General mycology

Last updated: April 13, 2022

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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.

Overview of mycological terminology [1]

  • Hyphae: tubular, branching filaments of fungal cells, with or without septae
  • Septa: hyphal cell wall divisions, typically porous
  • Pseudohyphae
    • A hypha-like filament formed by a chain of budding yeast cells that have not become detached from each other
    • Pseudohyphae can be identified by the presence of constrictions at the site of origin.
  • Mycelium: a haploid and multicellular network of hyphae forming a thread-like structure
  • Pseudomycelium: mycelium-like mass of pseudohyphae
  • Thallus: the vegetative body of a fungus
  • Sporangia: a spore-forming structure
  • Spores
    • Haploid, reproductive particles that can be formed on reproductive hyphae or mycelium
    • May result from asexual (e.g., sporangiospores) or sexual reproduction
  • Sporangiophore: modified hyphae bearing sporangia
  • Conidia
    • Asexual spore of. a fungus
    • May bud in clusters of chains
    • Produced by most pathogenic fungi
  • Conidiophore: simple or branched hyphae on which conidia are produced
  • Germ tube
    • An outgrowth produced by spores during germination
    • No constrictions at the site of origin
  • Anamorph: asexual reproductive state of a fungus
  • Teleomorph: sexual reproductive state of a fungus
  • Conidium: an asexual fungal spore formed from a vegetative yeast, hyphal cell, or a specialized conidiogenous cell
    • Microconidium: a small asexual fungal spore
    • Macroconidium: a large asexual fungal spore

Fungi structure and morphology [2]

Fungi vary widely in size and shape, from unicellular to multicellular forms. Microscopic fungi are either molds or yeasts or both.

  • General characteristics of fungi
    • Fungi are eukaryotes.
    • Most are obligate or facultative aerobes.
    • Can be unicellular, multicellular, or dimorphic
    • Divide asexually, sexually, or both
    • Fungi are chemotrophic organisms, i.e., they secrete enzymes to degrade organic substrates
  • Structure of fungi
    • Fungal cell wall: composed of chitin, glucans, and mannans
    • Fungal cell membrane: contains ergosterol (analogous to cholesterol in humans).
      • Cell membrane component unique to fungal species.
      • Key enzymes in its synthetic pathway include squalene epoxidase and 14–α–demethylase, which converts lanosterol to ergosterol.
  • Morphology of fungi

Fungi represent a kingdom separate from plants and animals. They extract energy (e.g., sugar and proteins) from living or dead organic matter.

To remember the temperatures at which the different forms of dimorphic fungi exist, think: Mold in the cold, yeast in the heat! Dimorphic fungi exist as molds at cooler temperatures (cold) and as yeasts at warmer temperatures (heat).

Diagnostics for fungal detection [1]

Fungi replication [1][3][4]


Fungi reproduce through sexually and/or asexually produced spores.

  • Asexual reproduction
    • Occurs through mitotic division
    • Produces unicellular spores that are genetically identical to the parent body
  • Sexual reproduction
    • Occurs through meiotic division
    • Produces zygospores, which result from the union of two compatible nuclei and are genetically different from the parent bodies
    • Introduces genetic diversity

Asexual reproduction of fungi

  • Mechanisms
    • Asexual spore production (most common mode of reproduction)
      • Spores may be released outside or within a special reproductive structure, where they grow independently.
      • A haploid cell is produced via mitosis and released from the parent body (e.g., hypha, sporogenous cell)
    • Fungal fragmentation: a portion of the mycelium splits from the body of the fungus, with the resulting fragment being capable of replication
    • Binary fission: a cell undergoes nuclear division and splits into two daughter cells capable of replicating
    • Budding
      • An outgrowth, bud, or appendage develops on the surface of the cell or the hypha, with its cytoplasm being continuous with that of the parent cell.
      • The nucleus of the parent cell divides and one daughter nucleus migrates into the bud.
      • This fragment eventually detaches from the parent cell after the nucleus divides via mitosis and is capable of replicating using the same process.
      • Yeasts (e.g., Candida spp.) mainly reproduce using this mechanism.
  • Types of asexual spores
    • Conidiospore: a single-cell, bicellular, or multicellular structure that arises on the tip or side of a hyphal structure called a “conidiophore” (e.g., Aspergillus)
    • Sporangiospore: produced in a sac-like structure called sporangia (e.g., Rhizopus)
    • Arthrospore: formed by the fragmentation of a disjunctor cell or splitting of a double septum (e.g., Trichosporidium, Coccididious immitis)
    • Chlamydospore: a thick-walled, single-cell spore in or on hyphae (e.g., Candida spp.)
    • Blastospore: a budding spore usually formed at the terminal end of a hypha (e.g., Candida albicans, Trichosporon spp., Paracoccidioides spp.)

Sexual reproduction of fungi

  • Stages: plasmogamy, karyogamy, and meiosis
  • Main methods of plasmogamy
    • Gametangium
      • An organ or cell in which gametes are produced
      • The fusion of the entire contents of two contacting gametangia takes place via a pore-like structure or by direct fusion.
    • Somatogamy: somatic hyphae take over the sexual function, come into contact, fuse, and exchange nuclei
    • Spermatization: fungi male fungal structures called spermatia become attached to the female receptive hyphae or gametangia
  • Types of sexual spores
    • Ascospores: produced in a sac-like structure called an “ascus” (e.g., Blastomyces, Histoplasma, Aspergillus)
    • Basidiospore: produced in a club-shaped structure called a “basidium” (e.g., Cryptococcus, Malassezia, Trichosporon)
    • Zygospore: formed when two sexually compatible hyphae or gametangia fuse (e.g., Rhizopus)
    • Oospores: a thick-walled spore, formed when a female gamete is fertilized by a male gamete nucleus. I.e., occurs solely in clinically nonrelevant fungi, e.g., Pythium, Phytophthora.

Sexual systems [5]

  • Overview
    • There are two main modes of reproduction: homothallism and heterothallism
    • Both modes share key reproductive features (e.g., ploidy changes, meiosis) but differ in features involving aspects of cell or hyphal fusion.
  • Homothallism
    • The possession of resources to reproduce sexually in a single fungus; i.e., the thallus contains both male and female sex organs, thus enabling self-fertilization
    • Examples: Aspergillus nidulans, P. jirovecii
  • Heterothallism
    • The division of sexes between fungi of a single (self-sterile) species; reproduction occurs between two separate mycelia
    • Example: Saccharomyces cerevisiae (baker's yeast)

Fungal metabolism [1][6]


  • Fungi have a variety of metabolic pathways enabling them to digest and synthesize compounds.
  • Fungi derive their energy from the breakdown of organic compounds.
  • Organic compound breakdown is achieved via enzyme secretion (e.g., hydrolytic, oxidative, peroxidative)

Substances synthesized by fungi

Overview of the most common opportunistic fungal infections
Pathogen Risk factors Clinical features Diagnostics Treatment
  • Cryptococcus neoformans
  • AIDS
  • Exposure to pigeon droppings/soil
  • Transmission via inhalation
Pneumocystis pneumonia


  • Imaging
    • Assess the extent of tissue damage and organ involvement
    • Head CT: sinusitis with orbital and intracranial involvement
  • Tissue biopsy (confirmatory): wide-angled branching of irregularly shaped, broad, nonseptate hyphae

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.

Dermatomycoses are mycotic infections of tissue with high keratin content (skin, nails, hair) caused mainly by dermatophytes, but may also result from opportunistic infection with other species of fungus (e.g., Malassezia).

Overview of the most common cutaneous fungal infections
Pathogen Risk factors Clinical features Diagnostics Treatment
Tinea versicolor (pityriasis versicolor)
  • Hot or humid weather conditions
  • Best initial: KOH showing short hyphae and spores that have a “spaghetti and meatballs” appearance

Overview of the most common systemic fungal infections
Pathogen Risk factors Clinical features Diagnostics Treatment
  • Histoplasma capsulatum
  • Endemic areas: Mississippi and the Ohio river valley
  • Exposure to bird or bat droppings in endemic areas through activities such as spelunking (cave exploration)
  • Immunosuppression (e.g., AIDS)
Coccidioidomycosis (valley fever)
  • Coccidioides immitis
  • Coccidioides posadasii
  • Travel to Southwestern United States, California
  • Soil/dust exposure in endemic areas (e.g., during windstorms, earthquakes, archeological explorations) [8]
  • Paracoccidioides species
    • Paracoccidioides brasiliensis
    • Paracoccidioides lutzii
  • Travel to South and Central America
  • > [10]
  • KOH/calcofluor staining on smears or silver/PAS-staining on tissue biopsy
    • Budding yeast with “captain's wheel” formation
    • Fungi are identified by comparing their size to that of an RBC (fungal size > RBC)
  • Cultures have low sensitivity.


  • Blastomyces dermatitidis
  • Travel to Southeastern, Central, Eastern, and the Great Lakes region of the United States
  • KOH or culture (confirmatory) of sputum, urine, or body fluids showing:
    • Yeast form (at body temperature or > 37°C): broad-based buds
    • Fungi are identified by comparing their size to that of an RBC (fungal size ≈ RBC)
    • Mold form (at room temperature): circular fungal cells with filamentous hyphae

History of the hidden Ohio and Mississippi river valleys:” Histoplasma is hidden within macrophages and Ohio and Mississippi river valleys are the endemic regions of histoplasma.

Paracoccidiomycosis steers the ship to South and Central America at the captain's wheel: ”Paracoccidiomycosis is endemic in South and Central America and its budding yeast has a captain's wheel appearance.

The yeast form of Blastomycosis forms broad-based buds.

Unlike most other dimorphic fungi, Blastomyces can cause disseminated disease even in immunocompetent hosts.

Sporotrichosis (Rose gardener disease)

“A rose gardener plants roses in a pot while smoking a cigar:” sporotrichosis is associated with traumatic gardening injuries, treatment includes potassium iodide, and Sporothrix appears as a cigar-shaped yeast in culture.

Overview of the most important dermatophytes
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

Overview of the most important yeasts
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

  1. Money NP. The Fungi. Elsevier ; 2016 : p. 67-97
  2. Reproductive processes of fungi. Updated: February 27, 2020. Accessed: November 5, 2021.
  3. Brooks G, Carroll KC, Butel J, Morse S, Mietzner TA. Jawetz Melnick & Adelbergs Medical Microbiology. McGraw Hill Professional ; 2012
  4. Ni M, Feretzaki M, Sun S, Wang X, Heitman J. Sex in Fungi. Annu Rev Genet. 2011; 45 (1): p.405-430. doi: 10.1146/annurev-genet-110410-132536 . | Open in Read by QxMD
  5. Walker GM, White NA. Introduction to Fungal Physiology. John Wiley & Sons, Inc. ; 2017 : p. 1-35
  6. Cole. Medical Microbiology. Medical Microbiology. 1996 .
  7. Zhang P, Lian L, Wang F. Magnetic resonance imaging features of gelatinous pseudocysts in cryptococcal meningoencephalitis. Acta Neurol Belg. 2018; 119 (2): p.265-267. doi: 10.1007/s13760-018-1033-6 . | Open in Read by QxMD
  8. Thompson G, Brown J, Benedict K, Park B. Coccidioidomycosis: epidemiology. Clinical Epidemiology. 2013 : p.185. doi: 10.2147/clep.s34434 . | Open in Read by QxMD
  9. Arora NP, Taneja V, ReyesSacin C, Bhanot R, Natesan SK. Coccidioidomycosis masquerading as malignancy.. BMJ case reports. 2012; 2012 . doi: 10.1136/bcr.12.2011.5357 . | Open in Read by QxMD
  10. Paracoccidioidomycosis. Updated: January 1, 2009. Accessed: April 22, 2020.
  11. Blastomycosis. Updated: January 1, 2009. Accessed: May 2, 2020.
  12. Kumar V, Abbas AK, Aster JC. Robbins & Cotran Pathologic Basis of Disease. Elsevier Saunders ; 2014

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