Additional Information
Book Details
Abstract
Perfect your lab skills with the gold standard in microbiology! Serving as both the #1 bench reference for practicing microbiologists and as a favorite text for students in clinical laboratory science programs, Bailey & Scott’s Diagnostic Microbiology, 14th Edition covers all the topical information and critical thinking practice you need for effective laboratory testing. This new edition also features hundreds step-by-step procedures, updated visuals, new case studies, and new material on the latest trends and equipment in clinical microbiology — including automation, automated streaking, MALDI-TOF, and incubator microscopes. It’s everything you need to get quality lab results in class and in clinical practice!
- More than 800 detailed, full-color illustrations aid comprehension and help in visualizing concepts.
- Expanded sections on parasitology, mycology, and virology eliminate the need to purchase separate books on this material.
- General and Species boxes in the organism chapters highlight the important topics that will be discussed in the chapter.
- Case studies provide the opportunity to apply information to a variety of diagnostic scenarios, and help improve decision-making and critical thinking skills.
- Hands-on procedures include step-by-step instructions, full-color photos, and expected results.
- A glossary of terms is found at the back of the book for quick reference.
- Learning objectives begin each chapter, offering a measurable outcome to achieve by the completing the material.
- Learning resources on the Evolve companion website enhance learning with review questions and procedures.
- NEW! Coverage of automation, automated streaking, MALDI-TOF, and incubator microscopes keeps you in the know on these progressing topics.
- NEW! Updated images provide a more vivid look into book content and reflect the latest procedures.
- NEW! Thoroughly reviewed and updated chapters equip you with the most current information.
- NEW! Significant lab manual improvements provide an excellent learning resource at no extra cost.
- NEW! 10 extra case studies on the Evolve companion website offer more opportunities to improve critical thinking skills.
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover Page | Cover | ||
| Front matter | iii | ||
| Bailey & scott’s diagnostic microbiology | iii | ||
| Copyright | iv | ||
| Dedication | v | ||
| Reviewers | vi | ||
| Contributors | viii | ||
| Preface | x | ||
| Acknowledgments | xi | ||
| Table of contents | xii | ||
| Part I Basic Medical Microbiology | 1 | ||
| 1 Microbial taxonomy | 1 | ||
| Objectives | 1 | ||
| Classification | 2 | ||
| Family | 2 | ||
| Genus | 2 | ||
| Species | 2 | ||
| Nomenclature | 2 | ||
| Identification | 3 | ||
| Identification methods | 3 | ||
| Bibliography | 4 | ||
| 2 Bacterial genetics, metabolism, and structure | 5 | ||
| Objectives | 5 | ||
| Bacterial genetics | 5 | ||
| Nucleic acid structure and organization | 5 | ||
| Nucleotide structure and sequence | 6 | ||
| DNA molecular structure | 6 | ||
| Genes and the genetic code | 6 | ||
| Chromosomes | 6 | ||
| Nonchromosomal elements | 6 | ||
| Replication and expression of genetic information | 8 | ||
| Replication | 8 | ||
| Expression of genetic information | 9 | ||
| Transcription | 9 | ||
| Translation | 10 | ||
| Regulation and control of gene expression | 11 | ||
| Genetic exchange and diversity | 13 | ||
| Mutation | 14 | ||
| Genetic recombination | 14 | ||
| Genetic exchange | 14 | ||
| Transformation. | 14 | ||
| Transduction | 14 | ||
| Conjugation | 15 | ||
| Bacterial metabolism | 17 | ||
| Fueling | 17 | ||
| Acquisition of nutrients | 17 | ||
| Production of precursor metabolites | 17 | ||
| Energy production | 17 | ||
| Oxidative phosphorylation | 19 | ||
| Biosynthesis | 19 | ||
| Polymerization and assembly | 20 | ||
| Structure and function of the bacterial cell | 20 | ||
| Eukaryotic and prokaryotic cells | 20 | ||
| Bacterial morphology | 20 | ||
| Bacterial cell components | 21 | ||
| Cell envelope | 21 | ||
| Outer membrane | 21 | ||
| Cell wall (murein layer) | 21 | ||
| Periplasmic space | 22 | ||
| Cytoplasmic (inner) membrane | 22 | ||
| Cellular appendages | 22 | ||
| Cell interior | 23 | ||
| Bibliography | 23 | ||
| 3 Host-microorganism interactions | 24 | ||
| Objectives | 24 | ||
| The encounter between host and microorganism | 25 | ||
| The human host’s perspective | 25 | ||
| Microbial reservoirs and transmission | 25 | ||
| Human and microbe interactions | 26 | ||
| Animals as microbial reservoirs | 26 | ||
| Insects as vectors | 27 | ||
| The environment as a microbial reservoir | 27 | ||
| The microorganism’s perspective | 27 | ||
| Microorganism colonization of host surfaces | 27 | ||
| The host’s perspective | 27 | ||
| Skin and skin structures | 27 | ||
| Mucous membranes | 28 | ||
| General protective characteristics | 29 | ||
| Specific protective characteristics | 29 | ||
| The microorganism’s perspective | 30 | ||
| Microbial colonization | 30 | ||
| Microorganism entry, invasion, and dissemination | 30 | ||
| The host’s perspective | 30 | ||
| Disruption of surface barriers | 30 | ||
| Responses to microbial invasion of deeper tissues | 31 | ||
| Nonspecific responses | 31 | ||
| Phagocytes | 31 | ||
| Inflammation | 32 | ||
| Specific responses—the immune system | 33 | ||
| Components of the immune system | 33 | ||
| Two branches of the immune system | 33 | ||
| The microorganism’s perspective | 35 | ||
| Colonization and infection | 35 | ||
| Pathogens and virulence | 35 | ||
| Microbial virulence factors | 36 | ||
| Attachment | 36 | ||
| Invasion. | 36 | ||
| Survival against inflammation | 36 | ||
| Survival against the immune system | 37 | ||
| Microbial toxins | 37 | ||
| Genetics of virulence: Pathogenicity islands | 38 | ||
| Biofilm formation | 38 | ||
| Outcome and prevention of infectious diseases | 39 | ||
| Outcome of infectious diseases | 39 | ||
| Prevention of infectious diseases | 39 | ||
| Immunization | 40 | ||
| Epidemiology | 41 | ||
| Bibliography | 41 | ||
| Part II General Principles in Clinical Microbiology | 42 | ||
| Section 1 Safety and Specimen Management | 42 | ||
| 4 Laboratory safety | 42 | ||
| Objectives | 42 | ||
| Sterilization, disinfection, and decontamination | 42 | ||
| Methods of sterilization | 43 | ||
| Methods of disinfection | 43 | ||
| Physical methods of disinfection | 43 | ||
| Chemical methods of disinfection | 44 | ||
| Antiseptics | 45 | ||
| Chemical safety | 45 | ||
| Fire safety | 46 | ||
| Electrical safety | 46 | ||
| Handling of compressed gases | 46 | ||
| Biosafety | 47 | ||
| Exposure control plan | 47 | ||
| Employee education and orientation | 48 | ||
| Disposal of hazardous waste | 48 | ||
| Standard precautions | 48 | ||
| Engineering controls | 49 | ||
| Laboratory environment | 49 | ||
| Biologic safety cabinet | 50 | ||
| Personal protective equipment | 51 | ||
| Postexposure control | 52 | ||
| Classification of biologic agents based on hazard | 52 | ||
| Mailing biohazardous materials | 53 | ||
| Bibliography | 55 | ||
| 5 Specimen management | 56 | ||
| Objectives | 56 | ||
| General concepts for specimen collection and handling | 56 | ||
| Appropriate collection techniques | 57 | ||
| Specimen transport | 57 | ||
| Specimen preservation | 57 | ||
| Specimen storage | 57 | ||
| Specimen labeling | 66 | ||
| Specimen requisition | 66 | ||
| Rejection of unacceptable specimens | 66 | ||
| Specimen processing | 66 | ||
| Gross examination of specimen | 67 | ||
| Direct microscopic examination | 67 | ||
| Selection of culture media | 67 | ||
| Specimen preparation | 69 | ||
| Inoculation on solid media | 69 | ||
| Incubation conditions | 69 | ||
| Specimen workup | 69 | ||
| Extent of identification required | 69 | ||
| Communication of laboratory findings | 70 | ||
| Critical (panic) values | 70 | ||
| Expediting results reporting: Computerization | 70 | ||
| Bibliography | 71 | ||
| Section 2 Approaches to Diagnosis of Infectious Diseases | 72 | ||
| 6 Role of microscopy | 72 | ||
| Objectives | 72 | ||
| Bright-field (light) microscopy | 72 | ||
| Principles of light microscopy | 72 | ||
| Magnification | 73 | ||
| Resolution | 73 | ||
| Contrast | 74 | ||
| Direct and indirect smears | 74 | ||
| Staining techniques | 75 | ||
| Gram stain | 75 | ||
| Procedure overview | 75 | ||
| Principle | 75 | ||
| Gram stain examination (direct smear) | 76 | ||
| Gram stain of bacteria grown in culture (indirect smear) | 79 | ||
| Acid-fast stains | 79 | ||
| Principle | 79 | ||
| Procedure overview | 79 | ||
| Phase-contrast microscopy | 79 | ||
| Fluorescent microscopy | 80 | ||
| Principle of fluorescent microscopy | 80 | ||
| Staining techniques for fluorescent microscopy | 81 | ||
| Fluorochroming | 81 | ||
| Acridine orange | 82 | ||
| Auramine-rhodamine | 82 | ||
| Calcofluor white | 82 | ||
| Immunofluorescence | 82 | ||
| Dark-field microscopy | 83 | ||
| Electron microscopy | 84 | ||
| Digital automated microscopy | 85 | ||
| Bibliography | 85 | ||
| 7 Traditional cultivation and identification | 86 | ||
| Objectives | 86 | ||
| Organism identification | 86 | ||
| Principles of bacterial cultivation | 86 | ||
| Nutritional requirements | 87 | ||
| General concepts of culture media | 87 | ||
| Phases of growth media | 87 | ||
| Media classifications and functions | 88 | ||
| Summary of artificial media for routine bacteriology | 89 | ||
| Brain-heart infusion | 89 | ||
| Chocolate agar | 89 | ||
| Columbia cna with blood | 89 | ||
| Gram-negative broth | 92 | ||
| Hektoen enteric agar | 92 | ||
| Macconkey agar | 92 | ||
| Phenylethyl alcohol agar | 93 | ||
| Sheep blood agar | 93 | ||
| Modified thayer-martin agar | 93 | ||
| Thioglycollate broth | 93 | ||
| Xylose-lysine-deoxycholate agar | 94 | ||
| Preparation of artificial media | 94 | ||
| Media sterilization | 94 | ||
| Cell cultures | 95 | ||
| Environmental requirements | 95 | ||
| Oxygen and carbon dioxide availability | 95 | ||
| Temperature | 95 | ||
| Ph | 95 | ||
| Moisture | 95 | ||
| Methods for providing optimal incubation conditions | 95 | ||
| Bacterial cultivation | 96 | ||
| Isolation of bacteria from specimens | 96 | ||
| Evaluation of colony morphologies | 96 | ||
| Type of media supporting bacterial growth | 98 | ||
| Relative quantities of each colony type | 98 | ||
| Colony characteristics | 98 | ||
| Indirect gram stain and subcultures | 99 | ||
| Principles of identification | 99 | ||
| Organism identification using genotypic criteria | 100 | ||
| Organism identification using phenotypic criteria | 101 | ||
| Microscopic morphology and staining characteristics | 101 | ||
| Macroscopic (colony) morphology | 102 | ||
| Environmental requirements for growth | 102 | ||
| Resistance or susceptibility to antimicrobial agents | 102 | ||
| Nutritional requirements and metabolic capabilities | 103 | ||
| Establishing enzymatic capabilities | 103 | ||
| Types of enzyme-based tests | 103 | ||
| Single enzyme tests | 103 | ||
| Catalase test | 103 | ||
| Oxidase test | 103 | ||
| Indole test | 104 | ||
| Urease test | 104 | ||
| Pyr test | 104 | ||
| Hippurate hydrolysis | 104 | ||
| Tests for the presence of metabolic pathways | 104 | ||
| Oxidation and fermentation tests | 104 | ||
| Amino acid degradation | 105 | ||
| Single substrate utilization | 106 | ||
| Establishing inhibitor profiles | 106 | ||
| Principles of phenotypic identification schemes | 106 | ||
| Selection and inoculation of identification test battery | 106 | ||
| Type of bacteria to be identified | 106 | ||
| Clinical significance of the bacterial isolate | 106 | ||
| Availability of reliable testing methods | 106 | ||
| Incubation for substrate utilization | 107 | ||
| Conventional identification | 107 | ||
| Rapid identification | 107 | ||
| Matrix-assisted laser desorption ionization time of flight mass spectrometry | 108 | ||
| Detection of metabolic activity | 109 | ||
| Colorimetry | 109 | ||
| Fluorescence | 109 | ||
| Turbidity | 109 | ||
| Analysis of metabolic profiles | 109 | ||
| Identification databases | 109 | ||
| Use of the database to identify unknown isolates | 110 | ||
| Confidence in identification | 111 | ||
| Commercial identification systems and automation | 111 | ||
| Advantages and examples of commercial system designs | 111 | ||
| Overview of commercial identification systems | 112 | ||
| Bibliography | 112 | ||
| 8 Nucleic acidbased analytic methods for microbial identification and characterization | 113 | ||
| Objectives | 113 | ||
| Overview of nucleic acid–based methods | 114 | ||
| Specimen collection and transport | 114 | ||
| Nucleic acid hybridization methods | 114 | ||
| Hybridization steps and components | 115 | ||
| Production and labeling of probe nucleic acid | 115 | ||
| Preparation of target nucleic acid | 117 | ||
| Mixture and hybridization of target and probe | 117 | ||
| Detection of hybridization | 118 | ||
| Hybridization formats | 118 | ||
| Liquid format | 118 | ||
| Solid support format | 118 | ||
| In situ hybridization | 119 | ||
| Peptide nucleic acid fluorescence in situ hybridization | 120 | ||
| Hybridization with signal amplification | 120 | ||
| Amplification methods—polymerase chain reaction–based | 122 | ||
| Overview of polymerase chain reaction and derivations | 122 | ||
| Extraction and denaturation of the target nucleic acid | 122 | ||
| Primer annealing | 122 | ||
| Extension of the primer-target duplex | 124 | ||
| Detection of polymerase chain reaction products | 124 | ||
| Derivations of the polymerase chain reaction method | 124 | ||
| Real-time polymerase chain reaction | 126 | ||
| Amplification methods: Non–polymerase chain reaction–based | 132 | ||
| Coupled target and signal (probe) amplification | 132 | ||
| Isothermal (constant temperature) amplification | 132 | ||
| Sequencing and enzymatic digestion of nucleic acids | 134 | ||
| Nucleic acid sequencing | 134 | ||
| Postamplification and traditional analysis | 135 | ||
| Nucleic acid electrophoresis | 135 | ||
| Pyrosequencing | 135 | ||
| High-density deoxyribonucleic acid (DNA) probes | 135 | ||
| Low- to moderate-density arrays | 135 | ||
| Enzymatic digestion and electrophoresis of nucleic acids | 135 | ||
| Applications of nucleic acid–based methods | 137 | ||
| Direct detection of microorganisms | 137 | ||
| Advantages and disadvantages | 138 | ||
| Analytical specificity | 138 | ||
| Analytical sensitivity | 138 | ||
| Applications for direct molecular detection of microorganisms | 139 | ||
| Identification of microorganisms grown in culture | 139 | ||
| Characterization of microorganisms beyond identification | 139 | ||
| Detection of antimicrobial resistance | 140 | ||
| Investigation of strain relatedness and pulsed-field gel electrophoresis | 140 | ||
| Automation and advances in molecular diagnostic instrumentation | 142 | ||
| Bibliography | 142 | ||
| 9 Overview of immunochemical methods used for organism detection | 144 | ||
| Objectives | 144 | ||
| Features of the immune response | 144 | ||
| Characteristics of antibodies | 145 | ||
| Features of the humoral immune response useful in diagnostic testing | 146 | ||
| Interpretation of serologic tests | 146 | ||
| Production of antibodies for use in laboratory testing | 147 | ||
| Polyclonal antibodies | 147 | ||
| Monoclonal antibodies | 147 | ||
| Igm clinical significance | 149 | ||
| Separating igm from igg for serologic testing | 149 | ||
| Principles of immunochemical methods used for organism detection | 149 | ||
| Precipitation tests | 150 | ||
| Double immunodiffusion | 150 | ||
| Single immunodiffusion | 150 | ||
| Particle agglutination | 150 | ||
| Coagglutination | 151 | ||
| Hemagglutination | 152 | ||
| Hemagglutination inhibition assays | 152 | ||
| Flocculation tests | 152 | ||
| Neutralization assays | 153 | ||
| Complement fixation assays | 153 | ||
| Immunofluorescent assays | 154 | ||
| Enzyme immunoassays | 156 | ||
| Solid-phase immunoassay | 156 | ||
| Membrane-bound solid-phase enzyme immunosorbent assay | 156 | ||
| Automated fluorescent immunoassays | 158 | ||
| Western blot immunoassays | 158 | ||
| Summary | 160 | ||
| Bibliography | 160 | ||
| Section 3 Evaluation of Antimicrobial Activity | 161 | ||
| 10 Principles of antimicrobial action and resistance | 161 | ||
| Objectives | 161 | ||
| Antimicrobial action | 161 | ||
| Principles | 161 | ||
| Mode of action of antibacterial agents | 163 | ||
| Inhibitors of cell wall synthesis | 163 | ||
| Beta-lactams | 164 | ||
| Fosfomycin | 165 | ||
| Glycopeptides and lipoglycopeptides | 165 | ||
| Inhibitors of cell membrane function | 166 | ||
| Lipopeptides | 166 | ||
| Inhibitors of protein synthesis | 166 | ||
| Aminoglycosides | 166 | ||
| Macrolide-lincosamide-streptogramin group | 167 | ||
| Ketolides | 167 | ||
| Oxazolidinones | 167 | ||
| Chloramphenicol | 167 | ||
| Tetracyclines | 167 | ||
| Glycylglycines | 167 | ||
| Inhibitors of deoxyribonucleic acid and ribonucleic acid synthesis | 168 | ||
| Fluoroquinolones | 168 | ||
| Metronidazole | 168 | ||
| Rifamycin | 168 | ||
| Inhibitors of other metabolic processes | 168 | ||
| Sulfonamides | 168 | ||
| Trimethoprim | 169 | ||
| Nitrofurantoin | 169 | ||
| Mechanisms of antibiotic resistance | 169 | ||
| Principles | 169 | ||
| Biologic versus clinical resistance | 169 | ||
| Environmentally mediated antimicrobial resistance | 169 | ||
| Microorganism-mediated antimicrobial resistance | 170 | ||
| Intrinsic resistance | 170 | ||
| Acquired resistance | 171 | ||
| Common pathways for antimicrobial resistance | 171 | ||
| Resistance to beta-lactam antibiotics | 171 | ||
| Resistance to glycopeptides | 174 | ||
| Resistance to aminoglycosides | 174 | ||
| Resistance to quinolones | 174 | ||
| Resistance to other antimicrobial agents | 174 | ||
| Emergence and dissemination of antimicrobial resistance | 175 | ||
| Bibliography | 176 | ||
| 11 Laboratory methods and strategies for antimicrobial susceptibility testing | 177 | ||
| Objectives | 177 | ||
| Goal and limitations | 177 | ||
| Standardization | 178 | ||
| Limitations of standardization | 178 | ||
| Testing methods | 178 | ||
| Principles | 178 | ||
| Methods that directly measure antimicrobial activity | 178 | ||
| Conventional testing methods: General considerations | 179 | ||
| Inoculum preparation | 179 | ||
| Selection of antimicrobial agents for testing | 179 | ||
| Conventional testing methods: Broth dilution | 180 | ||
| Procedures | 180 | ||
| Medium and antimicrobial agents. | 180 | ||
| Inoculation and incubation. | 180 | ||
| Reading and interpretation of results. | 180 | ||
| Advantages and disadvantages. | 180 | ||
| Conventional testing methods: Agar dilution | 183 | ||
| Conventional testing methods: Disk diffusion | 184 | ||
| Procedures | 185 | ||
| Medium and antimicrobial agents. | 185 | ||
| Inoculation and incubation. | 185 | ||
| Reading and interpretation of results. | 185 | ||
| Advantages and disadvantages. | 185 | ||
| Commercial susceptibility testing systems | 188 | ||
| Broth microdilution methods | 188 | ||
| Agar dilution derivations | 188 | ||
| Diffusion in agar derivations | 188 | ||
| Automated antimicrobial susceptibility test systems | 189 | ||
| Alternative approaches for enhancing resistance detection | 191 | ||
| Supplemental testing methods | 191 | ||
| Predictor antimicrobial agents | 193 | ||
| Methods that directly detect specific resistance mechanisms | 194 | ||
| Phenotypic methods | 194 | ||
| Beta-lactamase detection | 194 | ||
| Chloramphenicol acetyltransferase detection | 194 | ||
| Genotypic methods | 194 | ||
| Special methods for complex antimicrobial/organism interactions | 195 | ||
| Bactericidal tests | 195 | ||
| Minimal bactericidal concentration | 195 | ||
| Time-kill studies | 196 | ||
| Serum bactericidal test (schlichter test) | 196 | ||
| Tests for activity of antimicrobial combinations | 196 | ||
| Laboratory strategies for antimicrobial susceptibility testing | 197 | ||
| Relevance | 197 | ||
| When to perform a susceptibility test | 198 | ||
| Determining clinical significance | 198 | ||
| Predictability of antimicrobial susceptibility | 198 | ||
| Availability of reliable susceptibility testing methods | 199 | ||
| Selection of antimicrobial agents for testing | 199 | ||
| Accuracy | 199 | ||
| Use of accurate methodologies | 201 | ||
| Review of results | 201 | ||
| Components of results review strategies | 201 | ||
| Data review | 202 | ||
| Resolution | 203 | ||
| Accuracy and antimicrobial resistance surveillance | 203 | ||
| Communication | 203 | ||
| Reference | 204 | ||
| Bibliography | 204 | ||
| Part III Bacteriology | 205 | ||
| Section 1 Principles of Identification | 205 | ||
| 12 Overview of bacterial identification methods and strategies | 205 | ||
| Objectives | 205 | ||
| Rationale for approaching organism identification | 205 | ||
| Future trends of organism identification | 206 | ||
| Bibliography | 247 | ||
| Section 2 Catalase-Positive, Gram-Positive Cocci | 248 | ||
| 13 and similar organisms | 248 | ||
| Objectives | 248 | ||
| General characteristics | 248 | ||
| Epidemiology | 249 | ||
| Pathogenesis and spectrum of disease | 249 | ||
| Laboratory diagnosis | 252 | ||
| Specimen collection and transport | 252 | ||
| Specimen processing | 252 | ||
| Direct detection methods | 252 | ||
| Microscopy | 252 | ||
| Cultivation | 252 | ||
| Media of choice | 252 | ||
| Incubation conditions and duration | 253 | ||
| Colonial appearance | 253 | ||
| Approach to identification | 254 | ||
| Comments regarding specific organisms | 255 | ||
| Serodiagnosis | 257 | ||
| Molecular methods | 257 | ||
| Other identification methods | 259 | ||
| Antimicrobial susceptibility testing and therapy | 259 | ||
| Prevention | 261 | ||
| Bibliography | 262 | ||
| Section 3 Catalase-Negative, Gram-Positive Cocci | 264 | ||
| 14 and similar organisms | 264 | ||
| Objectives | 264 | ||
| General characteristics | 265 | ||
| Epidemiology | 265 | ||
| Pathogenesis and spectrum of disease | 266 | ||
| Beta-hemolytic streptococci | 266 | ||
| Streptococcus pneumoniae | 269 | ||
| Viridans streptococci | 269 | ||
| Enterococcus species | 269 | ||
| Miscellaneous other gram-positive cocci | 270 | ||
| Laboratory diagnosis | 270 | ||
| Specimen collection and transport | 270 | ||
| Specimen processing | 270 | ||
| Direct detection methods | 270 | ||
| Antigen detection | 270 | ||
| Molecular methods | 270 | ||
| Gram stain | 271 | ||
| Cultivation | 271 | ||
| Media of choice | 271 | ||
| Incubation conditions and duration | 274 | ||
| Colonial appearance | 274 | ||
| Approach to identification | 274 | ||
| Matrix-assisted laser desorption ionization time-of-flight mass spectrometry | 275 | ||
| Comments regarding specific organisms | 275 | ||
| Serodiagnosis | 277 | ||
| Antimicrobial susceptibility testing and therapy | 279 | ||
| Prevention | 281 | ||
| Bibliography | 282 | ||
| Section 4 Non-Branching, Catalase-Positive, Gram-Positive Bacilli | 283 | ||
| 15 and similar organisms | 283 | ||
| Objectives | 283 | ||
| General characteristics | 283 | ||
| Bacillus anthracis | 283 | ||
| Epidemiology | 284 | ||
| Pathogenesis and spectrum of disease | 284 | ||
| B. cereus group (not b. anthracis) | 286 | ||
| Epidemiology | 286 | ||
| Part IV Parasitology | 590 | ||
| 46 Overview of the methods and strategies in parasitology | 590 | ||
| Objectives | 590 | ||
| Epidemiology | 590 | ||
| Pathogenesis and spectrum of disease | 593 | ||
| Laboratory diagnosis | 601 | ||
| Specimen collection and transport | 601 | ||
| Specimen processing | 601 | ||
| Approach to identification | 606 | ||
| Microscopic examination | 608 | ||
| Intestinal tract | 614 | ||
| Ova and parasite examination | 614 | ||
| Recovery of the tapeworm scolex | 615 | ||
| Examination for pinworm | 616 | ||
| Sigmoidoscopy material | 619 | ||
| Duodenal drainage | 619 | ||
| Duodenal capsule technique (entero-test) | 620 | ||
| Urogenital tract specimens | 620 | ||
| Sputum | 620 | ||
| Aspirates | 620 | ||
| Biopsy specimens | 621 | ||
| Blood | 621 | ||
| Thin blood films | 623 | ||
| Thick blood films | 623 | ||
| Buffy coat films | 625 | ||
| Direct detection methods | 625 | ||
| Intestinal parasites | 625 | ||
| Blood parasites | 625 | ||
| Cultivation | 625 | ||
| Larval-stage nematodes | 627 | ||
| Blood protozoa | 627 | ||
| Serodiagnosis | 627 | ||
| Prevention | 627 | ||
| 47 Intestinal protozoa | 629 | ||
| Objectives | 629 | ||
| Amoebae | 629 | ||
| Entamoeba histolytica | 629 | ||
| General characteristics | 629 | ||
| Epidemiology | 636 | ||
| Pathogenesis and spectrum of disease | 637 | ||
| Asymptomatic infection | 637 | ||
| Intestinal disease | 637 | ||
| Hepatic disease | 639 | ||
| Metastatic amebiasis | 639 | ||
| Laboratory diagnosis | 641 | ||
| Routine methods | 641 | ||
| Antigen detection | 641 | ||
| Histology | 641 | ||
| Molecular methods | 641 | ||
| Antibody (serologic) detection | 642 | ||
| Reporting of results | 642 | ||
| Therapy | 642 | ||
| Asymptomatic infection | 642 | ||
| Prevention | 642 | ||
| Entamoeba coli | 642 | ||
| General characteristics | 642 | ||
| Epidemiology | 643 | ||
| Pathogenesis and spectrum of disease | 643 | ||
| Laboratory diagnosis | 644 | ||
| Therapy | 644 | ||
| Prevention | 644 | ||
| Entamoeba hartmanni | 644 | ||
| General characteristics | 644 | ||
| Epidemiology | 644 | ||
| Part V Mycology | 757 | ||
| 58 Overview of fungal identification methods and strategies | 757 | ||
| Objectives | 757 | ||
| Epidemiology | 758 | ||
| General features of the fungi | 758 | ||
| Taxonomy of the fungi | 758 | ||
| Clinical classification of the fungi | 759 | ||
| Practical working schema | 760 | ||
| Pathogenesis and spectrum of disease | 762 | ||
| Laboratory diagnosis | 762 | ||
| Collection, transport, and culturing of clinical specimens | 762 | ||
| Respiratory tract secretions | 763 | ||
| Cerebrospinal fluid | 763 | ||
| Blood | 763 | ||
| Eye (corneal scrapings or vitreous humor) | 763 | ||
| Hair, skin, and nail scrapings | 764 | ||
| Vaginal | 764 | ||
| Urine | 764 | ||
| Tissue, bone marrow, and sterile body fluids | 764 | ||
| Culture media and incubation requirements | 764 | ||
| Direct microscopic examination | 767 | ||
| Serologic testing | 770 | ||
| Molecular methods | 771 | ||
| Matrix-assisted laser desorption ionization mass spectrometry | 771 | ||
| General considerations for the identification of yeasts | 771 | ||
| General considerations for the identification of molds | 772 | ||
| General morphologic features of the molds | 774 | ||
| Clinical relevance for fungal identification | 776 | ||
| Laboratory safety | 779 | ||
| Prevention | 780 | ||
| Bibliography | 780 | ||
| 59 Hyaline molds, mucorales, entomophthorales, dermatophytes, and opportunistic and systemic mycoses | 782 | ||
| Objectives | 782 | ||
| The mucorales | 782 | ||
| General characteristics | 782 | ||
| Epidemiology and pathogenesis | 783 | ||
| Spectrum of disease | 783 | ||
| Laboratory diagnosis | 783 | ||
| Specimen collection, transport, and processing | 783 | ||
| Direct detection methods | 783 | ||
| Stains | 784 | ||
| Antigen-protein | 784 | ||
| Molecular methods | 784 | ||
| Cultivation | 784 | ||
| Approach to identification | 785 | ||
| Serologic testing | 785 | ||
| Matrix-assisted laser desorption ionization time-of-flight mass spectrometry | 786 | ||
| The entomophthorales | 786 | ||
| General characteristics | 786 | ||
| Epidemiology and pathogenesis | 786 | ||
| Spectrum of disease | 786 | ||
| Laboratory diagnosis | 786 | ||
| Specimen collection, transport, and processing | 786 | ||
| Direct detection methods | 786 | ||
| Antigen-protein | 786 | ||
| Molecular methods | 786 | ||
| Cultivation | 786 | ||
| Approach to identification | 786 | ||
| Serologic testing | 787 | ||
| The dermatophytes | 787 | ||
| General characteristics | 787 | ||
| Epidemiology and pathogenesis | 787 | ||
| Spectrum of disease | 787 | ||
| Trichophyton spp. | 787 | ||
| Laboratory diagnosis | 787 | ||
| Specimen collection, transport, and processing | 787 | ||
| Direct detection methods | 787 | ||
| Stains | 787 | ||
| Antigen-protein | 787 | ||
| Molecular methods | 788 | ||
| Cultivation | 788 | ||
| Approach to identification | 790 | ||
| Trichophyton spp. | 790 | ||
| Microsporum spp. | 792 | ||
| Epidermophyton sp. | 793 | ||
| Serologic testing | 793 | ||
| The opportunistic mycoses | 793 | ||
| General characteristics | 793 | ||
| Epidemiology and pathogenesis | 793 | ||
| Aspergillus spp. | 793 | ||
| Pathogenesis and spectrum of disease | 794 | ||
| Aspergillus spp. | 794 | ||
| Fusarium spp. and other hyaline septate opportunistic molds | 794 | ||
| Laboratory diagnosis | 795 | ||
| Specimen collection, transport, and processing | 795 | ||
| Direct detection methods | 795 | ||
| Stains | 795 | ||
| Antigen-protein | 795 | ||
| Molecular methods | 795 | ||
| Matrix-assisted laser desorption ionization time-of-flight mass spectrometry | 795 | ||
| Cultivation | 795 | ||
| Approach to identification | 796 | ||
| Aspergillus spp. | 796 | ||
| Serologic testing | 796 | ||
| Fusarium spp. | 797 | ||
| Geotrichum candidum | 797 | ||
| Acremonium spp. | 797 | ||
| Penicillium spp. and talaromyces marneffei | 797 | ||
| Paecilomyces spp. | 798 | ||
| Purpureocillium spp. | 798 | ||
| Scopulariopsis spp. | 798 | ||
| Serologic testing | 798 | ||
| Systemic mycoses | 798 | ||
| General characteristics | 799 | ||
| Epidemiology | 799 | ||
| Blastomyces spp. | 799 | ||
| Coccidioides spp. | 799 | ||
| Emmonsia spp. | 799 | ||
| Histoplasma capsulatum | 799 | ||
| Paracoccidioides brasiliensis | 799 | ||
| Talaromyces marneffei | 800 | ||
| Sporothrix spp. | 800 | ||
| Pathogenesis and spectrum of disease | 800 | ||
| Blastomyces spp. | 800 | ||
| Coccidioides spp. | 800 | ||
| Emmonsia spp. | 800 | ||
| Histoplasma capsulatum | 800 | ||
| Paracoccidioides brasiliensis | 800 | ||
| Talaromyces marneffei | 801 | ||
| Sporothrix spp. | 801 | ||
| Laboratory diagnosis | 801 | ||
| Specimen collection, transport, and processing | 801 | ||
| Direct detection methods | 801 | ||
| Stains | 801 | ||
| Blastomyces spp. | 801 | ||
| Coccidioides spp. | 801 | ||
| Emmonsia spp. | 801 | ||
| Histoplasma capsulatum. | 801 | ||
| Paracoccidioides brasiliensis. | 801 | ||
| Talaromyces marneffei. | 803 | ||
| Sporothrix spp. | 803 | ||
| Antigen-protein | 803 | ||
| Molecular methods | 803 | ||
| Cultivation | 803 | ||
| Blastomyces dermatitidis. | 803 | ||
| Coccidioides spp. | 803 | ||
| Emmonsia spp. | 803 | ||
| Histoplasma capsulatum. | 803 | ||
| Paracoccidioides brasiliensis. | 804 | ||
| Talaromyces marneffei. | 804 | ||
| Sporothrix spp. | 804 | ||
| Approach to identification | 805 | ||
| Blastomyces dermatitidis | 805 | ||
| Coccidioides spp. | 805 | ||
| Emmonsia spp. | 806 | ||
| Histoplasma capsulatum | 806 | ||
| Paracoccidioides brasiliensis | 806 | ||
| Talaromyces marneffei | 806 | ||
| Sporothrix spp. | 807 | ||
| Serologic testing | 807 | ||
| References | 810 | ||
| Bibliography | 810 | ||
| 60 Dematiaceious (melanized) molds | 812 | ||
| Objectives | 812 | ||
| General characteristics | 812 | ||
| Epidemiology and pathogenesis | 812 | ||
| Superficial infections | 812 | ||
| Mycetoma | 812 | ||
| Chromoblastomycosis | 813 | ||
| Phaeohyphomycosis | 813 | ||
| Pathogenesis and spectrum of disease | 813 | ||
| Laboratory diagnosis | 815 | ||
| Specimen collection, transport, and processing | 815 | ||
| Direct detection method | 815 | ||
| Stains | 815 | ||
| Superficial infections | 815 | ||
| Chromoblastomycosis | 815 | ||
| Mycetoma and phaeohyphomycosis | 815 | ||
| Serologic testing | 815 | ||
| Molecular methods | 815 | ||
| Matrix-assisted laser desorption ionization time-of-flight mass spectrometry | 816 | ||
| Cultivation | 816 | ||
| Superficial infections | 816 | ||
| Mycetoma | 816 | ||
| White grain mycetoma. | 816 | ||
| Black grain mycetoma. | 816 | ||
| Chromoblastomycosis | 816 | ||
| Phaeohyphomycosis | 817 | ||
| Approach to identification | 817 | ||
| Superficial infections | 817 | ||
| Mycetoma | 817 | ||
| White grain mycetoma: pseudallescheria boydii and acremonium spp. | 817 | ||
| Black grain mycetoma: exophiala jeanselmei, curvularia spp., and madurella spp. | 818 | ||
| Chromoblastomycosis: cladosporium, phialophora, and fonsecaea spp. | 818 | ||
| Phaeohyphomycosis: alternaria, bipolaris, cladophialophora, curvularia, exophiala, exserohilum, and phialophora spp. | 819 | ||
| Alternaria spp. | 819 | ||
| Bipolaris spp. | 819 | ||
| Cladophialophora spp. | 819 | ||
| Curvularia spp. | 819 | ||
| Exophiala spp. | 819 | ||
| Exserohilum spp. | 819 | ||
| Antifungal susceptibilities | 820 | ||
| Bibliography | 821 | ||
| 61 Opportunistic atypical fungus: | 822 | ||
| Objectives | 822 | ||
| General characteristics | 822 | ||
| Epidemiology | 822 | ||
| Pathogenesis and spectrum of disease | 822 | ||
| Laboratory diagnosis | 823 | ||
| Specimen collection and transport | 823 | ||
| Specimen processing | 823 | ||
| Direct detection methods | 823 | ||
| Stains | 823 | ||
| Direct detection of (1-3)-beta-d-glucan | 824 | ||
| Molecular methods | 824 | ||
| Cultivation | 824 | ||
| Approach to identification | 824 | ||
| Serologic testing | 824 | ||
| References | 824 | ||
| Bibliography | 824 | ||
| 62 The yeasts | 825 | ||
| Objectives | 825 | ||
| General characteristics | 825 | ||
| Epidemiology | 826 | ||
| Blastoschizomyces spp. | 826 | ||
| Candida spp. | 827 | ||
| Cryptococcus spp. | 827 | ||
| Malassezia, pseudozyma, rhodotorula, saccharomyces, sporobolomyces, and trichosporon spp. | 827 | ||
| Pathogenesis and spectrum of disease | 827 | ||
| Blastoschizomyces spp. | 827 | ||
| Candida albicans | 827 | ||
| Non-albicans candida | 828 | ||
| Cryptococcus neoformans | 828 | ||
| Genus cryptococcus | 828 | ||
| Cryptococcus gattii | 829 | ||
| Malassezia spp. | 829 | ||
| Pseudozyma spp. | 829 | ||
| Rhodotorula spp. | 829 | ||
| Saccharomyces cerevisiae | 829 | ||
| Sporobolomyces spp. | 830 | ||
| Trichosporon spp. | 830 | ||
| Laboratory diagnosis | 830 | ||
| Specimen collection, transport, and processing | 830 | ||
| Stains | 830 | ||
| Candida spp. | 830 | ||
| Cryptococcus spp. | 830 | ||
| Malassezia spp. | 831 | ||
| Trichosporon spp. | 831 | ||
| Antigen detection | 831 | ||
| Molecular methods | 831 | ||
| Cultivation | 832 | ||
| Part VI Virology | 844 | ||
| 64 Overview of the methods and strategies in virology | 844 | ||
| Objectives | 844 | ||
| General characteristics | 845 | ||
| Viral structure | 845 | ||
| Virus taxonomy | 847 | ||
| Viral replication | 847 | ||
| Epidemiology | 848 | ||
| Pathogenesis and spectrum of disease | 848 | ||
| Prevention and therapy | 849 | ||
| Antiviral agents | 849 | ||
| Viruses that cause human diseases | 849 | ||
| Laboratory diagnosis | 849 | ||
| Designing a clinical virology laboratory | 849 | ||
| Specimen selection and collection | 851 | ||
| General principles | 851 | ||
| Throat, nasopharyngeal swab, or aspirate | 852 | ||
| Bronchial and bronchoalveolar washes | 855 | ||
| Rectal swabs and stool specimens | 855 | ||
| Urine | 855 | ||
| Skin and mucous membrane lesions | 855 | ||
| Sterile body fluids other than blood | 855 | ||
| Blood | 855 | ||
| Bone marrow | 855 | ||
| Tissue | 856 | ||
| Genital specimens | 856 | ||
| Serum for antibody testing | 856 | ||
| Specimen transport and storage | 856 | ||
| Specimen processing | 856 | ||
| General principles | 856 | ||
| Processing based on specimen type | 858 | ||
| Lip and genital specimens | 858 | ||
| Urine | 858 | ||
| Stool | 858 | ||
| Respiratory tract | 858 | ||
| Specimens from neonatal patients | 859 | ||
| Cerebrospinal fluid | 859 | ||
| Blood | 859 | ||
| Processing based on requests for specific viruses | 859 | ||
| Arboviruses | 859 | ||
| Cytomegalovirus | 859 | ||
| Enteroviruses | 860 | ||
| Epstein-barr virus | 860 | ||
| Hepatitis viruses | 860 | ||
| Herpes simplex virus | 861 | ||
| Human immunodeficiency virus and other retroviruses | 861 | ||
| Influenza a and b viruses | 862 | ||
| Pediatric respiratory viruses | 862 | ||
| Gastroenteritis viruses | 864 | ||
| Torch | 864 | ||
| Varicella-zoster virus | 864 | ||
| Virus detection methods | 866 | ||
| Cytology and histology | 866 | ||
| Electron microscopy | 866 | ||
| Immunodiagnosis (antigen detection) | 866 | ||
| Enzyme-linked virus-inducible system | 871 | ||
| Molecular methods | 871 | ||
| Cell culture | 872 | ||
| Conventional cell culture | 872 | ||
| Shell vial cell culture | 874 | ||
| Identification of viruses detected in cell culture | 875 | ||
| Serologic testing | 875 | ||
| General principles | 875 | ||
| Immune status testing | 878 | ||
| Serology panels | 879 | ||
| Preservation and storage of viruses | 879 | ||
| Bibliography | 879 | ||
| 65 Viruses in human disease | 881 | ||
| Objectives | 881 | ||
| Viruses in human disease | 881 | ||
| Adenoviruses | 881 | ||
| Arenaviruses | 883 | ||
| Bunyaviruses | 884 | ||
| Caliciviruses | 885 | ||
| Coronaviruses | 886 | ||
| Filoviruses | 887 | ||
| Flaviviruses | 888 | ||
| Hepevirus | 890 | ||
| Hepadnaviruses | 891 | ||
| Herpes viruses | 892 | ||
| Orthomyxoviruses | 897 | ||
| Papillomaviruses | 899 | ||
| Paramyxoviruses | 900 | ||
| Parvoviruses | 902 | ||
| Picornaviruses | 903 | ||
| Polyomaviruses | 905 | ||
| Poxviruses | 906 | ||
| Reoviruses | 907 | ||
| Retroviruses | 908 | ||
| Rhabdoviruses | 910 | ||
| Togaviruses | 911 | ||
| Miscellaneous viruses | 911 | ||
| Interpretation of laboratory test results | 911 | ||
| Viruses in tissue and body fluids | 911 | ||
| Viruses in the respiratory tract | 911 | ||
| Viruses in the eye | 912 | ||
| Detection of epstein-barr virus | 912 | ||
| Detection of enteroviruses | 912 | ||
| Detection of hepatitis viruses | 912 | ||
| Detection of varicella-zoster virus and herpes simplex virus | 912 | ||
| Detection of cytomegalovirus | 913 | ||
| Detection of human immunodeficiency virus | 913 | ||
| Prions in human disease | 913 | ||
| Bibliography | 914 | ||
| 66 Antiviral therapy, susceptibility testing, and prevention | 916 | ||
| Objectives | 916 | ||
| Antiviral therapy | 916 | ||
| Antiviral resistance | 916 | ||
| Methods of antiviral susceptibility testing | 917 | ||
| Phenotypic assays | 917 | ||
| Plaque reduction assay | 917 | ||
| Dye uptake assay | 917 | ||
| Deoxyribonucleic acid hybridization | 917 | ||
| Enzyme immunoassay | 918 | ||
| Flow cytometry | 918 | ||
| Neuraminidase inhibition assay | 918 | ||
| Recombinant virus assays | 918 | ||
| Genotypic susceptibility assays | 918 | ||
| Pyrosequencing | 918 | ||
| Next generation sequencing | 919 | ||
| Human immunodeficiency virus | 919 | ||
| Influenza | 919 | ||
| Prevention of other viral infections | 920 | ||
| Vaccination | 920 | ||
| Immune prophylaxis and therapy | 921 | ||
| Eradication | 922 | ||
| Bibliography | 922 | ||
| Part VII Diagnosis by Organ System | 924 | ||
| 67 Bloodstream infections | 924 | ||
| Objectives | 924 | ||
| General considerations | 925 | ||
| Etiology | 925 | ||
| Bacteria | 925 | ||
| Fungi | 926 | ||
| Parasites | 926 | ||
| Viruses | 926 | ||
| Types of bacteremia | 926 | ||
| Types of bloodstream infections | 927 | ||
| Intravascular infections | 927 | ||
| Endocarditis | 927 | ||
| Mycotic aneurysm and suppurative thrombophlebitis | 927 | ||
| Intravenous catheter–associated bacteremia. | 927 | ||
| Extravascular infections | 928 | ||
| Clinical manifestations | 930 | ||
| Immunocompromised patients | 931 | ||
| Detection of bacteremia | 931 | ||
| Specimen collection | 931 | ||
| Preparation of the site | 931 | ||
| Antisepsis | 931 | ||
| Precautions | 932 | ||
| Specimen volume | 932 | ||
| Adults | 932 | ||
| Children | 932 | ||
| Number of blood cultures | 932 | ||
| Timing of collection | 932 | ||
| Miscellaneous matters | 932 | ||
| Anticoagulation | 932 | ||
| Dilution | 933 | ||
| Blood culture media | 933 | ||
| Types of blood culture bottles | 933 | ||
| Culture techniques | 933 | ||
| Conventional blood cultures | 933 | ||
| Incubation conditions | 933 | ||
| Self-contained subculture system | 934 | ||
| Lysis centrifugation | 934 | ||
| Instrument-based systems | 934 | ||
| Bactec systems | 934 | ||
| Bact/alert microbial detection system | 936 | ||
| Versa trek system | 936 | ||
| Techniques to detect intravenous catheter–associated infections | 936 | ||
| Handling positive blood cultures | 937 | ||
| Interpretation of blood culture results | 938 | ||
| Special considerations for other relevant organisms isolated from blood | 938 | ||
| Hacek (aacek) bacteria | 938 | ||
| Campylobacter and helicobacter | 938 | ||
| Fungi | 938 | ||
| Mycobacteria | 939 | ||
| Brucella | 939 | ||
| Spirochetes | 939 | ||
| Borrelia | 939 | ||
| Leptospira | 939 | ||
| Vitamin b6–dependent streptococci | 939 | ||
| Mycoplasma hominis | 939 | ||
| Bartonella | 940 | ||
| Bibliography | 940 | ||
| 68 Infections of the lower respiratory tract | 942 | ||
| Objectives | 942 | ||
| General considerations | 942 | ||
| Anatomy | 942 | ||
| Pathogenesis of the respiratory tract: Basic concepts | 943 | ||
| Host factors | 943 | ||
| Microorganism virulence factors | 944 | ||
| Adherence | 944 | ||
| Toxins | 944 | ||
| Microorganism growth | 945 | ||
| Avoiding the host response | 945 | ||
| Diseases of the lower respiratory tract | 945 | ||
| Bronchitis | 945 | ||
| Acute | 945 | ||
| Chronic versus acute | 946 | ||
| Bronchiolitis | 946 | ||
| Pneumonia | 946 | ||
| Pathogenesis | 947 | ||
| Clinical manifestations | 947 | ||
| Epidemiology and etiologic agents | 947 | ||
| Community-acquired pneumonia | 947 | ||
| Children. | 947 | ||
| Young adults. | 947 | ||
| Adults (viral pneumonia) | 949 | ||
| Adults (fungal pneumonia) | 949 | ||
| Chronic lower respiratory tract infections | 949 | ||
| Immunocompromised patients | 949 | ||
| Patients with neoplasms. | 949 | ||
| Transplant recipients. | 949 | ||
| Patients with human immunodeficiency virus. | 949 | ||
| Pleural infections | 950 | ||
| Laboratory diagnosis of lower respiratory tract infections | 950 | ||
| Specimen collection and transport | 950 | ||
| Sputum | 951 | ||
| Expectorated | 951 | ||
| Induced | 951 | ||
| Endotracheal or tracheostomy suction specimens | 951 | ||
| Bronchoscopy | 951 | ||
| Transtracheal aspirates | 952 | ||
| Other invasive procedures | 952 | ||
| Specimen processing | 952 | ||
| Direct visual examination | 952 | ||
| Routine culture | 955 | ||
| Bibliography | 955 | ||
| 69 Upper respiratory tract infections and other infections of the oral cavity and neck | 957 | ||
| Objectives | 957 | ||
| General considerations | 957 | ||
| Anatomy | 957 | ||
| Pathogenesis | 957 | ||
| Diseases of the upper respiratory tract, oral cavity, and neck | 957 | ||
| Upper respiratory tract | 957 | ||
| Laryngitis | 957 | ||
| Laryngotracheobronchitis | 958 | ||
| Epiglottitis | 958 | ||
| Pharyngitis, tonsillitis, and peritonsillar abscesses | 958 | ||
| Pharyngitis and tonsillitis | 958 | ||
| Clinical manifestations. | 958 | ||
| Pathogenesis. | 958 | ||
| Epidemiology and etiologic agents. | 958 | ||
| Peritonsillar abscesses | 960 | ||
| Rhinitis | 960 | ||
| Miscellaneous infections caused by other agents | 960 | ||
| Corynebacterium diphtheriae | 960 | ||
| Bordetella pertussis | 960 | ||
| Klebsiella spp. | 960 | ||
| Oral cavity | 960 | ||
| Stomatitis | 960 | ||
| Thrush | 961 | ||
| Periodontal infections | 961 | ||
| Types | 961 | ||
| Etiologic agents | 961 | ||
| Salivary gland infections | 961 | ||
| Neck | 961 | ||
| Diagnosis of upper respiratory tract infections | 961 | ||
| Collection and transport of specimens | 961 | ||
| Direct visual examination or detection | 962 | ||
| Culture | 963 | ||
| Streptococcus pyogenes (beta-hemolytic group a streptococci) | 963 | ||
| Corynebacterium diphtheriae | 963 | ||
| Bordetella pertussis | 963 | ||
| Neisseria spp. | 963 | ||
| Epiglottitis | 963 | ||
| Diagnosis of infections in the oral cavity and neck | 963 | ||
| Collection and transport | 963 | ||
| Direct visual examination | 964 | ||
| Culture | 964 | ||
| Bibliography | 964 | ||
| 70 Meningitis and other infections of the central nervous system | 965 | ||
| Objectives | 965 | ||
| General considerations | 965 | ||
| Anatomy | 965 | ||
| Coverings and spaces of the central nervous system | 965 | ||
| Cerebrospinal fluid | 966 | ||
| Routes of infection | 966 | ||
| Diseases of the central nervous system | 966 | ||
| Meningitis | 966 | ||
| Purulent meningitis | 966 | ||
| Pathogenesis. | 966 | ||
| Clinical manifestations. | 966 | ||
| Acute. | 968 | ||
| Chronic. | 968 | ||
| Epidemiology and etiologic agents of acute meningitis. | 968 | ||
| Aseptic meningitis | 969 | ||
| Encephalitis/meningoencephalitis | 969 | ||
| Viral encephalitis | 970 | ||
| Parasitic infections | 970 | ||
| Brain abscess | 970 | ||
| Shunt infections | 970 | ||
| Laboratory diagnosis of central nervous system infections | 971 | ||
| Meningitis | 971 | ||
| Specimen collection and transport | 971 | ||
| Initial processing | 971 | ||
| Cerebrospinal fluid laboratory results | 971 | ||
| Visual detection of etiologic agents | 972 | ||
| Stained smear of sediment | 972 | ||
| Wet preparation | 972 | ||
| India ink stain | 972 | ||
| Direct detection of etiologic agents | 972 | ||
| Antigen | 972 | ||
| Bacteria. | 972 | ||
| Cryptococcus neoformans. | 972 | ||
| Molecular methods | 973 | ||
| Miscellaneous tests | 973 | ||
| Culture | 974 | ||
| Bacteria and fungi | 974 | ||
| Parasites and viruses | 974 | ||
| Brain abscess/biopsies | 974 | ||
| Specimen collection, transport, and processing. | 974 | ||
| Bibliography | 975 | ||
| 71 Infections of the eyes, ears, and sinuses | 976 | ||
| Objectives | 976 | ||
| Eyes | 976 | ||
| Anatomy | 976 | ||
| Resident microbiota | 976 | ||
| Diseases | 977 | ||
| Pathogenesis | 977 | ||
| Epidemiology and etiology of disease | 977 | ||
| Blepharitis | 977 | ||
| Conjunctivitis | 977 | ||
| Keratitis | 979 | ||
| Endophthalmitis | 980 | ||
| Periocular | 980 | ||
| Uveitis | 981 | ||
| Other infections | 981 | ||
| Laboratory diagnosis | 982 | ||
| Specimen collection and transport | 982 | ||
| Direct visual examination | 982 | ||
| Culture | 982 | ||
| Nonculture methods | 983 | ||
| Ears | 983 | ||
| Anatomy | 983 | ||
| Resident microbiota | 983 | ||
| Diseases, epidemiology, and etiology of disease | 983 | ||
| Otitis externa (external ear infections) | 983 | ||
| Otitis media (middle ear infections) | 984 | ||
| Pathogenesis | 984 | ||
| Laboratory diagnosis | 984 | ||
| Specimen collection and transport | 984 | ||
| Direct visual examination | 984 | ||
| Culture and nonculture methods | 984 | ||
| Sinuses | 984 | ||
| Anatomy | 984 | ||
| Diseases | 985 | ||
| Pathogenesis | 985 | ||
| Epidemiology and etiology of disease | 985 | ||
| Laboratory diagnosis | 985 | ||
| Matrix-assisted laser desorption ionization time-of-flight mass spectrometry | 986 | ||
| Bibliography | 986 | ||
| 72 Infections of the urinary tract | 987 | ||
| Objectives | 987 | ||
| General considerations | 987 | ||
| Anatomy | 987 | ||
| Resident microbiota of the urinary tract | 987 | ||
| Infections of the urinary tract | 988 | ||
| Epidemiology | 988 | ||
| Etiologic agents | 988 | ||
| Community-acquired | 988 | ||
| Hospital- and health care–associated | 988 | ||
| Miscellaneous | 989 | ||
| Pathogenesis | 989 | ||
| Routes of infection | 989 | ||
| The host-pathogen relationship | 990 | ||
| Types of infection and their clinical manifestations | 991 | ||
| Urethritis | 991 | ||
| Ureteritis | 991 | ||
| Asymptomatic bacteriuria | 991 | ||
| Cystitis | 992 | ||
| Acute urethral syndrome | 992 | ||
| Pyelonephritis | 992 | ||
| Urosepsis | 992 | ||
| Laboratory diagnosis of urinary tract infections | 992 | ||
| Specimen collection | 992 | ||
| Clean-catch midstream urine | 992 | ||
| Straight catheterized urine | 992 | ||
| Suprapubic bladder aspiration | 993 | ||
| Indwelling catheter | 993 | ||
| Specimen transport | 993 | ||
| Screening procedures | 993 | ||
| Gram or methylene blue stain | 993 | ||
| Pyuria | 994 | ||
| Indirect indices | 994 | ||
| Nitrate reductase (greiss) test | 994 | ||
| Leukocyte esterase test | 994 | ||
| Catalase | 994 | ||
| Automated and semiautomated systems | 994 | ||
| General comments regarding screening procedures | 994 | ||
| Urine culture | 995 | ||
| Inoculation and incubation of urine cultures | 995 | ||
| Interpretation of urine cultures | 995 | ||
| Bibliography | 998 | ||
| 73 Genital tract infections | 999 | ||
| Objectives | 999 | ||
| General considerations | 999 | ||
| Anatomy | 999 | ||
| Resident microbiota | 999 | ||
| Sexually transmitted diseases and other genital tract infections | 1000 | ||
| Genital tract infections | 1001 | ||
| Sexually transmitted diseases and other lower genital tract infections | 1001 | ||
| Epidemiology and etiologic agents | 1001 | ||
| Routes of transmission | 1001 | ||
| Sexually transmitted | 1001 | ||
| Other routes | 1002 | ||
| Clinical manifestations | 1002 | ||
| Asymptomatic | 1002 | ||
| Dysuria | 1002 | ||
| Urethral discharge | 1002 | ||
| Lesions of the skin and mucous membranes | 1002 | ||
| Vaginitis | 1004 | ||
| Cervicitis | 1005 | ||
| Anorectal lesions | 1005 | ||
| Bartholinitis | 1005 | ||
| Infections of the reproductive organs and other upper genital tract infections | 1005 | ||
| Females | 1005 | ||
| Pelvic inflammatory disease | 1006 | ||
| Infections after gynecologic surgery | 1006 | ||
| Infections associated with pregnancy | 1006 | ||
| Males | 1007 | ||
| Gonorrhea | 1007 | ||
| Syphilis | 1007 | ||
| Laboratory diagnosis of genital tract infections | 1007 | ||
| Lower genital tract infections | 1007 | ||
| Urethritis, cervicitis, and vaginitis | 1007 | ||
| Specimen collection | 1007 | ||
| Urethral. | 1007 | ||
| Cervical and vaginal. | 1007 | ||
| Transport. | 1007 | ||
| Direct microscopic examination | 1009 | ||
| Culture | 1010 | ||
| Nonculture methods | 1011 | ||
| Genital skin and mucous membrane lesions | 1011 | ||
| Buboes | 1012 | ||
| Infections of the reproductive organs | 1012 | ||
| Pelvic inflammatory disease | 1012 | ||
| Miscellaneous infections | 1012 | ||
| Infections of neonates and human products of conception | 1012 | ||
| Bibliography | 1013 | ||
| 74 Gastrointestinal tract infections | 1015 | ||
| Objectives | 1015 | ||
| Anatomy | 1015 | ||
| Resident gastrointestinal microbiome | 1017 | ||
| Gastroenteritis | 1017 | ||
| Pathogenesis | 1018 | ||
| Host factors | 1018 | ||
| Microbial factors | 1018 | ||
| Primary pathogenic mechanisms | 1018 | ||
| Toxins | 1019 | ||
| Enterotoxins. | 1019 | ||
| Cytotoxins. | 1019 | ||
| Neurotoxins. | 1020 | ||
| Attachment. | 1020 | ||
| Invasion. | 1020 | ||
| Miscellaneous virulence factors | 1023 | ||
| Clinical manifestations | 1023 | ||
| Epidemiology | 1024 | ||
| Institutional settings | 1024 | ||
| Traveler’s diarrhea | 1024 | ||
| Foodborne and waterborne outbreaks | 1024 | ||
| Immunocompromised hosts | 1025 | ||
| Etiologic agents | 1025 | ||
| Other infections of the gastrointestinal tract | 1025 | ||
| Esophagitis | 1025 | ||
| Gastritis | 1025 | ||
| Proctitis | 1028 | ||
| Miscellaneous | 1028 | ||
| Laboratory diagnosis of gastrointestinal tract infections | 1028 | ||
| Specimen collection and transport | 1028 | ||
| General comments | 1028 | ||
| Stool specimens for bacterial culture | 1028 | ||
| Stool specimens for ova and parasites | 1029 | ||
| Stool specimens for viruses | 1029 | ||
| Miscellaneous specimen types | 1029 | ||
| Direct detection of agents of gastroenteritis in feces | 1029 | ||
| Wet mounts | 1029 | ||
| Stains | 1029 | ||
| Antigen detection | 1029 | ||
| Molecular methods | 1029 | ||
| Culture of fecal material for isolation of etiologic agents | 1030 | ||
| Bacteria | 1030 | ||
| Organisms for routine culture | 1030 | ||
| Routine culture methods | 1030 | ||
| Salmonella and shigella. | 1030 | ||
| Campylobacter. | 1030 | ||
| Enrichment broths. | 1030 | ||
| Laboratory diagnosis of clostridium difficile–associated diarrhea | 1032 | ||
| Bibliography | 1033 | ||
| 75 Skin, soft tissue, and wound infections | 1034 | ||
| Objectives | 1034 | ||
| General considerations | 1034 | ||
| Anatomy of the skin | 1034 | ||
| Function of the skin | 1034 | ||
| Prevalence, etiology, and pathogenesis | 1035 | ||
| Skin and soft tissue infections | 1035 | ||
| Infections of the epidermis and dermis | 1035 | ||
| Infections in or around hair follicles | 1035 | ||
| Infections in the keratinized layer of the epidermis | 1035 | ||
| Infections in the deeper layers of the epidermis and dermis | 1036 | ||
| Infections of the subcutaneous tissues | 1036 | ||
| Infections of the muscle fascia and muscles | 1039 | ||
| Necrotizing fasciitis | 1039 | ||
| Progressive bacterial synergistic gangrene | 1039 | ||
| Myositis | 1039 | ||
| Wound infections | 1039 | ||
| Postoperative infections | 1039 | ||
| Bites | 1040 | ||
| Burns | 1040 | ||
| Special circumstances regarding skin and soft tissue infections | 1040 | ||
| Infections related to vascular and neurologic problems | 1041 | ||
| Sinus tracts and fistulas | 1041 | ||
| Systemic infections and skin manifestations | 1042 | ||
| Laboratory diagnostic procedures | 1042 | ||
| Infections of the epidermis and dermis | 1042 | ||
| Erysipeloid | 1042 | ||
| Superficial mycoses and erythrasma | 1042 | ||
| Erysipelas and cellulitis | 1043 | ||
| Vesicles and bullae | 1043 | ||
| Infections of the subcutaneous tissues | 1043 | ||
| Infections of the muscle fascia and muscles | 1043 | ||
| Wound infections | 1043 | ||
| Postoperative | 1043 | ||
| Bites | 1043 | ||
| Burns | 1043 | ||
| Bibliography | 1045 | ||
| 76 Normally sterile body fluids, bone and bone marrow, and solid tissues | 1046 | ||
| Objectives | 1046 | ||
| Specimens from sterile body sites | 1046 | ||
| Fluids | 1046 | ||
| Pleural fluid | 1046 | ||
| Peritoneal fluid | 1047 | ||
| Primary peritonitis | 1048 | ||
| Secondary peritonitis | 1048 | ||
| Peritoneal dialysis fluid | 1049 | ||
| Pericardial fluid | 1049 | ||
| Joint fluid | 1049 | ||
| Bone | 1050 | ||
| Bone marrow aspiration or biopsy | 1050 | ||
| Bone biopsy | 1050 | ||
| Solid tissues | 1051 | ||
| Laboratory diagnostic procedures | 1051 | ||
| Specimen collection and transport | 1051 | ||
| Fluids and aspirates | 1051 | ||
| Bone | 1052 | ||
| Tissue | 1052 | ||
| Specimen processing, direct examination, and culture | 1053 | ||
| Fluids and aspirates | 1053 | ||
| Bone | 1053 | ||
| Solid tissue | 1054 | ||
| Bibliography | 1054 | ||
| Part VIII Clinical Laboratory Management | 1055 | ||
| 77 Quality in the clinical microbiology laboratory | 1055 | ||
| Objectives | 1055 | ||
| Quality program | 1056 | ||
| Specimen collection and transport | 1056 | ||
| Standard operating procedure manual | 1057 | ||
| Personnel | 1057 | ||
| Reference laboratories | 1057 | ||
| Patient reports | 1057 | ||
| Proficiency testing | 1057 | ||
| Performance checks | 1058 | ||
| Instruments | 1058 | ||
| Commercially prepared media exempt from quality control | 1058 | ||
| User-prepared and nonexempt, commercially prepared media | 1058 | ||
| Antimicrobial susceptibility tests | 1058 | ||
| Stains and reagents | 1059 | ||
| Antisera | 1059 | ||
| Kits | 1059 | ||
| Maintenance of quality control records | 1059 | ||
| Maintenance of reference quality control stocks | 1059 | ||
| Bacteriology | 1059 | ||
| Mycology | 1059 | ||
| Mycobacteriology | 1060 | ||
| Virology | 1060 | ||
| Parasitology | 1060 | ||
| Quality assurance program | 1060 | ||
| Types of quality assurance audits | 1060 | ||
| Conducting a quality assurance audit | 1061 | ||
| Continuous daily monitoring | 1061 | ||
| Bibliography | 1061 | ||
| 78 Infection control | 1063 | ||
| Objectives | 1063 | ||
| Incidence of health care–associated infections | 1064 | ||
| Types of health care–associated infections | 1064 | ||
| Urinary tract infections | 1064 | ||
| Lung infections | 1065 | ||
| Surgical site infections | 1065 | ||
| Central line–associated bloodstream infection | 1065 | ||
| Emergence of antibiotic-resistant microorganisms | 1065 | ||
| Hospital infection control programs | 1065 | ||
| Role of the microbiology laboratory | 1066 | ||
| Characterizing strains involved in an outbreak | 1066 | ||
| Preventing health care–associated infections | 1068 | ||
| Surveillance methods | 1070 | ||
| Bibliography | 1070 | ||
| 79 Sentinel laboratory response to bioterrorism | 1072 | ||
| Objectives | 1072 | ||
| General considerations | 1072 | ||
| Bio crime | 1072 | ||
| Government laws and regulations | 1072 | ||
| Biosecurity | 1073 | ||
| Laboratory response network | 1073 | ||
| Role of the sentinel laboratory | 1074 | ||
| Bibliography | 1076 | ||
| Glossary | 1077 | ||
| Index | 1084 | ||
| A | 1084 | ||
| B | 1087 | ||
| C | 1089 | ||
| D | 1093 | ||
| E | 1093 | ||
| F | 1095 | ||
| G | 1096 | ||
| H | 1097 | ||
| I | 1099 | ||
| J | 1100 | ||
| K | 1100 | ||
| L | 1100 | ||
| M | 1101 | ||
| N | 1104 | ||
| O | 1105 | ||
| P | 1105 | ||
| Q | 1108 | ||
| R | 1108 | ||
| S | 1109 | ||
| T | 1112 | ||
| U | 1113 | ||
| V | 1114 | ||
| W | 1114 | ||
| X | 1115 | ||
| Y | 1115 | ||
| Z | 1115 |