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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 |