Medical Microbiology. 4th ed. - Chapter 10: Principles of DiagnosisBaron S, editor.
Galveston (TX): University of Texas Medical Branch at Galveston; 1996.
Co-Editors
Authors
Preface
Chapter 1. Immunology Overview
General Concepts
Evolution of the Immune System
Organization/Components/Functions
Molecular Communications in the Immune System
Cells of the Immune System
Immunoglobulin Supergene Family
Recognition of Self and Immune Tolerance
The Complement System
Defense against Infections
Diseases Due to Immune Responses to Infectious Agents
Ontogeny of Immunity
Maternal Immunologic Agents Transferred to the Recipient Infant
Immune Deficiencies
References
Section 1. Bacteriology
Introduction to Bacteriology
Chapter 2. Structure
General Concepts
Introduction
The Nucleoid
Surface Appendages
Surface Layers
Intracellular Components
References
Chapter 3. Classification
General Concepts
Introduction
Definitions
Approaches to Taxonomy
Phenotypic Characteristics Useful in Classification and Identification
Classification Below and Above the Species Level
Designation of New Species and Nomenclatural Changes
Assessing Newly Described Bacteria
Role of the Clinical Laboratory
Interfacing with Public Health Laboratories
Hazards of Clinical Laboratory Work
References
Chapter 4. Bacterial Metabolism
General Concepts
Introduction
Heterotrophic Metabolism
Respiration
Fermentation
Krebs Cycle
Glyoxylate Cycle
Electron Transport and Oxidative Phosphorylation
Mitchell or Proton Extrusion Hypothesis
Bacterial Photosynthesis
Autotrophy
Anerobic Respiration
The Nitrogen Cycle
References
Chapter 5. Genetics
General Concepts
Genetic Information in Microbes
Genome Organization
Mutation and Selection
Exchange of Genetic Information
Recombination DNA and Gene Cloning
Regulation of Gene Expression
References
Chapter 6. Normal Flora
General Concepts
Introduction
Significance of the Normal Flora
Normal Flora of Skin
Oral and Upper Respiratory Tract Flora
Gastrointestinal Tract Flora
Urogenital Flora
Conjunctival Flora
Host Infection by Elements of the Normal Flora
References
Chapter 7. Bacterial Pathogenesis
General Concepts
Introduction
Host Susceptibility
Pathogenic Mechanisms
Specific Virulence Factors
Biologic Activity of Endotoxin
Detection of Endotoxin in Medical Solutions
Epilogue
References
Chapter 8. Specific Acquired Immunity
General Concepts
Basis of Acquired Resistance
Primary vs Opportunistic Pathogens
Protective Antigens
Immune Mechanisms
Preventive Immunity
References
Chapter 9. Epidemiology
General Concepts
Introduction
Chain of Infection
Epidemiologic Methods
Epidemic Investigation
References
Chapter 10. Principles of Diagnosis
General Concepts
Introduction
Manifestations of Infection
Microbial Causes of Infection
Specimen Selection, Collection and Processing
Microbiologic Examination
References
Chapter 11. Antimicrobial Chemotherapy
General Concepts
Introduction
Biochemical Basis of Antimicrobial Action
Inhibition of Bacterial Cell Wall Synthesis
Antibiotics that Affect the Function of Cytoplasmic Membranes
Antibiotics that Inhibit Nucleic Acid Synthesis
Antimicrobial Inhibitors of Ribosome Function
Drugs that Inhibit Other Biochemical Targets
Antibacterial Agents that Affect Mycobacteria
Bacterial Resistance
Combinations of Antimicrobial Agents
Toxicology of Antimicrobial Agents
Mechanism to Reduce Bacterial Resistance
References
Chapter 12. Staphylococcus
General Concepts
Introduction
Taxonomy
Identification of Staphylococci in the Clinical laboratory
Epidemiology of Staphylococcus Aureus Infections
Clinical Manifestations of S Aureus
Pathogenesis of S Aureus Infections
Adherence
Avoidance of Host Defenses
Damage to the Host
Other Extracellular Proteins
Enzymes
Coagulase Negative Staphylococci
Resistance of Staphylococci to Antimicrobial Drugs
Future Prospects
References
Chapter 13. Streptococcus
General Concepts
Introduction
Clinical Manifestations
Classification, Antigenic Types and Extracellular Growth Products
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 14. Neisseria, Moraxella, Kingella and Eikenella
General Concepts
Introduction
Nesseria gonorrhoeae
Neisseria meningitidis
Moraxella
Kingella
Eikenella
References
Chapter 15. Bacillus
General Concepts
Introduction
Clinical Manifestions
Structure and Classification
Pathogenisis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 16. Miscellaneous Pathogenic Bacteria
GENERAL CONCEPTS
Introduction
Listeria Monocytogenes
Erysipelothrix Rhusiopathiae
Propionibacterium Acnes
Streptobacillus Moniliformis
Calymmatobacterium Granulomatis
References
Chapter 17. Anaerobes: General Characteristics
General Concepts
Introduction
Oxygen Toxicity
Pathogenic Anaerobes
Processing of Clinical Specimens
References
Chapter 18. Clostridia: Sporeforming Anaerobic Bacilli
General Concepts
Introduction
Gas Gangrene and Related Clostridial Wound Infections
Tetanus and Clostribium Tetani
Botulism and Clostridium Botulinum
Antibiotic-Associated Diarrhea, Pseudomembranous Colitis, and Clostridium Difficile
Other Pathogenic Clostridia Food Poisoning and Clostridium perfringens
References
Chapter 19. Anaerobic Cocci
General Concepts
Clinical Manifestations
Structure, Classification and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 20. Anaerobic Gram-Negative Bacilli
General Concepts
Introduction
Clinical Manifestations
Structure, Classification, and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 21. Salmonella
General Concepts
Introduction
Clinical Manifestations
Structure, Classification, and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 22. Shigella
General Concepts
Introduction
Clinical Presentation
Structure, Classification, and Antigenic Types
Pathogenesis
Host Defense
Epidemiology
Diagnosis
Treatment
Control
References
Chapter 23. Campylobacter and Helicobacter
General Concepts
Introduction
Campylobacter Jejuni and other Enteric Campylobacters
Helicobacter Pylori and other Gastric Helicobacter-Like Organisms
Other Pathogenic Helicobacter Species
References
Chapter 24. Cholera, Vibrio cholerae O1 and O139, and Other Pathogenic Vibrios
General Concepts
Introduction
Vibrio Cholerae
Other Vibrio Infections
References
Chapter 25. Escherichia Coli in Diarrheal Disease
General Concepts
Introduction
Noninflammatory Diarrheas Caused by Enterotoxigenic Escherichia Coli
Inflammatory Diarrheas Caused by Enteroinvasive, Cytotoxic, and Enteropathogenic Escherichia Coli
References
Chapter 26. Escherichia, Klebsiella, Enterobacter, Serratia, Citrobacter, and Proteus
General Concepts
Introduction
Clinical Manifestations
Distinctive Properties
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 27. Pseudomonas
General Concepts
Introduction
Clinical Manifestations
Structure, Classification, and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 28. Brucella
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 29. Pasteurella, Yersinia, and Francisella
General Concepts
Introduction
Pasteurella
Yersinia
Francisella
References
Chapter 30. Haemophilus Species
General Concepts
Introduction
Clinical Manifestations
Structure, Classification, and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 31. Bordetella
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 32. Corynebacterium Diphtheriae
General Concepts
Introduction
Clinical Manifestations
Structure, Classification, and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
Other Corynebacterium Species
Redesigning of Diphtheria Toxin for the Development of Eukaryotic Cell-Receptor Specific Cytotoxins
References
Chapter 33. Mycobacteria and Nocardia
General Concepts
Introduction
Mycobacterium tuberculosis Complex
Nontuberculous Mycobacteria
Mycobacterium leprae
Nocardia
References
Chapter 34. Actinomyces, Propionibacterium propionicus, and Streptomyces
General Concepts
Introduction
Actinomycosis
Streptomyces
References
Chapter 35. Leptospira
General Concepts
Introduction
Leptospira
Borrelia
Spirillum
References
Chapter 36. Treponema
General Concepts
Introduction
Clinical Manifestations
Structure and Biology
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
Other Treponematoses
References
Chapter 37. Mycoplasmas
General Concepts
Introduction
Clinical Presentation
Structure, Classification, and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 38. Rickettsiae
General Concepts
Introduction
Rickettsiae of the Spotted Fever and Typhus Groups
Orientia (Rickettsia) tsutsugamushi and Scrub Typhus
Ehrlichia
Coxiella burnetii and Q Fever
Bartonella
References
Chapter 39. Chlamydia
General Concepts
Introduction
Clinical Manifestations
Structure
Classification, and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 40. Legionella
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Section 2. Virology
Introduction to Virology
Chapter 41. Structure and Classification of Viruses
General Concepts
Structure and Function
Classification of Viruses
Virus Classification
References
Chapter 42. Multiplication
General Concepts
Initiation of Infection
The Strategies of Viral Multiplication
Single-stranded RNA viruses
Double-stranded RNA viruses
DNA virus genomes
Viruses differ with respect to their assembly, maturation and egress from infected cells
Variability in Viral Genomes and Viral Multiplication
References
Chapter 43. Viral Genetics
General Concepts
Introduction
Genetic Change in Viruses
Mutations
Recombination
References
Chapter 44. Effects on Cells
General Concepts
Introduction
Cytocidal Infections
Persistent Infections
Transforming Infections
References
Chapter 45. Viral Pathogenesis
General Concepts
Introduction
Cellular Pathogenesis
Tissue Tropism
Sequence of Virus Spread in the Host
Dissemination from the Portal of Entry
Incubation Period
Multiplication in Target Organs
Shedding of Virus
Congenital Infections
References
Chapter 46. Persistent Viral Infections
General Concepts
Introduction
Classification
Models of Virus Persistence in Vitro
Pathogenesis of Persistent Virus Infections
Reactivation of Persistent Viruses
Persistent Infections by Organ System
Control of Persistent Infections
References
Chapter 47. Tumor Viruses
General Concepts
Causation of Tumors
Human Oncogenic RNA Viruses (Retroviruses)
Oncogenic DNA Viruses
Vaccines in the Prevention of Virus-Associated Cancers
References
Chapter 48. Epidemiology and Evolution
General Concepts
Introduction
Portals of Entry and Exit
Viral Zoonoses
Epidemiologic Features of Viral Infections
Evolution of Viruses
References
Chapter 49. Nonspecific Defenses
General Concepts
Introduction
Defense Mechanisms that Precede Infection
Defense Mechanisms Evoked by Infection
Viral Interference and Interferon
Conclusion
References
Chapter 50. Immune Defenses
General Concepts
Introduction
Viral Activation of Immunity
Virus-Induced Immunopathology
Roles of Immune functions During Viral Infections
References
Chapter 51. Control of Viral Infections and Diseases
General Concepts
Introduction
Immunoprophylaxis
Sanitation and Vector Control
Antiviral Chemotherapy
Interferons: Cytokines With Antiviral Activity
Identifying New Effective Therapeutics
References
Chapter 52. Chemotherapy of Viral Infections
General Concepts
Introduction
Basic Mechanisms
Approved Antiviral Drugs
Future Antiviral Drugs
Main Targets for Antiviral Drugs
Limitations of Antiviral Drugs
References
Chapter 53. Picornaviruses
General Concepts
Introduction
Clinical Manifestations
Structure and Replication
Classification and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
Enteroviruses
References
Chapter 54. Alphaviruses (Togaviridae) and Flaviviruses (Flaviviridae)
General Concepts
Introduction
Alphaviruses
Flaviviruses
References
Chapter 55. Togaviruses: Rubella Virus
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 56. Bunyaviruses
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 57. Arenaviruses
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 58. Orthomyxoviruses
General Concepts
Introduction
Clinical Manifestation
Structure
Classification and Antigenic Types
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 59. Paramyxoviruses
General Concepts
Introduction
Parainfluenza Viruses
Respiratory Syncytial Virus
Mumps Virus
Measles Virus
References
Chapter 60. Coronaviruses
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 61. Rhabdoviruses: Rabies Virus
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 62. Human Retroviruses
General Concepts
Types of Endogenous and Exogenous Retroviruses
Human T-Cell Leukemia Viruses
Human Immunodeficiency Virus
References
Chapter 63. Rotaviruses, Reoviruses, Coltiviruses, and Orbiviruses
General Concepts
Introduction
Rotaviruses
Reoviruses
Coltiviruses and Orbiviruses
References
Chapter 64. Parvoviruses
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 65. Norwalk Virus and Other Caliciviruses
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 66. Papovaviruses
General Concepts
Introduction
Structure
Classification and Antigenic Types
Virus Multiplication and Cell Transformation
Polyomaviruses
Papillomaviruses
References
Chapter 67. Adenoviruses
General Concepts
Introduction
Clinical Manifestations
Structure
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
Vector in Human Somatic Gene Therapy
References
Chapter 68. Herpesviruses
General Concepts
Introduction
General Biologic Properties
Structure
Classification
Replication and Latency
Diagnosis
Herpes Simplex Viruses
Varicella-Zoster Virus
Cytomegalovirus
Epstein-Barr Virus
Human Herpesvirus 6 and 7
Kaposi's Sarcoma Herpesvirus
B-Virus
Control of Herpesvirus Infection
References
Chapter 69. Poxviruses
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 70. Hepatitis Viruses
General Concepts
Hepatitis A
Hepatitis E
Hepatitis B
Hepatitis D
Hepatitis C
The GB Hepatitis Viruses
References
Chapter 71. Subacute Spongiform Unconventional Virus Encephalopathies
General Concepts
Introduction
Unconventional Viruses
Scrapie
Kuru
Creutzfeldt-Jakob Disease
Concluding Comments
References
Chapter 72. Filoviruses
General Concepts
Introduction
Clinical Manifestation
Classification
Virus Structure
Virus Replication
Epidemiology
Pathogenesis
Host Defenses
Diagnosis
Patient Management, Therapy, and Control
References
Section 3. Mycology
Introduction to Mycology
General Concepts of Mycology
General Concepts
Clinical Presentation
Structure
Classification
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
Introduction to Mycology
General Concepts
Introduction
Physiology
Structure
Morphology
Propagules (Spores and Conidia)
Classification
References
Chapter 73. Basic Biology of Fungi
General Concepts
Introduction
Cell Walls
Filamentous Fungi and Filamentous Bacteria
Hyphal and Yeast Morphogenesis
Reproduction
References
Chapter 74. Disease of Mechanisms of Fungi
General Concepts
Introduction
Entry
Adaptation and Propagation
Dissemination
Host Factors
Fungal Factors
References
Chapter 75. Spectrum of Mycoses
General Concepts
Introduction
Superficial and Cutaneous Mycoses
Subcutaneous Mycoses
Deep Mycoses
References
Chapter 76. Antifungal Agents
General Concepts
Introduction
Polyene Antifungal Drugs
Azole Antifungal Drugs
5-Fluorocytosine
Other Antifungal Agents
Selection of Antifungal Agents
References
Section 4. Parasitology
Introduction to Parasitology
Chapter 77. Protozoa: Structure, Classification, Growth, and Development
General Concepts
Introduction
Structure
Classification
Life Cycle Stages
Reproduction
Nutrition
References
Chapter 78. Protozoa: Pathogenesis and Defenses
General Concepts
Introduction
Pathology
Immune Escape
References
Chapter 79. Intestinal Protozoa: Amebas
General Concepts
Introduction
Entamoeba Histolytica
References
Chapter 80. Other Intestinal Protozoa and Trichomonas Vaginalis
General Concepts
Introduction
Giardia Lamblia
Trichomonas Vaginalis
Other Trichomonads
Cryptosporidium
References
Chapter 81. Free-Living Amebas: Naegleria, Acanthamoeba and Balamuthia
General Concepts
Introduction
Naegleria Fowleri
Acanthamoeba/B Mandrillaris (Family Leptomyxidae)
References
Chapter 82. Hemoflagellates
General Concepts
Introduction
American Trypanosomiasis (Chagas Disease)
African Trypanosomiasis (Sleeping Sickness)
Cutaneous and Mucocutaneous Leishmaniasis
Visceral Leishmaniasis (Kala-Azar)
References
Chapter 83. Malaria
General Concepts
Introduction
Clinical Manifestations
Classification
Structure and Life Cycle
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 84. Toxoplasma Gondii
General Concepts
Introduction
Clinical Manifestations
Structure, Multiplication, and Life Cycle
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 85. Pneumocystis Carinii
General Concepts
Introduction
Clinical Manifestations
Structure
Classification and Antigenic Types
Multiplication
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 86. Helminths: Structure, Classification, Growth, and Development
General Concepts
Introduction
Flukes (Trematodes)
Tapeworms (Cestodes)
Roundworms (Nematodes)
References
Chapter 87. Helminths: Pathogenesis and Defenses
GENERAL CONCEPTS
Introduction
Infection
Pathogenesis
Defenses Against Infection
References
Chapter 88. Schistosomes and Other Trematodes
General Concepts
Introduction
Clinical Manifestations
Structure and Life Cycle
Pathogenesis
Host Defenses
Epidemiology
Diagnosis
Control
References
Chapter 89. Cestodes
General Concepts
Introduction
Taenia saginata, The Beef Tapeworm
Taenia solium, The Pork Tapeworm
Taenia multiceps, The Coenurus Tapeworm
Echinococcus granulosus, The Hydatid Tapeworm
Echinococcus multilocularis, The Multiloculate or Alveolar Hydatid Tapeworm
Hymenolepis nana, The Dwarf Tapeworm
Hymenolepis diminuta, The Rat Tapeworm
Dipylidium caninum, The Double-Pored Tapeworm
Diphyllobothrium latum, The Broad Fish Tapeworm
References
Chapter 90. Enteric Nematodes of Humans
General Concepts
Introduction
Ascaris Lumbricoides
Hookworms
Strongyloides Stercoralis
Trichuris Trichura
Enterobius Vermicularis
References
Chapter 91. Enteric Nematodes of Lower Animals Transmitted to Humans: Zoonoses
General Concepts
Introduction
Visceral and Ocular Larva Migrans
Cutaneous Larva Migrans
Trichinosis
References
Chapter 92. Filarial Nematodes
General Concepts
Introduction
Lymphatic Filariae Wuchereria Bancrofti and Brugia Malayi
Onchocerca Volvulus
Minor Filarial Infections
Dirofilaria Species
Dracunculus Medinensis
References
Section 5. Introduction to Infectious Diseases
Introduction to Infectious Diseases
Chapter 93. Infections of the Respiratory System
General Concepts
Upper Respiratory Infections
Lower Respiratory Infections
References
Chapter 94. Microbiology of the Circulatory System
General Concepts
Introduction
Clinical Syndromes
Blood Cultures
References
Chapter 95. Microbiology of the Gastrointestinal Tract
General Concepts
Composition and Distribution of the Microflora
Metabolic Activites of the Microflora
The Intestinal Microflora and Infection
Bacterial Diarrheas
Viral Diarrheas
Parasitic Diarrheas
Clinical Diagnosis of Diarrheal Disease
References
Chapter 96. Microbiology of the Nervous System
General Concepts
Introduction
Gross Anatomy
Blood-Brain Barrier
Immune System
Cellular Structure
Meningitis
Infection of the Brain Parenchyma
Encephalitis
Slow and Chronic Infection and Chronic Neurologic Disease
References
Chapter 97. Microbiology of the Genitourinary System
General Concepts
Introduction
Urethritis and Epididymitis
Vaginitis, Cervicitis, Endometritis, and Pelvic Inflammatory Disease
Genital Ulcer Disease
Urinary Tract Infections
References
Chapter 98. Microbial Infections of Skin and Nails
General Concepts
Introduction
Skin Infections
Methods for Laboratory Diagnosis
Bacterial Skin Infections
Treatment of the Pyodermas
Viral Skin Diseases
Fungal Skin Diseases
Nail
References
Chapter 99. Microbiology of Dental Decay and Periodontal Disease
General Concepts
Introduction
Dental Caries (Decay)
Periodontal Disease
References
Chapter 100. Bone, Joint, and Necrotizing Soft Tissue Infections
General Concepts
Introduction
Necrotizing Soft Tissue Infections
Joint Infections
Bone Infections
References