• Clinical science

General mycology


Mycoses are infections caused by fungi. They may be caused by dermatophytes (e.g., Trichophyton), yeast (e.g., Candida), or molds (e.g., Aspergillus). In immunocompetent individuals, mycoses usually result in local infection, which can be treated with local antifungals. Fungal infections may cause systemic infection in immunocompromised individuals (e.g., HIV-positive individuals, bone marrow transplant recipients), potentially leading to meningitis or severe sepsis.

Basics of mycology

Structure and characteristics of fungi

Fungi are not considered plants and are nonphotosynthetic. They extract energy (e.g., sugar and proteins) from living or dead organic matter.

Azoles target the synthesis of ergosterol, the principal sterol in fungal cell membranes. They inhibit the synthesis of ergosterol from lanosterol by interfering with 14α-demethylase (cytochrome P-450 enzyme).

Substances synthesized by fungi

Detection of fungal infections

  • Clinical features and microscopy → evaluation of fungal morphology
  • Additional characterization via:
    • Culture (e.g., Sabouraud agar)
    • Staining (e.g., silver stain)
    • Antigen detection (e.g., capsule components in serum)
    • Antibody detection plays a minor role.
  • Wood lamp examination: used to evaluate superficial fungal infections of the skin (e.g., tinea versicolor), which appear characteristically fluorescent under ultraviolet light
  • Latex agglutination test

Candida, Aspergillus, and Cryptococcus are opportunistic fungal pathogens with low inherent virulence. They commonly cause systemic mycoses in immunocompromised hosts but do not normally affect healthy hosts.

Fungi overview

Opportunistic fungal infections

Mycosis Etiology Clinical features Diagnosis Treatment
Pneumocystis pneumonia
  • Chest x-ray or CT: diffuse, bilateral ground-glass opacities
  • Bronchoalveolar lavage or lung biopsy (if sputum is negative): silver stain and immunofluorescence show disc-shaped yeasts


  • Pathogen: zygomycetes Mucor and Rhizopus
  • Risk factors: diabetic and immunocompromised patients
  • Patients with chronic sinus infection lasting for more than 3 months are predisposed to mucormycosis.
  • Head CT: sinusitis with orbital and intracranial involvement
  • Tissue biopsy (confirmatory): wide-angled branching of broad nonseptate hyphae

Cutaneous fungal infections

Mycosis Etiology Clinical features Diagnosis Treatment
Tinea versicolor (pityriasis versicolor)
  • Best initial: KOH showing short hyphae and spores that have a “spaghetti and meatballs” appearance

Systemic fungal infections

Mycosis Etiology Clinical features Diagnosis Treatment
  • Pathogen: Histoplasma capsulatum
  • Risk factors: AIDS and other immunocompromised patients, exposure to bird or bat droppings, especially in Mississippi and the Ohio river valley
  • AIDS-defining illness if disseminated or extrapulmonary
  • Chest x-ray: diffuse nodular densities, focal infiltrate or cavity, or lymphadenopathy
  • Best initial: positive urine and serum polysaccharide antigen test
  • Silver stain of biopsy or bronchoalveolar lavage showing macrophages filled with dimorphic fungus with septate hyphae
  • Culture (blood, sputum, bone marrow, lymph node, liver)
  • Liver biopsy: demonstrates disseminated disease with the presence of fungal organisms in the yeast-stage of development.
Coccidioidomycosis (valley fever)
  • Pathogen: Coccidioides immitis
  • Risk factors: travel to Southwestern United States, California
  • AIDS-defining illness if disseminated or extrapulmonary
  • Pathogen: Paracoccidioides species
    • Paracoccidioides brasiliensis
    • Paracoccidioides lutzii
  • Risk factors: travel to South and Central America
  • Infected patients often asymptomatic
  • Acute pneumonia
  • Painful nasal, pharyngeal, and laryngeal mucosal ulcerations
  • Lymphadenopathy (usually cervical)
  • Can disseminate → extrapulmonary manifestations (including verrucous skin lesions)
  • KOH/calcofluor staining on smears or silver/PAS-staining on tissue biopsy: budding yeast with “captain's wheel” formation
  • Cultures have a low sensitivity.


  • Pathogen: Blastomyces dermatitidis
  • Risk factors: travel to Southeastern and Central US
  • Pneumonia
  • Extrapulmonary: can disseminate to the skin (verrucous lesions and granulomatous nodules) and bones
  • KOH or culture (confirmatory) of sputum, urine, or body fluids showing:
    • yeast form (at body temperature or > 37°C): broad-based buds
    • Mold form (at room temperature): circular fungal cells with filamentous hyphae

Other fungal infections

Sporotrichosis (Rose gardener disease)



Important pathogens Characteristics Diseases Treatment

Trichophyton species

  • Occurs worldwide
  • Partial yellow-green fluorescence under Wood lamp

Epidermophyton species

  • Occurs worldwide
  • No typical fluorescence under Wood lamp

Microsporum species

  • Occurs worldwide
  • Partial blue-green fluorescence under Wood lamp


Important pathogens Characteristics Diseases Treatment

Candida species

Cryptococcus neoformans

  • Humans are infected via contaminated dust particles.
  • Possesses a capsule, which can be visualized using India Ink

Malassezia furfur


  • Pathogenicity
  • Morphology
    • Formation of monomorphic septate hyphae that branch at 45° and mycelium
    • Mold can infest food products and acquire a fuzzy appearance that is macroscopically visible.
Important pathogens Characteristics Diseases Treatment

Aspergillus fumigatus

  • Ubiquitous occurrence
  • Some species produce aflatoxins

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last updated 11/02/2020
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