Clinical Microbiology

  1. Clinical Virology
    1. Viral Structure and Classification
      1. Viral Components
        1. Nucleic Acid Genome
          1. DNA Viruses
            1. RNA Viruses
              1. Single-Stranded vs Double-Stranded
              2. Protein Capsid
                1. Capsomeres
                  1. Symmetry Types
                  2. Viral Envelope
                    1. Lipid Bilayer
                      1. Envelope Proteins
                        1. Glycoproteins
                      2. Viral Classification
                        1. Baltimore Classification
                          1. ICTV Classification System
                            1. Families and Genera
                            2. Viral Size and Morphology
                              1. Electron Microscopy
                                1. Size Comparisons
                              2. Viral Replication
                                1. Replication Cycle Steps
                                  1. Attachment and Entry
                                    1. Receptor Binding
                                      1. Membrane Fusion
                                        1. Endocytosis
                                        2. Uncoating
                                          1. Replication and Transcription
                                            1. DNA Virus Replication
                                              1. RNA Virus Replication
                                                1. Reverse Transcription
                                                2. Translation
                                                  1. Assembly
                                                    1. Release
                                                      1. Lysis
                                                        1. Budding
                                                      2. Host Cell Interactions
                                                        1. Cytopathic Effects
                                                          1. Persistent Infections
                                                            1. Latent Infections
                                                              1. Transformation
                                                            2. Laboratory Diagnosis of Viral Infections
                                                              1. Specimen Collection and Handling
                                                                1. Specimen Types
                                                                  1. Respiratory Specimens
                                                                    1. Stool Specimens
                                                                      1. Urine Specimens
                                                                        1. Blood Specimens
                                                                          1. Cerebrospinal Fluid
                                                                            1. Tissue Specimens
                                                                            2. Collection Timing
                                                                              1. Transport Media
                                                                                1. Storage Requirements
                                                                                2. Viral Culture
                                                                                  1. Cell Culture Systems
                                                                                    1. Primary Cell Cultures
                                                                                      1. Continuous Cell Lines
                                                                                        1. Semi-Continuous Cell Lines
                                                                                        2. Inoculation Methods
                                                                                          1. Incubation Conditions
                                                                                            1. Detection of Viral Growth
                                                                                              1. Cytopathic Effects
                                                                                                1. Hemadsorption
                                                                                                  1. Interference
                                                                                                2. Antigen Detection
                                                                                                  1. Direct Fluorescent Antibody
                                                                                                    1. Enzyme Immunoassays
                                                                                                      1. Rapid Antigen Tests
                                                                                                        1. Immunochromatographic Tests
                                                                                                        2. Nucleic Acid Detection
                                                                                                          1. Polymerase Chain Reaction
                                                                                                            1. Conventional PCR
                                                                                                              1. Real-Time PCR
                                                                                                                1. Multiplex PCR
                                                                                                                2. Nucleic Acid Sequencing
                                                                                                                  1. In Situ Hybridization
                                                                                                                  2. Serological Methods
                                                                                                                    1. Antibody Detection
                                                                                                                      1. IgM vs IgG Significance
                                                                                                                        1. Acute vs Convalescent Sera
                                                                                                                        2. Neutralization Tests
                                                                                                                          1. Complement Fixation
                                                                                                                            1. Hemagglutination Inhibition
                                                                                                                              1. Enzyme Immunoassays
                                                                                                                              2. Electron Microscopy
                                                                                                                                1. Negative Staining
                                                                                                                                  1. Immune Electron Microscopy
                                                                                                                                2. DNA Viruses
                                                                                                                                  1. Herpesviruses
                                                                                                                                    1. General Characteristics
                                                                                                                                      1. Large DNA Genome
                                                                                                                                        1. Latency
                                                                                                                                          1. Reactivation
                                                                                                                                          2. Herpes Simplex Viruses
                                                                                                                                            1. HSV-1 and HSV-2
                                                                                                                                              1. Clinical Manifestations
                                                                                                                                                1. Laboratory Diagnosis
                                                                                                                                                2. Varicella-Zoster Virus
                                                                                                                                                  1. Primary Infection (Chickenpox)
                                                                                                                                                    1. Reactivation (Shingles)
                                                                                                                                                      1. Laboratory Diagnosis
                                                                                                                                                      2. Cytomegalovirus
                                                                                                                                                        1. Clinical Manifestations
                                                                                                                                                          1. Congenital Infections
                                                                                                                                                            1. Laboratory Diagnosis
                                                                                                                                                            2. Epstein-Barr Virus
                                                                                                                                                              1. Infectious Mononucleosis
                                                                                                                                                                1. Associated Malignancies
                                                                                                                                                                  1. Laboratory Diagnosis
                                                                                                                                                                  2. Human Herpesvirus 6 and 7
                                                                                                                                                                    1. Roseola
                                                                                                                                                                      1. Clinical Significance
                                                                                                                                                                      2. Human Herpesvirus 8
                                                                                                                                                                        1. Kaposi's Sarcoma
                                                                                                                                                                      3. Adenoviruses
                                                                                                                                                                        1. General Characteristics
                                                                                                                                                                          1. Clinical Manifestations
                                                                                                                                                                            1. Laboratory Diagnosis
                                                                                                                                                                            2. Papillomaviruses
                                                                                                                                                                              1. Human Papillomavirus
                                                                                                                                                                                1. High-Risk vs Low-Risk Types
                                                                                                                                                                                  1. Cervical Cancer
                                                                                                                                                                                    1. Laboratory Diagnosis
                                                                                                                                                                                  2. Polyomaviruses
                                                                                                                                                                                    1. BK Virus
                                                                                                                                                                                      1. JC Virus
                                                                                                                                                                                        1. Clinical Significance
                                                                                                                                                                                        2. Poxviruses
                                                                                                                                                                                          1. Smallpox Virus
                                                                                                                                                                                            1. Molluscum Contagiosum
                                                                                                                                                                                            2. Parvoviruses
                                                                                                                                                                                              1. Parvovirus B19
                                                                                                                                                                                                1. Clinical Manifestations
                                                                                                                                                                                                  1. Laboratory Diagnosis
                                                                                                                                                                                                2. Hepatitis B Virus
                                                                                                                                                                                                  1. Viral Structure
                                                                                                                                                                                                    1. Replication Cycle
                                                                                                                                                                                                      1. Clinical Manifestations
                                                                                                                                                                                                        1. Laboratory Diagnosis
                                                                                                                                                                                                          1. Surface Antigen
                                                                                                                                                                                                            1. Core Antigen
                                                                                                                                                                                                              1. e Antigen
                                                                                                                                                                                                                1. Antibody Responses
                                                                                                                                                                                                                2. Chronic Infection
                                                                                                                                                                                                              2. RNA Viruses
                                                                                                                                                                                                                1. Orthomyxoviruses
                                                                                                                                                                                                                  1. Influenza Viruses
                                                                                                                                                                                                                    1. Types A, B, and C
                                                                                                                                                                                                                      1. Antigenic Variation
                                                                                                                                                                                                                        1. Clinical Manifestations
                                                                                                                                                                                                                          1. Laboratory Diagnosis
                                                                                                                                                                                                                            1. Pandemic Potential
                                                                                                                                                                                                                          2. Paramyxoviruses
                                                                                                                                                                                                                            1. Respiratory Syncytial Virus
                                                                                                                                                                                                                              1. Clinical Manifestations
                                                                                                                                                                                                                                1. Laboratory Diagnosis
                                                                                                                                                                                                                                2. Parainfluenza Viruses
                                                                                                                                                                                                                                  1. Measles Virus
                                                                                                                                                                                                                                    1. Clinical Manifestations
                                                                                                                                                                                                                                      1. Laboratory Diagnosis
                                                                                                                                                                                                                                      2. Mumps Virus
                                                                                                                                                                                                                                        1. Clinical Manifestations
                                                                                                                                                                                                                                          1. Laboratory Diagnosis
                                                                                                                                                                                                                                        2. Coronaviruses
                                                                                                                                                                                                                                          1. General Characteristics
                                                                                                                                                                                                                                            1. Common Cold Coronaviruses
                                                                                                                                                                                                                                              1. SARS-CoV
                                                                                                                                                                                                                                                1. MERS-CoV
                                                                                                                                                                                                                                                  1. SARS-CoV-2
                                                                                                                                                                                                                                                    1. COVID-19
                                                                                                                                                                                                                                                      1. Laboratory Diagnosis
                                                                                                                                                                                                                                                        1. Variants of Concern
                                                                                                                                                                                                                                                      2. Picornaviruses
                                                                                                                                                                                                                                                        1. Enteroviruses
                                                                                                                                                                                                                                                          1. Polioviruses
                                                                                                                                                                                                                                                            1. Coxsackieviruses
                                                                                                                                                                                                                                                              1. Echoviruses
                                                                                                                                                                                                                                                                1. Enterovirus 71
                                                                                                                                                                                                                                                                2. Rhinoviruses
                                                                                                                                                                                                                                                                  1. Hepatitis A Virus
                                                                                                                                                                                                                                                                    1. Clinical Manifestations
                                                                                                                                                                                                                                                                      1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                    2. Caliciviruses
                                                                                                                                                                                                                                                                      1. Noroviruses
                                                                                                                                                                                                                                                                        1. Gastroenteritis
                                                                                                                                                                                                                                                                          1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                        2. Reoviruses
                                                                                                                                                                                                                                                                          1. Rotaviruses
                                                                                                                                                                                                                                                                            1. Gastroenteritis
                                                                                                                                                                                                                                                                              1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                            2. Togaviruses
                                                                                                                                                                                                                                                                              1. Rubella Virus
                                                                                                                                                                                                                                                                                1. Clinical Manifestations
                                                                                                                                                                                                                                                                                  1. Congenital Rubella Syndrome
                                                                                                                                                                                                                                                                                    1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                                  2. Flaviviruses
                                                                                                                                                                                                                                                                                    1. Hepatitis C Virus
                                                                                                                                                                                                                                                                                      1. Clinical Manifestations
                                                                                                                                                                                                                                                                                        1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                                          1. Genotypes
                                                                                                                                                                                                                                                                                          2. West Nile Virus
                                                                                                                                                                                                                                                                                            1. Dengue Virus
                                                                                                                                                                                                                                                                                              1. Zika Virus
                                                                                                                                                                                                                                                                                              2. Retroviruses
                                                                                                                                                                                                                                                                                                1. Human Immunodeficiency Virus
                                                                                                                                                                                                                                                                                                  1. HIV-1 and HIV-2
                                                                                                                                                                                                                                                                                                    1. Replication Cycle
                                                                                                                                                                                                                                                                                                      1. Clinical Manifestations
                                                                                                                                                                                                                                                                                                        1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                                                          1. Antibody Testing
                                                                                                                                                                                                                                                                                                            1. Antigen Testing
                                                                                                                                                                                                                                                                                                              1. Nucleic Acid Testing
                                                                                                                                                                                                                                                                                                              2. Drug Resistance Testing
                                                                                                                                                                                                                                                                                                                1. Viral Load Monitoring
                                                                                                                                                                                                                                                                                                                2. Human T-Lymphotropic Viruses
                                                                                                                                                                                                                                                                                                                  1. HTLV-1 and HTLV-2
                                                                                                                                                                                                                                                                                                                    1. Clinical Significance
                                                                                                                                                                                                                                                                                                                  2. Arenaviruses
                                                                                                                                                                                                                                                                                                                    1. Lymphocytic Choriomeningitis Virus
                                                                                                                                                                                                                                                                                                                      1. Hemorrhagic Fever Viruses
                                                                                                                                                                                                                                                                                                                      2. Bunyaviruses
                                                                                                                                                                                                                                                                                                                        1. Hantaviruses
                                                                                                                                                                                                                                                                                                                          1. Rift Valley Fever Virus
                                                                                                                                                                                                                                                                                                                          2. Filoviruses
                                                                                                                                                                                                                                                                                                                            1. Ebola Virus
                                                                                                                                                                                                                                                                                                                              1. Marburg Virus
                                                                                                                                                                                                                                                                                                                              2. Rhabdoviruses
                                                                                                                                                                                                                                                                                                                                1. Rabies Virus
                                                                                                                                                                                                                                                                                                                                  1. Clinical Manifestations
                                                                                                                                                                                                                                                                                                                                    1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                                                                                2. Hepatitis Viruses
                                                                                                                                                                                                                                                                                                                                  1. Hepatitis A Virus
                                                                                                                                                                                                                                                                                                                                    1. RNA Virus
                                                                                                                                                                                                                                                                                                                                      1. Transmission
                                                                                                                                                                                                                                                                                                                                        1. Clinical Course
                                                                                                                                                                                                                                                                                                                                          1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                                                                                          2. Hepatitis B Virus
                                                                                                                                                                                                                                                                                                                                            1. DNA Virus
                                                                                                                                                                                                                                                                                                                                              1. Transmission
                                                                                                                                                                                                                                                                                                                                                1. Clinical Course
                                                                                                                                                                                                                                                                                                                                                  1. Laboratory Markers
                                                                                                                                                                                                                                                                                                                                                    1. Chronic Infection
                                                                                                                                                                                                                                                                                                                                                    2. Hepatitis C Virus
                                                                                                                                                                                                                                                                                                                                                      1. RNA Virus
                                                                                                                                                                                                                                                                                                                                                        1. Transmission
                                                                                                                                                                                                                                                                                                                                                          1. Clinical Course
                                                                                                                                                                                                                                                                                                                                                            1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                                                                                                              1. Genotyping
                                                                                                                                                                                                                                                                                                                                                              2. Hepatitis D Virus
                                                                                                                                                                                                                                                                                                                                                                1. Defective RNA Virus
                                                                                                                                                                                                                                                                                                                                                                  1. Co-infection with HBV
                                                                                                                                                                                                                                                                                                                                                                    1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                                                                                                                    2. Hepatitis E Virus
                                                                                                                                                                                                                                                                                                                                                                      1. RNA Virus
                                                                                                                                                                                                                                                                                                                                                                        1. Transmission
                                                                                                                                                                                                                                                                                                                                                                          1. Clinical Course
                                                                                                                                                                                                                                                                                                                                                                            1. Laboratory Diagnosis

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                                                                                                                                                                                                                                                                                                                                                                        8. Clinical Parasitology