Clinical Microbiology

  1. Clinical Mycology
    1. Fungal Biology and Structure
      1. Cell Structure
        1. Cell Wall Composition
          1. Chitin
            1. Beta-Glucans
              1. Mannoproteins
              2. Cell Membrane
                1. Ergosterol
                  1. Membrane Function
                  2. Cytoplasmic Organelles
                  3. Morphological Forms
                    1. Yeasts
                      1. Budding Reproduction
                        1. Pseudohyphae Formation
                        2. Molds
                          1. Hyphal Structure
                            1. Conidial Formation
                            2. Dimorphic Fungi
                              1. Temperature-Dependent Morphology
                                1. Tissue vs Mold Forms
                              2. Reproduction
                                1. Asexual Reproduction
                                  1. Budding
                                    1. Conidiation
                                      1. Fragmentation
                                      2. Sexual Reproduction
                                        1. Teleomorphs
                                          1. Genetic Recombination
                                      3. Classification of Medically Important Fungi
                                        1. Taxonomic Hierarchy
                                          1. Phyla and Classes
                                            1. Orders and Families
                                              1. Genera and Species
                                              2. Morphological Classification
                                                1. Yeasts and Yeast-like Fungi
                                                  1. Filamentous Fungi
                                                    1. Dimorphic Fungi
                                                    2. Clinical Classification
                                                      1. Superficial Mycoses
                                                        1. Cutaneous Mycoses
                                                          1. Subcutaneous Mycoses
                                                            1. Systemic Mycoses
                                                              1. Opportunistic Mycoses
                                                            2. Laboratory Diagnosis of Fungal Infections
                                                              1. Specimen Collection and Processing
                                                                1. Specimen Types
                                                                  1. Skin and Nail Specimens
                                                                    1. Hair Specimens
                                                                      1. Respiratory Specimens
                                                                        1. Blood and Sterile Body Fluids
                                                                          1. Tissue Specimens
                                                                          2. Collection Methods
                                                                            1. Transport and Storage
                                                                            2. Direct Microscopic Examination
                                                                              1. Potassium Hydroxide Preparation
                                                                                1. Principle and Procedure
                                                                                  1. Interpretation
                                                                                  2. Calcofluor White Stain
                                                                                    1. Fluorescent Detection
                                                                                    2. Gram Stain
                                                                                      1. Yeast Detection
                                                                                        1. Limitations
                                                                                        2. Histopathological Stains
                                                                                          1. Gomori Methenamine Silver
                                                                                            1. Periodic Acid-Schiff
                                                                                          2. Fungal Culture
                                                                                            1. Culture Media
                                                                                              1. Sabouraud Dextrose Agar
                                                                                                1. Potato Dextrose Agar
                                                                                                  1. Inhibitory Mold Agar
                                                                                                    1. Dermatophyte Test Medium
                                                                                                    2. Incubation Conditions
                                                                                                      1. Temperature Requirements
                                                                                                        1. Atmospheric Conditions
                                                                                                          1. Duration of Incubation
                                                                                                          2. Colony Morphology
                                                                                                            1. Texture and Topography
                                                                                                              1. Pigmentation
                                                                                                                1. Growth Rate
                                                                                                              2. Identification Methods
                                                                                                                1. Microscopic Morphology
                                                                                                                  1. Conidial Structures
                                                                                                                    1. Hyphal Characteristics
                                                                                                                      1. Reproductive Structures
                                                                                                                      2. Physiological Tests
                                                                                                                        1. Carbohydrate Assimilation
                                                                                                                          1. Nitrate Reduction
                                                                                                                            1. Urease Production
                                                                                                                            2. Molecular Methods
                                                                                                                              1. DNA Sequencing
                                                                                                                                1. PCR-Based Identification
                                                                                                                              2. Antigen Detection
                                                                                                                                1. Cryptococcal Antigen
                                                                                                                                  1. Histoplasma Antigen
                                                                                                                                    1. Aspergillus Galactomannan
                                                                                                                                      1. Beta-D-Glucan
                                                                                                                                      2. Serological Testing
                                                                                                                                        1. Antibody Detection
                                                                                                                                          1. Complement Fixation
                                                                                                                                            1. Immunodiffusion
                                                                                                                                          2. Clinically Significant Yeasts
                                                                                                                                            1. Candida Species
                                                                                                                                              1. General Characteristics
                                                                                                                                                1. Budding Yeasts
                                                                                                                                                  1. Pseudohyphae Formation
                                                                                                                                                    1. Germ Tube Test
                                                                                                                                                    2. Candida albicans
                                                                                                                                                      1. Identification Methods
                                                                                                                                                        1. Virulence Factors
                                                                                                                                                          1. Clinical Manifestations
                                                                                                                                                          2. Non-albicans Candida Species
                                                                                                                                                            1. Candida glabrata
                                                                                                                                                              1. Candida parapsilosis
                                                                                                                                                                1. Candida tropicalis
                                                                                                                                                                  1. Candida krusei
                                                                                                                                                                    1. Candida auris
                                                                                                                                                                    2. Laboratory Identification
                                                                                                                                                                      1. Germ Tube Test
                                                                                                                                                                        1. Chlamydospore Formation
                                                                                                                                                                          1. Carbohydrate Assimilation
                                                                                                                                                                            1. Chromogenic Media
                                                                                                                                                                          2. Cryptococcus Species
                                                                                                                                                                            1. Cryptococcus neoformans
                                                                                                                                                                              1. Capsule Detection
                                                                                                                                                                                1. India Ink Preparation
                                                                                                                                                                                  1. Urease Test
                                                                                                                                                                                    1. Clinical Manifestations
                                                                                                                                                                                    2. Cryptococcus gattii
                                                                                                                                                                                      1. Geographic Distribution
                                                                                                                                                                                        1. Clinical Differences
                                                                                                                                                                                      2. Other Yeasts
                                                                                                                                                                                        1. Malassezia Species
                                                                                                                                                                                          1. Lipid Requirements
                                                                                                                                                                                            1. Clinical Significance
                                                                                                                                                                                            2. Trichosporon Species
                                                                                                                                                                                              1. Rhodotorula Species
                                                                                                                                                                                                1. Saccharomyces cerevisiae
                                                                                                                                                                                              2. Clinically Significant Molds
                                                                                                                                                                                                1. Aspergillus Species
                                                                                                                                                                                                  1. General Characteristics
                                                                                                                                                                                                    1. Conidial Head Structure
                                                                                                                                                                                                      1. Thermotolerance
                                                                                                                                                                                                      2. Aspergillus fumigatus
                                                                                                                                                                                                        1. Morphology
                                                                                                                                                                                                          1. Clinical Significance
                                                                                                                                                                                                          2. Aspergillus flavus
                                                                                                                                                                                                            1. Aspergillus niger
                                                                                                                                                                                                              1. Aspergillus terreus
                                                                                                                                                                                                                1. Clinical Manifestations
                                                                                                                                                                                                                  1. Allergic Reactions
                                                                                                                                                                                                                    1. Invasive Aspergillosis
                                                                                                                                                                                                                      1. Aspergilloma
                                                                                                                                                                                                                    2. Zygomycetes
                                                                                                                                                                                                                      1. General Characteristics
                                                                                                                                                                                                                        1. Broad Nonseptate Hyphae
                                                                                                                                                                                                                          1. Sporangia Formation
                                                                                                                                                                                                                          2. Rhizopus Species
                                                                                                                                                                                                                            1. Mucor Species
                                                                                                                                                                                                                              1. Rhizomucor Species
                                                                                                                                                                                                                                1. Clinical Manifestations
                                                                                                                                                                                                                                  1. Rhinocerebral Mucormycosis
                                                                                                                                                                                                                                    1. Pulmonary Mucormycosis
                                                                                                                                                                                                                                  2. Fusarium Species
                                                                                                                                                                                                                                    1. Morphology
                                                                                                                                                                                                                                      1. Clinical Significance
                                                                                                                                                                                                                                      2. Penicillium Species
                                                                                                                                                                                                                                        1. Morphology
                                                                                                                                                                                                                                          1. Clinical Relevance
                                                                                                                                                                                                                                          2. Dermatophytes
                                                                                                                                                                                                                                            1. General Characteristics
                                                                                                                                                                                                                                              1. Keratinophilic
                                                                                                                                                                                                                                                1. Macroconidia and Microconidia
                                                                                                                                                                                                                                                2. Trichophyton Species
                                                                                                                                                                                                                                                  1. Trichophyton rubrum
                                                                                                                                                                                                                                                    1. Trichophyton mentagrophytes
                                                                                                                                                                                                                                                      1. Trichophyton tonsurans
                                                                                                                                                                                                                                                      2. Microsporum Species
                                                                                                                                                                                                                                                        1. Microsporum canis
                                                                                                                                                                                                                                                          1. Microsporum persicolor
                                                                                                                                                                                                                                                          2. Epidermophyton floccosum
                                                                                                                                                                                                                                                            1. Clinical Manifestations
                                                                                                                                                                                                                                                              1. Tinea Corporis
                                                                                                                                                                                                                                                                1. Tinea Pedis
                                                                                                                                                                                                                                                                  1. Tinea Capitis
                                                                                                                                                                                                                                                                    1. Tinea Unguium
                                                                                                                                                                                                                                                                    2. Laboratory Diagnosis
                                                                                                                                                                                                                                                                      1. KOH Examination
                                                                                                                                                                                                                                                                        1. Culture Methods
                                                                                                                                                                                                                                                                          1. Wood's Lamp Examination
                                                                                                                                                                                                                                                                      2. Dimorphic Fungi
                                                                                                                                                                                                                                                                        1. General Characteristics
                                                                                                                                                                                                                                                                          1. Temperature-Dependent Dimorphism
                                                                                                                                                                                                                                                                            1. Geographic Distribution
                                                                                                                                                                                                                                                                              1. Safety Considerations
                                                                                                                                                                                                                                                                              2. Histoplasma capsulatum
                                                                                                                                                                                                                                                                                1. Morphology
                                                                                                                                                                                                                                                                                  1. Mold Form
                                                                                                                                                                                                                                                                                    1. Yeast Form
                                                                                                                                                                                                                                                                                    2. Geographic Distribution
                                                                                                                                                                                                                                                                                      1. Clinical Manifestations
                                                                                                                                                                                                                                                                                        1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                                        2. Blastomyces dermatitidis
                                                                                                                                                                                                                                                                                          1. Morphology
                                                                                                                                                                                                                                                                                            1. Geographic Distribution
                                                                                                                                                                                                                                                                                              1. Clinical Manifestations
                                                                                                                                                                                                                                                                                                1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                                                2. Coccidioides Species
                                                                                                                                                                                                                                                                                                  1. Coccidioides immitis
                                                                                                                                                                                                                                                                                                    1. Coccidioides posadasii
                                                                                                                                                                                                                                                                                                      1. Morphology
                                                                                                                                                                                                                                                                                                        1. Geographic Distribution
                                                                                                                                                                                                                                                                                                          1. Clinical Manifestations
                                                                                                                                                                                                                                                                                                            1. Laboratory Safety
                                                                                                                                                                                                                                                                                                            2. Sporothrix schenckii Complex
                                                                                                                                                                                                                                                                                                              1. Morphology
                                                                                                                                                                                                                                                                                                                1. Clinical Manifestations
                                                                                                                                                                                                                                                                                                                  1. Laboratory Diagnosis
                                                                                                                                                                                                                                                                                                                  2. Paracoccidioides Species
                                                                                                                                                                                                                                                                                                                    1. Geographic Distribution
                                                                                                                                                                                                                                                                                                                      1. Clinical Manifestations
                                                                                                                                                                                                                                                                                                                    2. Antifungal Susceptibility Testing
                                                                                                                                                                                                                                                                                                                      1. Indications for Testing
                                                                                                                                                                                                                                                                                                                        1. Treatment Failures
                                                                                                                                                                                                                                                                                                                          1. Resistant Species
                                                                                                                                                                                                                                                                                                                            1. Clinical Trials
                                                                                                                                                                                                                                                                                                                            2. Testing Methods
                                                                                                                                                                                                                                                                                                                              1. Broth Microdilution
                                                                                                                                                                                                                                                                                                                                1. CLSI Methods
                                                                                                                                                                                                                                                                                                                                  1. EUCAST Methods
                                                                                                                                                                                                                                                                                                                                  2. Disk Diffusion
                                                                                                                                                                                                                                                                                                                                    1. E-test
                                                                                                                                                                                                                                                                                                                                    2. Antifungal Agents
                                                                                                                                                                                                                                                                                                                                      1. Polyenes
                                                                                                                                                                                                                                                                                                                                        1. Amphotericin B
                                                                                                                                                                                                                                                                                                                                          1. Nystatin
                                                                                                                                                                                                                                                                                                                                          2. Azoles
                                                                                                                                                                                                                                                                                                                                            1. Fluconazole
                                                                                                                                                                                                                                                                                                                                              1. Itraconazole
                                                                                                                                                                                                                                                                                                                                                1. Voriconazole
                                                                                                                                                                                                                                                                                                                                                  1. Posaconazole
                                                                                                                                                                                                                                                                                                                                                  2. Echinocandins
                                                                                                                                                                                                                                                                                                                                                    1. Caspofungin
                                                                                                                                                                                                                                                                                                                                                      1. Micafungin
                                                                                                                                                                                                                                                                                                                                                        1. Anidulafungin
                                                                                                                                                                                                                                                                                                                                                        2. Other Agents
                                                                                                                                                                                                                                                                                                                                                          1. Flucytosine
                                                                                                                                                                                                                                                                                                                                                            1. Terbinafine
                                                                                                                                                                                                                                                                                                                                                          2. Interpretation of Results
                                                                                                                                                                                                                                                                                                                                                            1. Clinical Breakpoints
                                                                                                                                                                                                                                                                                                                                                              1. Epidemiological Cutoff Values
                                                                                                                                                                                                                                                                                                                                                              2. Quality Control
                                                                                                                                                                                                                                                                                                                                                                1. Reference Strains
                                                                                                                                                                                                                                                                                                                                                                  1. Control Limits

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                                                                                                                                                                                                                                                                                                                                                              7. Clinical Virology