Section 1. Introduction
1. Introduction to Medical Microbiology
Historical Perspective
Viruses
Bacteria
Fungi
Parasites
Concept of Infectious Disease
Role of Diagnostic Microbiology Laboratory

2. Human Microbiome in Health and Disease
Human Microbiome Project
Core Microbiome
Evolution of the Microbiome and Normal Flora
Role of the Microbiome in Health and Disease
Diagnostics and Therapeutics
Perspective

3. Infection Control and Preventio
Infection Prevention and Control in the Hospital
Surveillance
Investigating Hospital Acquired Infections
Infection Prevention Program
Personal Protective Equipment
Antimicrobial/Diagnostic Stewardship
Disinfection, Sterilization
Infection Prevention and Control in the Community
Emerging Infectious Diseases
Personal Hygiene
Vaccines
Therapeutics

Section 2. General Principles of Laboratory Diagnosis
4. Traditional Diagnostic Methods
Microscopy
Culture
Identification and Antimicrobial Susceptibility Testing
Serology
Antibody detection
Antigen detection

5. Molecular and Proteomic Method
Microbial Detection
Microbial Identification
Epidemiologic Typing

Section 3. Basic Concepts in the Immune Response
6. Elements of Host Protective Responses
Overview of the immune system as a system
Soluble Activators and Stimulators of Innate and Immune Functions
Cells of the Immune Response

8. Innate Host Responses
Barriers to Infection
Soluble Components of Innate Responses
Cellular Components of Innate Responses
Activation of Innate Cellular Responses
Normal Flora–Associated Responses
Inflammation
Bridge to Antigen-Specific Immune Responses

9. Antigen-Specific Immune Responses
Immunogens, Antigens, and Epitopes
T Cells
Cell-Surface Receptors of T Cells
Development of T Cells
Initiation of T-Cell Responses
Activation of CD4 T Cells and Their Response to Antigen
CD8 T Cells
INNATE T Cells
B Cells and Humoral Immunity
B cells
Immunoglobulin Types and Structures
Immunogenetics
Antibody Response

10. Immune Responses to Infectious Agents
Antibacterial Responses
Antiviral Responses
Specific Immune Responses to Fungi
Specific Immune Responses to Parasites
Other Immune Responses
Immunopathogenesis
Autoimmune Responses
Immunodeficiency11. Antimicrobial Vaccines
Types of Immunizations
Immunization Programs

Section 4. Bacteriology
12. Bacterial Classification, Structure, and Replication
Differences between Eukaryotes and Prokaryotes
Bacterial Classification
Bacterial Structure
Bacterial metabolism
Bacterial Genetics

13. Bacterial Metabolism and Genetics
Bacterial Metabolism
Human Bacterial Metabolism
Bacterial Genes and Expression
Bacterial Genetics

14. Pathogenesis of Bacterial Diseases
Entry into the Human Body
Colonization, Adhesion, and Invasion
Pathogenic Actions of Bacteria
Immunopathogenesis
Mechanisms for Escaping Host Defenses
Summary

15. Role of Bacteria in Disease

16. Laboratory Diagnosis of Bacterial Diseases

17. Antibacterial Agents
Inhibition of Cell Wall Synthesis
Inhibition of Protein Synthesis
Inhibition of Nucleic Acid Synthesis
Other Antibiotics

18. Staphylococcus and Related Gram-Positive Cocci
Physiology and Structure
Pathogenesis and Immunity
Epidemiology
Clinical Diseases
Staphylococcus aureus
Staphylococcus, other species
Laboratory Diagnosis
Treatment, Prevention, and Control

19. Streptococcus and Enterococcus
General Properties
Streptococcus pyogenes
Streptococcus agalactiae
Other ß-Hemolytic Streptococci
Viridans Streptococci
Streptococcus pneumoniae
Enterococcus

20. Bacillus
Bacillus anthracis
Bacillus cereus

21. Listeria and Related Gram-Positive Bacteria
Listeria monocytogenes
Erysipelothrix rhusiopathiae
Corynebacterium diphtheriae

22. Mycobacterium and Related Acid-Fast Bacteria
Physiology and Structure of Mycobacteria
Mycobacterium Tuberculosis
Other Slow-Growing Mycobacteria
Rapidly Growing Mycobacteria
Nocardia
Other Weakly Acid-Fast Bacteria

23. Neisseria and Related Genera
Neisseria gonorrhoeae and Neisseria meningitidis
Other Neisseria Species

24. Haemophilus and Related Bacteria
Haemophilus

25. Enterobacteriales
General Properties
Escherichia coli
Salmonella
Shigella
Yersinia
Other Enterobacteriales
Other General Properties

26. Vibrio and Related Bacteria
Vibrio
Aeromonas

27. Pseudomonas and Related Bacteria
Pseudomonas
Burkholderia
Stenotrophomonas maltophilia
Acinetobacter
Moraxella

28. Campylobacter and Helicobacter
Campylobacter
Helicobacter

29. Miscellaneous Gram-Negative Rods
Bartonella
Bordetella
Other Bordetella Species
Brucella
Cardiobacterium
Francisella
Legionella
Streptobacillus

30. Clostridium
Clostridium difficile
Clostridium perfringens
Clostridium tetani
Clostridium botulinum
Other Clostridial Species

31. Non–Spore-Forming Anaerobic Bacteria
Anaerobic Gram-Positive Cocci
Anaerobic Gram-Positive Rods
Anaerobic Gram-Negative Cocci
Anaerobic Gram-Negative Rods

32. Treponema, Borrelia, and Leptospira
Treponema
Borrelia
Leptospira

33. Mycoplasma
Physiology and Structure
Pathogenesis and Immunity
Epidemiology
Clinical Diseases
Laboratory Diagnosis
Treatment, Prevention, and Control

34. Rickettsia, Ehrlichia, and Related Bacteria
Rickettsiaceae
Anaplasmataceae
Coxiellaceae

35. Chlamydia
Physiology and Structure
Chlamydia trachomatis
Chlamydia pneumoniae
Chlamydia psittaci

Section 5. Virology
36. Viral Classification, Structure, and Replication
Classification
Virion Structure
Viral Replication
Viral Genetics
Viral Vectors for Therapy

37. Pathogenesis of Viral Diseases
Basic Steps in Viral Disease
Infection of the Target Tissue
Viral Pathogenesis
Viral Disease
Epidemiology
Control of Viral Spread38. Role of Viruses in Disease
Viral Diseases
Chronic and Potentially Oncogenic Infections
Infections in Immunocompromised Patients
Congenital, Neonatal, and Perinatal Infections

39. Laboratory Diagnosis of Viral Diseases
Specimen Collection
Cytology
Electron Microscopy
Viral Isolation and Growth
Detection of Viral Genetic Material
Detection of Viral Proteins
Viral Serology

40. Antiviral Agents and Infection Control
Targets for Antiviral Drugs
Nucleoside Analogs
Nonnucleoside Polymerase Inhibitors
Protease Inhibitors
Antiinfluenza Drugs
Immunomodulators
Infection Control

41. Papillomaviruses and Polyomaviruses
Human Papillomaviruses
Polyomaviridae

42. Adenoviruses
Structure and Replication
Pathogenesis and Immunity
Epidemiology
Clinical Syndromes
Laboratory Diagnosis
Treatment, Prevention, and Control
Therapeutic Adenoviruses

43. Human Herpesviruses
Structure of Herpesviruses
Herpesvirus Replication
Herpes Simplex Virus
Varicella-Zoster Virus
Epstein-Barr Virus
Cytomegalovirus
Human Herpesviruses 6 and 7
Other Human Herpesviruses

44. Poxviruses
Structure and Replication
Pathogenesis and Immunity
Epidemiology
Clinical Syndromes

45. Parvoviruses
Structure and Replication
Pathogenesis and Immunity
Epidemiology
Clinical Syndromes
Laboratory Diagnosis
Treatment, Prevention, and Control

46. Picornaviruses
Structure
Replication
Enteroviruses
Rhinoviruses

47. Coronaviruses and Noroviruses
Coronaviruses
Noroviruses

48. Paramyxoviruses
Structure and Replication
Measles Virus
Parainfluenza Viruses
Mumps Virus
Respiratory Syncytial Virus
Human Metapneumovirus
Nipah and Hendra Viruses

49. Orthomyxoviruses
Structure and Replication
Pathogenesis and Immunity
Epidemiology
Clinical Syndromes
Laboratory Diagnosis
Treatment, Prevention, and Control

50. Rhabdoviruses, Filoviruses, and Bornaviruses
Rhabdoviruses
Filoviruses
Borna Disease Virus

51. Reoviruses
Structure
Replication
Rotaviruses
Orthoreoviruses (Mammalian Reoviruses)
Coltiviruses and Orbiviruses

52. Togaviruses and Flaviviruses
Alphaviruses and Flaviviruses
Rubella Virus

53. Bunyaviridae and Arenaviridae
Bunyaviridae
Arenaviruses

54. Retroviruses
Classification
Structure
Replication
Human Immunodeficiency Virus
Human T-Cell Lymphotropic Virus and Other Oncogenic Retroviruses
Endogenous Retroviruses

55. Hepatitis Viruses
Hepatitis A Virus
Hepatitis B Virus
Hepatitis C and G Viruses
Hepatitis G Virus
Hepatitis D Virus
Hepatitis E Virus

56. Prion Diseases
Structure and Physiology
Pathogenesis
Epidemiology
Clinical Syndromes
Laboratory Diagnosis
Treatment, Prevention, and Control

Section 6. Mycology
57. Fungal Classification, Structure, and Replication
The Importance of Fungi
Fungal Taxonomy, Structure, and Replication
Ascomycota (Ascomycetes)
Basidiomycota (Basidiomycetes)
Glomerulomycota (Mucormycetes, formerly Zygomycetes)
Microspora (Microsporidia)
Classification of Human Mycoses
Summary

58. Pathogenesis of Fungal Disease
Primary Fungal Pathogens
Opportunistic Pathogens

59. Role of Fungi in Disease


60. Laboratory Diagnosis of Fungal Disease
Clinical Recognition of Fungal Infections
Conventional Laboratory Diagnosis
Immunologic, Molecular, and Biochemical Markers for Direct Detection of Invasive Fungal Infections

61. Antifungal Agents
Systemically Active Antifungal Agents
Topical Antifungal Agents
Investigational Antifungal Agents
Combinations of Antifungal Agents in the Treatment of Mycoses
Mechanisms of Resistance to Antifungal Agents

62. Superficial and Cutaneous Mycoses
Superficial Mycoses
Cutaneous Mycoses

63. Subcutaneous Mycoses
Lymphocutaneous Sporotrichosis
Chromoblastomycosis
Eumycotic Mycetoma
Subcutaneous Entomophthoromycosis
Subcutaneous Phaeohyphomycosis

64. Systemic Mycoses Caused by Dimorphic Fungi
Blastomycosis
Coccidioidomycosis
Emergomycosis and Adiaspiromycosis
Histoplasmosis
Paracoccidioidomycosis
Talaromycosis (Penicilliosis) marneffei

65. Opportunistic Mycoses
Candidiasis
Opportunistic Mycoses Caused by Cryptococcus Neoformans and Other Noncandidal Yeastlike Fungi
Microsporidia
Aspergillosis
Mucormycosis
Mycoses Caused by Other Hyaline Molds
Phaeohyphomycosis
Pneumocystosis

66. Fungal and Fungal-Like Infections of Unusual or Uncertain Etiology
Adiaspiromycosis
Chlorellosis
Lacaziosis (Lobomycosis)
Protothecosis
Pythiosis Insidiosi
Lagenidiosis
Rhinosporidiosis

Section 7. Parasitology
67. Parasitic Classification, Structure, and Replication
Importance of Parasites
Classification and Structure
Physiology and Replication
Summary

68. Pathogenesis of Parasitic Diseases
Exposure and Entry
Adherence and Replication
Cell and Tissue Damage
Disruption, Evasion, and Inactivation of Host Defenses

69. Role of Parasites in Disease

70. Laboratory Diagnosis of Parasitic Disease
Parasite Life Cycle as an Aid in Diagnosis
General Diagnostic Considerations
Parasitic Infections of the Intestinal and Urogenital Tracts
Parasitic Infections of Blood and Tissue
Alternatives to Microscopy

71. Antiparasitic Agents
Targets for Antiparasite Drug Action
Drug Resistance
Antiparasitic Agents

72. Intestinal and Urogenital Protozoa
Amebae (Amoebozoa)
Ciliates (Metamonada [Formerly Flagellates] and Ciliophora)
Sporozoa (Apicomplexa)

73. Blood and Tissue Protozoa
Plasmodium Species
Babesia Species
Toxoplasma gondii
Sarcocystis lindemanni
Free-Living Amebae
Leishmania
Trypanosomes

74. Nematodes
Enterobius vermicularis
Ascaris lumbricoides
Toxocara and Baylisascaris
Trichuris trichiura
Hookworms
Strongyloides stercoralis
Trichinella spiralis
Wuchereria bancrofti and Brugia malayi
Loa loa
Mansonella Species
Onchocerca volvulus
Dirofilaria immitis
Dracunculus medinensis

75. Trematodes
Fasciolopsis buski
Fasciola hepatica
Clonorchis sinensis
Paragonimus westermani
Schistosomes

76. Cestodes
Taenia solium
Cysticercosis
Taenia saginata
Diphyllobothrium latum
Sparganosis
Echinococcus granulosus
Echinococcus multilocularis
Hymenolepis nana
Hymenolepis diminuta
Dipylidium caninum

77. Arthropods
Myriapoda
Crustacea
Pentastomida
Chelicerata (Arachnida)
Hexapoda (Insecta)

Section 8. Infectious Diseases by Organ System
78. Sepsis and Cardiovascular Infections
Vignette
Specific specimen sites and the collection/transport of the specimens summary table
most likely pathogens summary table

79. Ear, Nose, and Throat Infections
Vignette
Specific specimen sites and the collection/transport of the specimens summary table
most likely pathogens summary table

80. Lower Respiratory Tract Infections
Vignette
Specific specimen sites and the collection/transport of the specimens summary table
most likely pathogens summary table

81. Ocular and Central Nervous System Infections
Vignette
Specific specimen sites and the collection/transport of the specimens summary table
most likely pathogens summary table

82. Genitourinary Tract Infections
Urinary tract infections
Vignette
Specific specimen sites and the collection/transport of the specimens summary table
most likely pathogens summary table
Sexually transmitted genital infections
Vignette
Specific specimen sites and the collection/transport of the specimens summary table
most likely pathogens summary table

83. Gastrointestinal Tract Infections
Vignette
Specific specimen sites and the collection/transport of the specimens summary table
most likely pathogens summary table

84. Intraabdominal Infections
Vignette
Specific specimen sites and the collection/transport of the specimens summary table
most likely pathogens summary table

85. Musculoskeletal, Skin, and Soft Tissue Infections
Vignette
Specific specimen sites and the collection/transport of the specimens summary table
most likely pathogens summary table

APPENDIX
Classic References to Know (ASM manual, CDC, Trop Dis, etc)