
| Use of Accurate Methodologies | 188 | ||
| Review of Results | 190 | ||
| Components of Results Review Strategies | 190 | ||
| Data Review. | 190 | ||
| Resolution. | 191 | ||
| Accuracy and Antimicrobial Resistance Surveillance | 191 | ||
| Communication | 192 | ||
| Chapter Review | 192.e1 | ||
| Reference | 192 | ||
| Bibliography | 192 | ||
| III Bacteriology | 193 | ||
| 1 Principles of Identification | 193 | ||
| 13 Overview of Bacterial Identification Methods and Strategies | 193 | ||
| Objectives | 193 | ||
| Rationale for Approaching Organism Identification | 193 | ||
| Future Trends of Organism Identification | 196 | ||
| Bibliography | 231 | ||
| 2 Catalase-Positive, Gram-Positive Cocci | 232 | ||
| 14 Staphylococcus, Micrococcus, and Similar Organisms | 232 | ||
| Objectives | 232 | ||
| General Characteristics | 232 | ||
| Epidemiology | 232 | ||
| Pathogenesis and Spectrum of Disease | 233 | ||
| Laboratory Diagnosis | 235 | ||
| Specimen Collection and Transport | 235 | ||
| Specimen Processing | 235 | ||
| Direct Detection Methods | 235 | ||
| Microscopy | 235 | ||
| Nucleic Acid Testing | 236 | ||
| Cultivation | 236 | ||
| Media of Choice | 236 | ||
| Incubation Conditions and Duration | 237 | ||
| Colonial Appearance | 237 | ||
| Approach to Identification | 237 | ||
| Comments Regarding Specific Organisms | 238 | ||
| Serodiagnosis | 240 | ||
| Antimicrobial Susceptibility Testing and Therapy | 242 | ||
| Prevention | 244 | ||
| Chapter Review | 244.e1 | ||
| Bibliography | 246 | ||
| 3 Catalase-Negative, Gram-Positive Cocci | 247 | ||
| 15 Streptococcus, Enterococcus, and Similar Organisms | 247 | ||
| Objectives | 247 | ||
| General Characteristics | 247 | ||
| Epidemiology | 248 | ||
| Pathogenesis and Spectrum of Disease | 248 | ||
| Beta-Hemolytic Streptococci | 248 | ||
| Streptococcus Pneumoniae and Viridans Streptococci | 251 | ||
| Enterococci | 251 | ||
| Miscellaneous Other Gram-Positive Cocci | 252 | ||
| Laboratory Diagnosis | 252 | ||
| Specimen Collection and Transport | 252 | ||
| Specimen Processing | 252 | ||
| Direct Detection Methods | 252 | ||
| Antigen Detection | 252 | ||
| Molecular Diagnostic Testing | 252 | ||
| Gram Stain | 253 | ||
| Cultivation | 253 | ||
| Media of Choice | 253 | ||
| Incubation Conditions and Duration | 255 | ||
| Colonial Appearance | 255 | ||
| Approach to Identification | 255 | ||
| Comments Regarding Specific Organisms | 255 | ||
| Serodiagnosis | 259 | ||
| Antimicrobial Susceptibility Testing and Therapy | 260 | ||
| Prevention | 262 | ||
| Chapter Review | 262.e1 | ||
| Bibliography | 264 | ||
| 4 Non-Branching, Catalase-Positive, Gram-Positive Bacilli | 265 | ||
| 16 Bacillus and Similar Organisms | 265 | ||
| Objectives | 265 | ||
| General Characteristics | 265 | ||
| Bacillus Anthracis | 265 | ||
| Epidemiology | 265 | ||
| IV Parasitology | 546 | ||
| 1 Principles of Identification | 546 | ||
| 47 Laboratory Methods for Diagnosis of Parasitic Infections: Overview | 546 | ||
| Objectives | 546 | ||
| Epidemiology | 546 | ||
| Pathogenesis and Spectrum of Disease | 546 | ||
| Laboratory Diagnosis | 549 | ||
| Specimen Collection and Transport | 558 | ||
| Specimen Processing | 558 | ||
| Approach to Identification | 563 | ||
| Microscopic Examination | 563 | ||
| Intestinal Tract | 565 | ||
| O&P Examination. | 571 | ||
| Recovery of the Tapeworm Scolex. | 572 | ||
| Examination for Pinworm. | 572 | ||
| Sigmoidoscopy Material. | 572 | ||
| Duodenal Drainage. | 573 | ||
| Duodenal Capsule Technique (Entero-Test). | 573 | ||
| Urogenital Tract Specimens | 573 | ||
| Sputum | 575 | ||
| Aspirates | 575 | ||
| Biopsy Specimens | 576 | ||
| Blood | 578 | ||
| Thin Blood Films. | 578 | ||
| Thick Blood Films. | 580 | ||
| Blood Film Stains. | 580 | ||
| Buffy Coat Films. | 580 | ||
| Direct Detection Methods | 580 | ||
| Intestinal Parasites | 581 | ||
| Blood Parasites | 581 | ||
| Cultivation | 581 | ||
| Larval-Stage Nematodes | 581 | ||
| Protozoa | 581 | ||
| Serodiagnosis | 581 | ||
| Prevention | 583 | ||
| Chapter Review | 583.e1 | ||
| Bibliography | 583 | ||
| 48 Intestinal Protozoa | 585 | ||
| Objectives | 585 | ||
| Amebae | 585 | ||
| Entamoeba histolytica | 585 | ||
| General Characteristics | 585 | ||
| Epidemiology | 590 | ||
| Pathogenesis and Spectrum of Disease | 590 | ||
| Asymptomatic Infection. | 593 | ||
| Intestinal Disease. | 593 | ||
| Hepatic Disease. | 593 | ||
| Laboratory Diagnosis | 595 | ||
| Routine Methods. | 595 | ||
| Antigen Detection. | 595 | ||
| Antibody Detection. | 595 | ||
| Histology. | 595 | ||
| Nucleic Acid-Based Techniques | 595 | ||
| Therapy | 595 | ||
| Asymptomatic Infection. | 596 | ||
| Mild to Moderate Disease. | 596 | ||
| Severe Intestinal Disease. | 596 | ||
| Hepatic Disease. | 596 | ||
| Prevention | 596 | ||
| Entamoeba coli | 596 | ||
| General Characteristics | 596 | ||
| Epidemiology | 596 | ||
| Pathogenesis and Spectrum of Disease | 596 | ||
| Laboratory Diagnosis | 596 | ||
| Therapy | 596 | ||
| Prevention | 597 | ||
| Entamoeba hartmanni | 597 | ||
| General Characteristics | 597 | ||
| Epidemiology | 598 | ||
| Pathogenesis and Spectrum of Disease | 598 | ||
| Laboratory Diagnosis | 598 | ||
| Endolimax nana | 598 | ||
| General Characteristics | 598 | ||
| Epidemiology | 599 | ||
| Pathogenesis and Spectrum of Disease | 599 | ||
| Laboratory Diagnosis | 599 | ||
| Iodamoeba bütschlii | 599 | ||
| General Characteristics | 599 | ||
| Epidemiology | 600 | ||
| Pathogeneis and Spectrum of Disease | 600 | ||
| Laboratory Diagnosis | 600 | ||
| Therapy | 600 | ||
| Prevention (E. hartmanni, E. nana, I. bütschlii) | 601 | ||
| Blastocystis hominis | 601 | ||
| General Characteristics | 601 | ||
| Epidemiology | 602 | ||
| Pathogenesis and Spectrum of Disease | 602 | ||
| Laboratory Diagnosis | 602 | ||
| Routine Methods. | 602 | ||
| Antigen Detection. | 602 | ||
| Antibody Detection. | 603 | ||
| Therapy | 603 | ||
| Prevention | 603 | ||
| Flagellates | 603 | ||
| Giardia lamblia | 603 | ||
| General Characteristics | 603 | ||
| Epidemiology | 603 | ||
| Pathogenesis and Spectrum of Disease | 604 | ||
| Asymptomatic Infection. | 604 | ||
| Intestinal Disease. | 605 | ||
| Chronic Disease. | 607 | ||
| Antigenic Variation. | 607 | ||
| Laboratory Diagnosis | 607 | ||
| Routine Methods. | 607 | ||
| Antigen Detection. | 607 | ||
| Antibody Detection. | 607 | ||
| Histology. | 607 | ||
| Nucleic Acid-Based Techniques | 608 | ||
| V Mycology | 705 | ||
| 59 Overview of Fungal Identification Methods and Strategies | 705 | ||
| Objectives | 705 | ||
| Epidemiology | 705 | ||
| General Features of the Fungi | 706 | ||
| Taxonomy of the Fungi | 706 | ||
| Clinical Classification of the Fungi | 707 | ||
| Practical Working Schema | 709 | ||
| Pathogeneis and Spectrum of Disease | 709 | ||
| Laboratory Diagnosis | 712 | ||
| Collection, Transport, and Culturing of Clinical Specimens | 712 | ||
| Respiratory Tract Secretions | 713 | ||
| Cerebrospinal Fluid | 713 | ||
| Blood | 714 | ||
| Hair, Skin, and Nail Scrapings | 714 | ||
| Vaginal | 714 | ||
| Urine | 714 | ||
| Tissue, Bone Marrow, and Sterile Body Fluids | 714 | ||
| Culture Media and Incubation Requirements | 714 | ||
| Direct Microscopic Examination | 717 | ||
| Serodiagnosis | 717 | ||
| Molecular Detection | 717 | ||
| MALDI-TOF (Matrix-Assisted Laser Desorption Ionization) | 717 | ||
| General Considerations for the Identification of Yeasts | 717 | ||
| General Considerations for the Identification of Molds | 721 | ||
| General Morphologic Features of the Molds | 722 | ||
| Clinical Relevance for Fungal Identification | 725 | ||
| Laboratory Safety | 726 | ||
| Prevention | 730 | ||
| Chapter Review | 730.e1 | ||
| Bibliography | 730 | ||
| 60 Hyaline Molds, Mucorales (Zygomycetes), Dermatophytes, and Opportunistic and Systemic Mycoses | 732 | ||
| Objectives | 732 | ||
| The Mucorales | 732 | ||
| General Characteristics | 732 | ||
| Epidemiology and Pathogenesis | 732 | ||
| Spectrum of Disease | 732 | ||
| Laboratory Diagnosis | 733 | ||
| Specimen Collection and Transport | 733 | ||
| Specimen Processing | 733 | ||
| Direct Detection Methods | 733 | ||
| Stains. | 733 | ||
| Antigen-Protein. | 733 | ||
| Nucleic Acid Amplification. | 733 | ||
| Cultivation. | 733 | ||
| Approach to Identification | 733 | ||
| Serodiagnosis | 734 | ||
| The Dermatophytes | 734 | ||
| General Characteristics | 734 | ||
| Epidemiology and Pathogenesis | 734 | ||
| Spectrum of Disease | 734 | ||
| Trichophyton spp. | 734 | ||
| Laboratory Diagnosis | 734 | ||
| Specimen Collection and Transport | 734 | ||
| Specimen Processing | 734 | ||
| Direct Detection Methods | 734 | ||
| Stains. | 734 | ||
| Antigen-Protein. | 735 | ||
| Nucleic Acid Amplification. | 735 | ||
| Cultivation. | 735 | ||
| Approach to Identification | 735 | ||
| Trichophyton spp. | 735 | ||
| Microsporum spp. | 739 | ||
| Epidermophyton sp. | 740 | ||
| Serodiagnosis | 740 | ||
| The Opportunistic Mycoses | 740 | ||
| General Characteristics | 740 | ||
| Epidemiology and Pathogenesis | 741 | ||
| VI Virology | 786 | ||
| 65 Overview of the Methods and Strategies in Virology* | 786 | ||
| Objectives | 786 | ||
| General Characteristics | 787 | ||
| Viral Structure | 787 | ||
| Virus Taxonomy | 787 | ||
| Viral Replication | 789 | ||
| Epidemiology | 790 | ||
| Pathogenesis and Spectrum of Disease | 790 | ||
| Prevention and Therapy | 790 | ||
| Antiviral Agents | 790 | ||
| Viruses That Cause Human Diseases | 791 | ||
| Laboratory Diagnosis | 791 | ||
| Setting Up a Clinical Virology Laboratory | 791 | ||
| Specimen Selection and Collection | 792 | ||
| General Principles | 792 | ||
| Throat, Nasopharyngeal Swab, or Aspirate | 796 | ||
| Bronchial and Bronchoalveolar Washes | 796 | ||
| Rectal Swabs and Stool Specimens | 796 | ||
| Urine | 796 | ||
| Skin and Mucous Membrane Lesions | 796 | ||
| Sterile Body Fluids Other Than Blood | 796 | ||
| Blood | 796 | ||
| Bone Marrow | 797 | ||
| Tissue | 797 | ||
| Genital Specimens | 797 | ||
| Serum for Antibody Testing | 797 | ||
| Specimen Transport and Storage | 797 | ||
| Specimen Processing | 798 | ||
| General Principles | 798 | ||
| Processing Based on Specimen Type | 798 | ||
| Lip and Genital Specimens. | 798 | ||
| Urine. | 798 | ||
| Stool. | 798 | ||
| Respiratory Tract. | 799 | ||
| Specimens from Neonatal Patients. | 799 | ||
| Cerebrospinal Fluid. | 799 | ||
| Blood. | 799 | ||
| Processing Based on Requests for Specific Viruses | 799 | ||
| Arboviruses. | 799 | ||
| Cytomegalovirus. | 800 | ||
| Enteroviruses. | 800 | ||
| Epstein-Barr Virus. | 800 | ||
| Hepatitis Viruses. | 800 | ||
| Herpes Simplex Virus. | 801 | ||
| Human Immunodeficiency Virus and Other Retroviruses. | 802 | ||
| Influenza A and B Viruses. | 802 | ||
| Pediatric Respiratory Viruses. | 802 | ||
| Gastroenteritis Viruses. | 802 | ||
| TORCH. | 803 | ||
| Varicella-Zoster Virus. | 804 | ||
| Virus Detection Methods | 805 | ||
| Cytology and Histology | 805 | ||
| Electron Microscopy | 807 | ||
| Immunodiagnosis (Antigen Detection) | 807 | ||
| Enzyme-Linked Virus-Inducible System | 809 | ||
| Molecular Detection Using Nucleic Acid Probes and Polymerase Chain Reaction Assays | 809 | ||
| Cell Culture | 812 | ||
| Conventional Cell Culture. | 812 | ||
| Shell Vial Cell Culture. | 814 | ||
| Identification of Viruses Detected in Cell Culture. | 814 | ||
| Viral Serology | 816 | ||
| General Principles | 816 | ||
| Immune Status Testing | 818 | ||
| Serology Panels | 819 | ||
| Preservation and Storage of Viruses | 819 | ||
| Chapter Review | 819.e2 | ||
| Bibliography | 820 | ||
| 66 Viruses in Human Disease | 821 | ||
| Objectives | 821 | ||
| Viruses in Human Disease | 821 | ||
| Adenoviruses | 821 | ||
| Arenaviruses | 822 | ||
| Bunyaviruses | 824 | ||
| Caliciviruses | 825 | ||
| Coronaviruses | 826 | ||
| Filoviruses | 827 | ||
| Flaviviruses | 827 | ||
| Hepevirus | 829 | ||
| Hepadnaviruses | 830 | ||
| Herpes Viruses | 831 | ||
| Orthomyxoviruses | 836 | ||
| Papillomaviruses | 838 | ||
| Paramyxoviruses | 839 | ||
| Parvoviruses | 841 | ||
| Picornaviruses | 841 | ||
| Polyomaviruses | 843 | ||
| Poxviruses | 844 | ||
| Reoviruses | 845 | ||
| Retroviruses | 846 | ||
| Rhabdoviruses | 847 | ||
| Togaviruses | 849 | ||
| Miscellaneous Viruses | 849 | ||
| Interpretation of Laboratory Test Results | 849 | ||
| Viruses in Tissue and Body Fluids | 850 | ||
| Viruses in the Respiratory Tract | 850 | ||
| Viruses in the Eye | 850 | ||
| Detection of Epstein-Barr Virus | 850 | ||
| Detection of Enteroviruses | 850 | ||
| Detection of Hepatitis Viruses | 850 | ||
| Detection of Varicella-Zoster Virus and Herpes Simplex Virus | 851 | ||
| Detection of Cytomegalovirus | 851 | ||
| Detection of Human Immunodeficiency Virus | 851 | ||
| Chapter Review | 851.e1 | ||
| Bibliography | 852 | ||
| 67 Antiviral Therapy, Susceptibility Testing, and Prevention | 853 | ||
| Objectives | 853 | ||
| Antiviral Therapy | 853 | ||
| Antiviral Resistance | 853 | ||
| Methods of Antiviral Susceptibility Testing | 854 | ||
| Phenotypic Assays | 854 | ||
| Plaque Reduction Assay | 854 | ||
| DU Assay | 854 | ||
| DNA Hybridization | 854 | ||
| Enzyme Immunoassay | 854 | ||
| Flow Cytometry | 854 | ||
| Neuraminidase Inhibition Assay | 854 | ||
| Genotypic Susceptibility Assays | 855 | ||
| Pyrosequencing | 855 | ||
| Human Immunodeficiency Virus | 855 | ||
| Influenza | 855 | ||
| Prevention of Other Viral Infections | 857 | ||
| Vaccination | 857 | ||
| Immune Prophylaxis and Therapy | 858 | ||
| Eradication | 858 | ||
| Chapter Review | 858.e1 | ||
| Bibliography | 858 | ||
| VII Diagnosis by Organ System | 860 | ||
| 68 Bloodstream Infections | 860 | ||
| Objectives | 860 | ||
| General Considerations | 860 | ||
| Etiology | 860 | ||
| Bacteria | 860 | ||
| Fungi | 861 | ||
| Parasites | 861 | ||
| Viruses | 861 | ||
| Types of Bacteremia | 862 | ||
| Types of Bloodstream Infections | 862 | ||
| Intravascular Infections | 862 | ||
| Infective Endocarditis. | 862 | ||
| Mycotic Aneurysm and Suppurative Thrombophlebitis. | 863 | ||
| Intravenous Catheter–Associated Bacteremia. | 863 | ||
| Extravascular Infections | 865 | ||
| Clinical Manifestations | 865 | ||
| Immunocompromised Patients | 866 | ||
| Detection of Bacteremia | 866 | ||
| Specimen Collection | 866 | ||
| Preparation of the Site | 866 | ||
| Antisepsis. | 866 | ||
| Precautions. | 867 | ||
| Specimen Volume | 867 | ||
| Adults. | 867 | ||
| Children. | 867 | ||
| Number of Blood Cultures | 867 | ||
| Timing of Collection | 868 | ||
| Miscellaneous Matters | 868 | ||
| Anticoagulation. | 868 | ||
| Dilution. | 868 | ||
| Blood Culture Media. | 868 | ||
| Types of Blood Culture Bottle | 868 | ||
| Culture Techniques | 869 | ||
| Conventional Blood Cultures | 869 | ||
| Incubation Conditions. | 869 | ||
| Self-Contained Subculture System | 869 | ||
| Lysis Centrifugation | 869 | ||
| Instrument-Based Systems | 870 | ||
| BACTEC Systems. | 870 | ||
| BacT/ALERT Microbial Detection System. | 870 | ||
| Versa TREK System. | 870 | ||
| Techniques to Detect IV Catheter–Associated Infections | 870 | ||
| Handling Positive Blood Cultures | 872 | ||
| Interpretation of Blood Culture Results | 873 | ||
| Special Considerations for Other Relevant Organisms Isolated From Blood | 874 | ||
| HACEK (AACEK) Bacteria | 874 | ||
| Campylobacter and Helicobacter | 874 | ||
| Fungi | 874 | ||
| Mycobacteria | 874 | ||
| Brucella | 875 | ||
| Spirochetes | 875 | ||
| Borrelia | 875 | ||
| Leptospira | 875 | ||
| Vitamin B6-Dependent Streptococci | 875 | ||
| Mycoplasma Hominis | 875 | ||
| Bartonella | 875 | ||
| Chapter Review | 876.e1 | ||
| Bibliography | 876 | ||
| 69 Infections of the Lower Respiratory System | 878 | ||
| Objectives | 878 | ||
| General Considerations | 878 | ||
| Anatomy | 878 | ||
| Pathogenesis of the Respiratory Tract: Basic Concepts | 878 | ||
| Host Factors | 878 | ||
| Microorganism Factors | 879 | ||
| Adherence. | 879 | ||
| Toxins. | 880 | ||
| Microorganism Growth. | 880 | ||
| Avoiding the Host Response. | 880 | ||
| Diseases of the Lower Respiratory Tract | 881 | ||
| Bronchitis | 881 | ||
| Acute | 881 | ||
| Chronic versus Acute | 881 | ||
| Bronchiolitis | 882 | ||
| Pneumonia | 882 | ||
| Pathogenesis | 882 | ||
| Clinical Manifestations | 883 | ||
| Epidemiology/Etiologic Agents | 883 | ||
| Community-Acquired Pneumonia. | 883 | ||
| Children. | 883 | ||
| Young Adults. | 883 | ||
| Adults (Viral pneumonia). | 884 | ||
| Adults (Fungal pneumonia). | 884 | ||
| Chronic Lower Respiratory Tract Infections. | 885 | ||
| Immunocompromised Patients. | 885 | ||
| Patients with Neoplasms. | 885 | ||
| Transplant Recipients. | 885 | ||
| HIV-Infected Patients. | 885 | ||
| Pleural Infections | 885 | ||
| Laboratory Diagnosis of Lower Respiratory Tract Infections | 886 | ||
| Specimen Collection and Transport | 886 | ||
| Sputum | 886 | ||
| Expectorated. | 886 | ||
| Induced. | 886 | ||
| Endotracheal or Tracheostomy Suction Specimens | 887 | ||
| Bronchoscopy. | 887 | ||
| Transtracheal Aspirates. | 887 | ||
| Other Invasive Procedures. | 887 | ||
| Specimen Processing | 889 | ||
| Direct Visual Examination | 889 | ||
| Routine Culture | 890 | ||
| Chapter Review | 890.e1 | ||
| Bibliography | 891 | ||
| 70 Upper Respiratory Tract Infections and Other Infections of the Oral Cavity and Neck | 892 | ||
| Objectives | 892 | ||
| General Considerations | 892 | ||
| Anatomy | 892 | ||
| Pathogenesis | 892 | ||
| Diseases of the Upper Respiratory Tract, Oral Cavity, and Neck | 892 | ||
| Upper Respiratory Tract | 892 | ||
| Laryngitis | 892 | ||
| Laryngotracheobronchitis | 892 | ||
| Epiglottitis | 893 | ||
| Pharyngitis, Tonsillitis, and Peritonsillar Abscesses | 893 | ||
| Pharyngitis and Tonsillitis. | 893 | ||
| Clinical Manifestations. | 893 | ||
| Pathogenesis. | 893 | ||
| Epidemiology/Etiologic Agents. | 893 | ||
| Peritonsillar Abscesses. | 894 | ||
| Rhinitis | 894 | ||
| Miscellaneous Infections Caused by Other Agents. | 894 | ||
| Corynebacterium diphtheriae. | 894 | ||
| Bordetella pertussis. | 894 | ||
| Klebsiella spp. | 895 | ||
| Oral Cavity | 895 | ||
| Stomatitis | 895 | ||
| Thrush | 895 | ||
| Periodontal Infections | 895 | ||
| Types. | 895 | ||
| Etiologic Agents. | 895 | ||
| Salivary Gland Infections | 895 | ||
| Neck | 895 | ||
| Diagnosis of Upper Respiratory Tract Infections | 896 | ||
| Collection and Transport of Specimens | 896 | ||
| Direct Visual Examination or Detection | 896 | ||
| Culture | 897 | ||
| Streptococcus pyogenes (Beta-Hemolytic Group A Streptococci) | 897 | ||
| Corynebacterium diphtheriae | 897 | ||
| Bordetella pertussis | 897 | ||
| Neisseria | 898 | ||
| Epiglottitis | 898 | ||
| Diagnosis of Infections in the Oral Cavity and Neck | 898 | ||
| Collection and Transport | 898 | ||
| Direct Visual Examination | 898 | ||
| Culture | 898 | ||
| Chapter Review | 898.e1 | ||
| Bibliography | 898 | ||
| 71 Meningitis, Encephalitis, and Other Infections of the Central Nervous System | 899 | ||
| Objectives | 899 | ||
| General Considerations | 899 | ||
| Anatomy | 899 | ||
| Coverings and Spaces of the CNS | 899 | ||
| Cerebrospinal Fluid | 899 | ||
| Routes of Infection | 899 | ||
| Diseases of the Central Nervous System | 901 | ||
| Meningitis | 901 | ||
| Purulent Meningitis. | 901 | ||
| Pathogenesis. | 901 | ||
| Clinical Manifestations. | 902 | ||
| Acute. | 902 | ||
| Chronic. | 902 | ||
| Epidemiology/Etiologic Agents-Acute Meningitis. | 902 | ||
| Aseptic Meningitis. | 903 | ||
| Encephalitis/Meningoencephalitis | 903 | ||
| Viral. | 903 | ||
| Parasitic | 905 | ||
| Brain Abscess | 905 | ||
| SHUNT INFECTIONS | 905 | ||
| Laboratory Diagnosis of Central Nervous System Infections | 905 | ||
| Meningitis | 905 | ||
| Specimen Collection and Transport | 905 | ||
| Initial Processing | 906 | ||
| CSF Laboratory Results | 906 | ||
| Visual Detection of Etiologic Agents | 906 | ||
| Stained Smear of Sediment. | 906 | ||
| Wet Preparation. | 907 | ||
| India Ink Stain. | 907 | ||
| Direct Detection of Etiologic Agents | 907 | ||
| Antigen. | 907 | ||
| Bacteria. | 907 | ||
| Cryptococcus neoformans. | 908 | ||
| Molecular Methods. | 908 | ||
| Miscellaneous Tests | 908 | ||
| Culture | 908 | ||
| Bacteria and Fungi. | 908 | ||
| Parasites and Viruses. | 908 | ||
| Brain Abscess/Biopsies | 908 | ||
| Specimen Collection, Transport and Processing. | 908 | ||
| Chapter Review | 908.e1 | ||
| Bibliography | 909 | ||
| 72 Infections of the Eyes, Ears, and Sinuses | 910 | ||
| Objectives | 910 | ||
| Eyes | 910 | ||
| Anatomy | 910 | ||
| Resident Microbial Flora | 910 | ||
| Diseases | 910 | ||
| Pathogenesis | 910 | ||
| Epidemiology and Etiology of Disease | 911 | ||
| Blepharitis | 911 | ||
| Conjunctivitis | 911 | ||
| Keratitis | 913 | ||
| Endophthalmitis | 913 | ||
| Periocular | 913 | ||
| Other Infections | 914 | ||
| Laboratory Diagnosis | 914 | ||
| Specimen Collection and Transport | 914 | ||
| Direct Visual Examination | 914 | ||
| Culture | 914 | ||
| Nonculture Methods | 915 | ||
| Ears | 915 | ||
| Anatomy | 915 | ||
| Resident Microbial Flora | 915 | ||
| Diseases, Epidemiology, and Etiology of Disease | 915 | ||
| Otitis Externa (External Ear Infections) | 915 | ||
| Otitis Media (Middle Ear Infections) | 916 | ||
| Pathogenesis | 916 | ||
| Laboratory Diagnosis | 916 | ||
| Specimen Collection and Transport | 916 | ||
| Direct Visual Examination | 917 | ||
| Culture and Nonculture Methods | 917 | ||
| Sinuses | 917 | ||
| Anatomy | 917 | ||
| Diseases | 917 | ||
| Pathogenesis | 917 | ||
| Epidemiology and Etiology of Disease | 917 | ||
| Laboratory Diagnosis | 918 | ||
| Chapter Review | 918.e1 | ||
| Bibliography | 918 | ||
| 73 Infections of the Urinary Tract | 919 | ||
| Objectives | 919 | ||
| General Considerations | 919 | ||
| Anatomy | 919 | ||
| Resident Microorganisms of the Urinary Tract | 919 | ||
| Infections of the Urinary Tract | 919 | ||
| Epidemiology | 919 | ||
| Etiologic Agents | 920 | ||
| Community-Acquired | 920 | ||
| Hospital-Acquired | 920 | ||
| Miscellaneous | 920 | ||
| Pathogenesis | 921 | ||
| Routes of Infection | 921 | ||
| The Host-Parasite Relationship | 921 | ||
| Types of Infection and Their Clinical Manifestations | 922 | ||
| Urethritis | 922 | ||
| Ureteritis | 923 | ||
| Asymptomatic Bacteriuria | 923 | ||
| Cystitis | 923 | ||
| Acute Urethral Syndrome | 923 | ||
| Pyelonephritis | 923 | ||
| Urosepsis | 923 | ||
| Laboratory Diagnosis of Urinary Tract Infections | 923 | ||
| Specimen Collection | 923 | ||
| Clean-Catch Midstream Urine | 923 | ||
| Straight Catheterized Urine | 924 | ||
| Suprapubic Bladder Aspiration | 924 | ||
| Indwelling Catheter | 924 | ||
| Specimen Transport | 924 | ||
| Screening Procedures | 924 | ||
| Gram Stain | 925 | ||
| Pyuria | 925 | ||
| Indirect Indices | 925 | ||
| Nitrate Reductase (Greiss) Test. | 925 | ||
| Leukocyte Esterase Test. | 925 | ||
| Catalase. | 925 | ||
| Automated and Semiautomated Systems | 925 | ||
| General Comments Regarding Screening Procedures | 926 | ||
| Urine Culture | 926 | ||
| Inoculation and Incubation of Urine Cultures | 926 | ||
| Interpretation of Urine Cultures | 927 | ||
| Chapter Review | 929.e1 | ||
| Bibliography | 929 | ||
| 74 Genital Tract Infections | 931 | ||
| Objectives | 931 | ||
| General Considerations | 931 | ||
| Anatomy | 931 | ||
| Resident Microbial Flora | 931 | ||
| Sexually Transmitted Diseases and Other Genital Tract Infections | 931 | ||
| Genital Tract Infections | 932 | ||
| Sexually Transmitted Diseases and Other Lower Genital Tract Infections | 932 | ||
| Epidemiology/Etiologic Agents | 932 | ||
| Routes of Transmission | 932 | ||
| Sexually Transmitted. | 933 | ||
| Other Routes. | 933 | ||
| Clinical Manifestations | 934 | ||
| Asymptomatic. | 934 | ||
| Dysuria. | 934 | ||
| Urethral Discharge. | 934 | ||
| Lesions of the Skin and Mucous Membranes. | 934 | ||
| Vaginitis. | 935 | ||
| Cervicitis. | 936 | ||
| Anorectal Lesions. | 936 | ||
| Bartholinitis. | 937 | ||
| Infections of the Reproductive Organs and Other Upper Tract Infections | 937 | ||
| Females. | 937 | ||
| Pelvic Inflammatory Disease. | 937 | ||
| Infections after Gynecologic Surgery. | 937 | ||
| Infections Associated with Pregnancy. | 937 | ||
| Males. | 938 | ||
| Gonorrhea. | 938 | ||
| Syphilis. | 938 | ||
| Laboratory Diagnosis of Genital Tract Infections | 938 | ||
| Lower Genital Tract Infections | 938 | ||
| Urethritis, Cervicitis, and Vaginitis | 938 | ||
| Specimen Collection. | 938 | ||
| Urethral. | 938 | ||
| Cervical/Vaginal. | 939 | ||
| Transport. | 940 | ||
| Direct Microscopic Examination. | 940 | ||
| Culture. | 941 | ||
| Nonculture Methods. | 942 | ||
| Genital Skin and Mucous Membrane Lesions | 942 | ||
| Bubo | 943 | ||
| Infections of the Reproductive Organs | 943 | ||
| Pelvic Inflammatory Disease | 943 | ||
| Miscellaneous Infections | 943 | ||
| Infections of Neonates and Human Products of Conception | 943 | ||
| Chapter Review | 944.e1 | ||
| Bibliography | 944 | ||
| 75 Gastrointestinal Tract Infections | 945 | ||
| Objectives | 945 | ||
| Anatomy | 945 | ||
| Resident Microbial Flora | 945 | ||
| Gastroenteritis | 947 | ||
| Pathogenesis | 947 | ||
| Host Factors | 947 | ||
| Microbial Factors | 948 | ||
| Primary Pathogenic Mechanisms. | 948 | ||
| Toxins | 948 | ||
| Enterotoxins. | 948 | ||
| Cytotoxins. | 949 | ||
| Neurotoxins. | 949 | ||
| Attachment. | 951 | ||
| Invasion. | 951 | ||
| Miscellaneous Virulence Factors. | 953 | ||
| Clinical Manifestations | 953 | ||
| Epidemiology | 953 | ||
| Institutional Settings | 953 | ||
| Traveler’s Diarrhea | 953 | ||
| Food- and Water-Borne Outbreaks | 954 | ||
| Immunocompromised Hosts | 954 | ||
| Etiologic Agents | 954 | ||
| Other Infections of the Gastrointestinal Tract | 954 | ||
| Esophagitis | 954 | ||
| Gastritis | 954 | ||
| Proctitis | 954 | ||
| Miscellaneous | 954 | ||
| Laboratory Diagnosis of Gastrointestinal Tract Infections | 956 | ||
| Specimen Collection and Transport | 956 | ||
| General Comments | 956 | ||
| Stool Specimens for Bacterial Culture | 956 | ||
| Stool Specimens for Ova and Parasites | 956 | ||
| Stool Specimens for Viruses | 956 | ||
| Miscellaneous Specimen Types | 956 | ||
| Direct Detection of Agents of Gastroenteritis in Feces | 957 | ||
| Wet Mounts | 957 | ||
| Stains | 957 | ||
| Antigen Detection | 957 | ||
| Molecular Biologic Techniques | 957 | ||
| Culture of Fecal Material for Isolation of Etiologic Agents | 957 | ||
| Bacteria | 957 | ||
| Organisms for Routine Culture. | 957 | ||
| Routine Culture Methods. | 958 | ||
| Salmonella/Shigella. | 958 | ||
| Campylobacter. | 958 | ||
| Enrichment Broths. | 958 | ||
| Laboratory Diagnosis of Clostridium Difficile–associated Diarrhea | 958 | ||
| Chapter Review | 960.e1 | ||
| Bibliography | 960 | ||
| 76 Skin, Soft Tissue, and Wound Infections | 961 | ||
| Objectives | 961 | ||
| General Considerations | 961 | ||
| Anatomy of the Skin | 961 | ||
| Function of the Skin | 961 | ||
| Prevalence, Etiology, and Pathogenesis | 961 | ||
| Skin and Soft Tissue Infections | 962 | ||
| Infections of the Epidermis and Dermis | 962 | ||
| Infections in or around Hair Follicles | 962 | ||
| Infections in the Keratinized Layer of the Epidermis | 962 | ||
| Infections in the Deeper Layers of the Epidermis and Dermis | 962 | ||
| Infections of the Subcutaneous Tissues | 963 | ||
| Infections of the Muscle Fascia and Muscles | 965 | ||
| Necrotizing Fasciitis | 965 | ||
| Progressive Bacterial Synergistic Gangrene | 965 | ||
| Myositis | 965 | ||
| Wound Infections | 966 | ||
| Postoperative Infections | 966 | ||
| Bites | 966 | ||
| Burns | 967 | ||
| Special Circumstances Regarding Skin and Soft Tissue Infections | 967 | ||
| Infections Related to Vascular and Neurologic Problems | 967 | ||
| Sinus Tracts and Fistulas | 968 | ||
| Systemic Infections and Skin Manifestations | 969 | ||
| Laboratory Diagnostic Procedures | 969 | ||
| Infections of the Epidermis and Dermis | 969 | ||
| Erysipeloid | 969 | ||
| Superficial Mycoses and Erythrasma | 969 | ||
| Erysipelas and Cellulitis | 969 | ||
| Vesicles and Bullae | 969 | ||
| Infections of the Subcutaneous Tissues | 970 | ||
| Infections of the Muscle Fascia and Muscles | 970 | ||
| Wound Infections | 970 | ||
| Postoperative | 970 | ||
| Bites | 970 | ||
| Burns | 970 | ||
| Chapter Review | 970.e2 | ||
| Bibliography | 972 | ||
| 77 Normally Sterile Body Fluids, Bone and Bone Marrow, and Solid Tissues | 973 | ||
| Objectives | 973 | ||
| Specimens From Sterile Body Sites | 973 | ||
| Fluids | 973 | ||
| Pleural Fluid | 973 | ||
| Peritoneal Fluid | 973 | ||
| Primary Peritonitis. | 974 | ||
| Secondary Peritonitis. | 975 | ||
| Peritoneal Dialysis Fluid | 975 | ||
| Pericardial Fluid | 976 | ||
| Joint Fluid | 976 | ||
| Bone | 977 | ||
| Bone Marrow Aspiration or Biopsy | 977 | ||
| Bone Biopsy | 977 | ||
| Solid Tissues | 978 | ||
| Laboratory Diagnostic Procedures | 978 | ||
| Specimen Collection and Transport | 978 | ||
| Fluids and Aspirates | 978 | ||
| Bone | 979 | ||
| Tissue | 979 | ||
| Specimen Processing, Direct Examination, and Culture | 979 | ||
| Fluids and Aspirates | 979 | ||
| Bone | 980 | ||
| Solid Tissue | 981 | ||
| Chapter Review | 981.e1 | ||
| Bibliography | 981 | ||
| VIII Clinical Laboratory Managementy | 982 | ||
| 78 Quality in the Clinical Microbiology Laboratory | 982 | ||
| Objectives | 982 | ||
| Quality Program | 983 | ||
| Specimen Collection and Transport | 983 | ||
| Standard Operating Procedure Manual | 983 | ||
| Personnel | 983 | ||
| Reference Laboratories | 984 | ||
| Patient Reports | 984 | ||
| Proficiency Testing (PT) | 984 | ||
| Performance Checks | 984 | ||
| Instruments | 984 | ||
| Commercially Prepared Media Exempt From QC | 985 | ||
| User-Prepared and Nonexempt, Commercially Prepared Media | 985 | ||
| Antimicrobial Susceptibility Tests | 985 | ||
| Stains and Reagents | 985 | ||
| Antisera | 985 | ||
| Kits | 986 | ||
| Maintenance of QC Records | 986 | ||
| Maintenance of Reference QC Stocks | 986 | ||
| Bacteriology | 986 | ||
| Mycology | 986 | ||
| Mycobacteriology | 986 | ||
| Virology | 986 | ||
| Parasitology | 986 | ||
| QA Program | 986 | ||
| Q-Probes | 987 | ||
| In-House QA Audits | 987 | ||
| Conducting a QA Audit | 987 | ||
| Continuous Daily Monitoring | 987 | ||
| Chapter Review | 987.e1 | ||
| Bibliography | 988 | ||
| 79 Infection Control | 989 | ||
| Objectives | 989 | ||
| Incidence of HAI | 989 | ||
| Types of HAI | 990 | ||
| Urinary Tract Infections | 990 | ||
| Lung Infections | 990 | ||
| Surgical Site Infections | 990 | ||
| Central Line-Associated Bloodstream Infection | 990 | ||
| Emergence of Antibiotic-Resistant Microorganisms | 991 | ||
| Hospital Infection Control Programs | 991 | ||
| Role of the Microbiology Laboratory | 991 | ||
| Characterizing Strains Involved in an Outbreak | 992 | ||
| Preventing HAI | 992 | ||
| Surveillance Methods | 994 | ||
| Chapter Review | 995.e1 | ||
| Bibliography | 996 | ||
| 80 Sentinel Laboratory Response to Bioterrorism | 997 | ||
| Objectives | 997 | ||
| General Considerations | 997 | ||
| Biocrime | 997 | ||
| Government Laws and Regulations | 997 | ||
| Biosecurity | 998 | ||
| Laboratory Response Network | 998 | ||
| Role of the Sentinel Laboratory | 999 | ||
| Chapter Review | 1000.e1 | ||
| Bibliography | 1000 | ||
| Glossary | 1003 | ||
| Index | 1013 | ||
| A | 1013 | ||
| B | 1015 | ||
| C | 1017 | ||
| D | 1020 | ||
| E | 1021 | ||
| F | 1022 | ||
| G | 1023 | ||
| H | 1024 | ||
| I | 1025 | ||
| J | 1026 | ||
| K | 1026 | ||
| L | 1026 | ||
| M | 1027 | ||
| N | 1029 | ||
| O | 1030 | ||
| P | 1031 | ||
| Q | 1032 | ||
| R | 1032 | ||
| S | 1033 | ||
| T | 1036 | ||
| U | 1037 | ||
| V | 1037 | ||
| W | 1038 | ||
| X | 1038 | ||
| Y | 1038 | ||
| Z | 1038 | ||
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