General Mycology

Fungal Characteristics

Eukaryotic, true nucleus + organelles. Cell wall: chitin, β-glucans (not peptidoglycan). Membrane: ergosterol (not cholesterol) — antifungal drug target. No chlorophyll. Reproduce by asexual/sexual spores.

Morphological Forms

Yeast: round/oval, buds separate from parent. E.g. Cryptococcus neoformans.

Yeast-like: bud stays attached, elongates → pseudohyphae (constrictions at septa distinguish from true hyphae). E.g. Candida.

Molds: hyphae (2-10 µm), septate or non-septate/coenocytic. Form mycelium — aerial (spores) + vegetative (nutrient absorption). E.g. Dermatophytes, Aspergillus, Penicillium, Rhizopus, Mucor.

Dimorphic fungi: mold at 25°C (environment), yeast at 37°C (body). Histoplasma, Blastomyces, Coccidioides, Paracoccidioides, Penicillium marneffei, Sporothrix schenckii.

Taxonomic Classification (by sexual spore)

Zygomycota — zygospores, aseptate hyphae — Rhizopus, Mucor Ascomycota — ascospores, septate hyphae — Aspergillus Basidiomycota — basidiospores — Cryptococcus Deuteromycota (Fungi imperfecti) — no known sexual stage — most medically important fungi

Laboratory Diagnosis — Microscopy

KOH prep: 10% (skin/scraping), 20-40% (nail), overnight 10% (biopsy) — digests keratin, hyphae visible. Pitfall: confuse with collagen/cotton fiber/hair.

Gram stain — yeasts (Cryptococcus, Candida) = Gram+ budding.

India ink/nigrosin — negative stain, Cryptococcus capsule = clear halo.

Calcofluor white — binds cellulose/chitin, fluoresces UV, more sensitive than KOH.

PAS stain — recommended for fungi, magenta-pink, stains only LIVE fungi.

GMS (Gomori methenamine silver) — alternative to PAS, black fungi/pale green background, stains LIVE + DEAD fungi.

Mucicarmine — Cryptococcus + Rhinosporidium cell wall.

LPCB (lactophenol cotton blue) — phenol (disinfectant) + lactic acid (preserves morphology) + glycerol (prevents drying) + cotton blue (stains) — used for CULTURE mounts, not direct specimens.

Culture

SDA (Sabouraud dextrose agar) — 4% dextrose, pH 5.6 — standard medium.

Emmons’ modification — neutral pH, lower dextrose — broader fungal support.

Corn meal/rice starch agar — nutrient-deficient, stimulates chlamydospores (Candida albicans ID).

BHI agar/blood agar — fastidious fungi (Histoplasma, Cryptococcus).

Niger seed/bird seed agar — selective for Cryptococcus (turns brown, phenol-oxidase).

CHROMagar Candida — colour-differentiates Candida species.

Conditions: 25-30°C most fungi; dimorphic fungi tested at BOTH 25°C and 37°C. Incubation 2-3 weeks. Antibacterial agents added (cycloheximide, chloramphenicol, gentamicin).

Identification: Macroscopic — growth rate (rapid <5d = yeasts/opportunists; slow 1-4wk = dermatophytes/systemic/subcutaneous agents), pigmentation, texture, topography.

Microscopic — teased mount, slide culture (most accurate, in-situ), cellophane tape mount. Read: hyphae type (septate/aseptate, hyaline/pigmented), sporulation pattern.

Species-specific: Germ tube test/carbohydrate assimilation (Candida); Hair perforation test (dermatophytes); Urease test (Cryptococcus).

Immunological/Molecular

Antigen detection: Cryptococcal capsular Ag (CSF, latex agglutination); Aspergillus galactomannan (serum/urine); β-D-glucan assay (broad invasive fungal marker — EXCEPT zygomycetes, Blastomyces, Cryptococcus — negative in these even if truly infected).

Automation: MALDI-TOF, VITEK for yeast ID.

Molecular: PCR, real-time PCR, sequencing.

Antifungal Agents

Polyenes (Amphotericin B, Nystatin) — bind ergosterol, disrupt membrane. Ampho B = systemic; Nystatin = topical.

Azoles — inhibit ergosterol synthesis. Imidazoles (clotrimazole, ketoconazole) = topical/limited systemic. Triazoles (fluconazole, itraconazole, voriconazole, posaconazole) = systemic, broadening spectrum.

Echinocandins (caspofungin, micafungin) — inhibit β-glucan synthesis (no human equivalent — well tolerated).

Flucytosine — antimetabolite → fluorouracil, blocks DNA synthesis. Combined with Ampho B.

Griseofulvin — disrupts mitotic spindle. Dermatophytoses only.

Allylamines (terbinafine) — inhibit ergosterol synthesis, topical.

Overview of Fungal Diseases

Superficial mycoses:

• Tinea versicolor — Malassezia furfur — hypo/hyperpigmented scaly patches
• Tinea nigra — Hortaea werneckii — black palm/sole patches
• Piedra — black (Trichosporon beigelii) / white (Piedraia hortae) hair nodules
• Dermatophytosis — Trichophyton (skin+hair+nail), Microsporum (skin+hair), Epidermophyton (skin+nail)

Subcutaneous mycoses:

• Mycetoma — swelling+sinuses+granules triad. Eumycetoma (fungal, Madurella) vs Actinomycetoma (bacterial, Nocardia)
• Sporotrichosis — Sporothrix schenckii — “rose gardener’s disease,” nodulo-ulcerative
• Chromoblastomycosis — dematiaceous fungi, sclerotic body
• Phaeohyphomycosis — dematiaceous fungi, broader category
• Rhinosporidiosis — Rhinosporidium seeberi — friable nasal polyps

Systemic mycoses (dimorphic fungi): Histoplasma, Blastomyces, Coccidioides, Paracoccidioides — inhaled spores → pulmonary → disseminate.

Opportunistic mycoses:

• Candidiasis — Candida spp. — commonest human fungal disease. Risk: steroids, immunosuppression, transplant, HIV
• Cryptococcosis — C. neoformans — fatal meningitis in HIV. India ink CSF.
• Zygomycosis/Mucormycosis — Rhizopus, Mucor. Risk: diabetic ketoacidosis. Rhinocerebral form classic.
• Aspergillosis — A. fumigatus/flavus/niger. Risk: glucocorticoids, neutropenia.
• Penicilliosis — P. marneffei (only dimorphic Penicillium) — wart-like skin lesions, HIV.
• Pneumocystosis — P. jirovecii pneumonia, HIV.

Others:

• Mycotoxicosis — toxin-contaminated food (aflatoxin/A. flavus → hepatocellular carcinoma)
• Mycetism — poisonous mushroom ingestion
• Microsporidiosis — reclassified from protozoa to fungi; GI/musculoskeletal/ocular disease

What Sets Fungi Apart

Fungi are eukaryotic organisms — they possess a true nucleus and organelles such as mitochondria, unlike bacteria — but they differ from human cells in ways that matter directly for antifungal therapy. Their cell wall is rigid, built from chitin, β-glucans, and other polysaccharides rather than peptidoglycan; their cell membrane carries ergosterol in place of the cholesterol human membranes use, which is exactly the structural difference most antifungal drugs are designed to exploit. Fungi lack chlorophyll, may be unicellular or multicellular, and reproduce by asexual and/or sexual spore formation.

Morphological Forms

Fungi present in four basic growth forms, and correctly recognizing which one an isolate belongs to is usually the first step in identification:

• Yeasts grow as round-to-oval single cells that reproduce by budding — a daughter cell protrudes, enlarges, and eventually separates from the parent. Cryptococcus neoformans is the medically important pathogenic example.
• Yeast-like fungi also reproduce by budding, but the daughter cell stays attached and elongates, and repeated budding in this attached state produces chains of elongated cells called pseudohyphae — distinguished from true hyphae by visible constrictions at each septum. Candida is the classic example.
• Molds grow as long branching filaments (hyphae), 2–10 µm wide, which may be septate (with cross-walls) or non-septate/coenocytic (multinucleated, no cross-walls). Hyphae proliferate into a tangled mass called a mycelium, split functionally into aerial mycelium (projecting above the medium surface, typically bearing the spores used for identification) and vegetative mycelium (growing into the medium itself, absorbing nutrients). Dermatophytes, Aspergillus, Penicillium, Rhizopus, and Mucor are all true molds.
• Dimorphic fungi switch form with temperature — growing as a mold at ambient temperature (25°C, as they exist in soil and the environment) but converting to a yeast form at body temperature (37°C, as they exist once they have infected human tissue). This group includes essentially every classic systemic mycosis agent: Histoplasma capsulatum, Blastomyces dermatitidis, Coccidioides immitis, Paracoccidioides brasiliensis, Penicillium (Talaromyces) marneffei, and Sporothrix schenckii.

Taxonomic Classification

Beyond gross morphology, fungi are formally classified by the type of sexual spore they produce, splitting the medically relevant kingdom into four phyla: Zygomycota (lower fungi, aseptate hyphae, producing zygospores — Rhizopus, Mucor), Ascomycota (septate hyphae, producing ascospores — Aspergillus), Basidiomycota (producing basidiospores — Cryptococcus), and Deuteromycota, the historical catch-all “Fungi imperfecti” for the majority of medically important fungi whose sexual stage has never been identified or simply does not exist.

Laboratory Diagnosis

Direct Microscopy

Specimen choice follows the site of suspected infection — skin scraping, hair, or nail for superficial disease; sputum or blood for systemic disease; CSF specifically for suspected cryptococcal meningitis.

Potassium hydroxide (KOH) preparation is the simplest and most widely used direct method: 10% KOH (higher, 20–40%, for slow-dissolving material like nail; overnight incubation in 10% KOH for biopsy tissue) digests the host’s keratin, leaving fungal hyphae clearly visible against the cleared background. The main pitfall is mistaking collagen fibers, cotton fibers, or hair fragments in the specimen for fungal hyphae.

Beyond plain KOH, several stains sharpen or specialize the view: Gram stain shows yeasts and yeast-like fungi (Cryptococcus, Candida) as Gram-positive budding cells; India ink and nigrosin are negative stains that reveal the Cryptococcus neoformans capsule as a clear halo against a dark background; calcofluor white binds cellulose and chitin in the fungal wall and fluoresces under UV, giving better sensitivity than plain KOH. For histopathological sections, periodic acid-Schiff (PAS) is the standard recommended fungal stain (fungi appear magenta-pink against blue nuclei) and stains only live fungi; Gomori methenamine silver (GMS) is the usual alternative, staining both live and dead fungal elements black against a pale green background; mucicarmine specifically picks out the carminophilic walls of Cryptococcus and Rhinosporidium; and lactophenol cotton blue (LPCB) — a mixture combining a disinfectant (phenol), a morphology-preserving agent (lactic acid), an anti-drying agent (glycerol), and the stain itself (cotton blue) — is the standard mount used to examine fungal colonies grown in culture, not direct clinical specimens.

Culture

Sabouraud’s dextrose agar (SDA) — high dextrose (4%), low pH (5.6) — is the mycology workhorse, though a small number of fastidious fungi need richer media instead: Emmons’ neutral SDA modification (neutral pH, lower dextrose) supports a broader range; corn meal agar and rice starch agar, both nutritionally deficient, are used specifically to stimulate chlamydospore formation for Candida albicans identification; brain heart infusion agar and blood agar support genuinely fastidious fungi such as Histoplasma and Cryptococcus; niger seed (bird seed) agar selects specifically for Cryptococcus, which turns the medium brown from its phenol-oxidase activity; and CHROMagar Candida differentiates Candida species directly by colony colour.

Culture conditions matter: most fungi grow at 25–30°C, while dimorphic fungi specifically need testing at both 25°C (mold form) and 37°C (yeast form) to demonstrate their defining dimorphism; incubation runs 2–3 weeks, far longer than routine bacterial culture; and antibacterial agents (cycloheximide, chloramphenicol, gentamicin) are added to suppress bacterial overgrowth of the plate.

Identification from culture combines macroscopic reading of the colony — growth rate (rapid, under 5 days, typical of yeasts and opportunists; slow, 1–4 weeks, typical of dermatophytes and systemic/subcutaneous agents), pigmentation on the reverse side, texture (glabrous, velvety, cottony, granular), and surface topography — with microscopic examination of a teased mount, slide culture (the most accurate technique, growing the fungus directly on a coverslip for undisturbed in-situ morphology), or a cellophane-tape mount. What is actually being read microscopically is the nature of the hyphae (septate/aseptate, hyaline/pigmented, narrow/wide) and the pattern of sporulation. Species-specific supplementary tests exist too — the germ tube test and carbohydrate assimilation/fermentation profiles for Candida speciation, hair perforation testing for dermatophyte identification, and a urease test for urease-producing genera such as Cryptococcus.

Immunological and Molecular Methods

Antibody detection (ELISA, immunodiffusion, agglutination, complement fixation) and antigen detection both have a role where culture is slow or the fungus is difficult to isolate: cryptococcal capsular antigen from CSF by latex agglutination is a fast, sensitive route to diagnosing cryptococcal meningitis without waiting on culture; Aspergillus galactomannan antigen in serum or urine flags invasive aspergillosis; and the β-D-glucan assay detects a cell-wall component shared broadly across invasive fungal infections, though notably not by zygomycetes, Blastomyces, or Cryptococcus, since their walls lack or under-express this component — a gap worth remembering when the assay comes back negative in a genuinely suspicious case. Automated platforms (MALDI-TOF, VITEK) now handle much of yeast identification and increasingly some mold identification too, and PCR-based molecular methods (including real-time PCR and sequencing) offer the fastest, most specific route where they are available.

Antifungal Agents

Antifungal drug classes map cleanly onto the fungal cell’s structural differences from a human cell. Polyenes (amphotericin B, nystatin) bind ergosterol directly and disrupt the membrane — amphotericin B systemically for essentially any invasive mycosis, nystatin topically. Azoles (imidazoles like clotrimazole and ketoconazole for topical/limited systemic use; triazoles like fluconazole, itraconazole, voriconazole, and posaconazole for systemic disease, each with a progressively broader spectrum) inhibit ergosterol synthesis rather than binding it directly. Echinocandins (caspofungin, micafungin) take a different route entirely, inhibiting β-glucan synthesis in the fungal cell wall — a target with no human equivalent at all, which is part of why they are so well tolerated. Flucytosine, an antimetabolite converted in the body to fluorouracil, blocks fungal DNA synthesis and is used in combination with amphotericin B rather than alone. Griseofulvin, reserved for dermatophytoses, disrupts the fungal mitotic spindle. Allylamines (terbinafine) inhibit ergosterol synthesis topically.

Overview of Fungal Disease Categories

Fungal disease is organized clinically by depth and pattern of tissue involvement, and this classification determines both the likely causative agents and how urgently the infection needs treating.

Superficial mycoses stay confined to skin, hair, nail, and mucosa — tinea versicolor (Malassezia furfur, hypo/hyperpigmented scaly patches), tinea nigra (Hortaea werneckii, painless black palm/sole patches), piedra (nodules on the hair shaft — black from Trichosporon beigelii, white from Piedraia hortae), and dermatophytosis itself (ringworm), caused by Trichophyton (skin, hair, nail), Microsporum (skin, hair only), and Epidermophyton (skin, nail only) — a division of labour worth remembering precisely, since it is exactly the kind of detail exams test.

Subcutaneous mycoses result from traumatic inoculation of an environmental saprophyte into skin and subcutaneous tissue, staying largely confined there — mycetoma (a chronic triad of swelling, discharging sinuses, and granules in the discharge, split into eumycetoma from true fungi like Madurella mycetomatis and actinomycetoma from bacteria like Nocardia), sporotrichosis (Sporothrix schenckii, subcutaneous nodulo-ulcerative lesions, “rose gardener’s disease”), chromoblastomycosis (dematiaceous/pigmented fungi producing a characteristic sclerotic body), phaeohyphomycosis (a broader category of dematiaceous fungal infection), and rhinosporidiosis (Rhinosporidium seeberi, friable nasal polyps).

Systemic mycoses are caused specifically by the thermally dimorphic fungi — Histoplasma, Blastomyces, Coccidioides, Paracoccidioides — which are inhaled as spores, establish pulmonary infection, and can disseminate from there to multiple organs regardless of the host’s immune status, though disease is generally more severe when immunity is impaired.

Opportunistic mycoses are caused by organisms that are ordinarily commensal or environmental and cause disease specifically when host defenses are down — candidiasis (Candida species, the single most common human fungal disease, predisposed to by steroids, immunosuppression, transplantation, and HIV), cryptococcosis (Cryptococcus neoformans, notorious for fatal meningitis in HIV-infected patients, diagnosed by India ink capsule staining of CSF), zygomycosis/mucormycosis (Rhizopus, Mucor, and related genera, strongly associated with diabetic ketoacidosis and presenting classically as rhinocerebral disease with eye and facial pain progressing to orbital involvement), aspergillosis (A. fumigatus, A. flavus, A. niger, driven by glucocorticoid use and profound neutropenia), penicilliosis (Penicillium marneffei, the one dimorphic Penicillium species, causing wart-like skin lesions in HIV-infected patients), and pneumocystosis (Pneumocystis jirovecii pneumonia in HIV-infected patients).

Other mycoses round out the category: mycotoxicosis (illness from ingesting food contaminated by fungal toxins, such as aflatoxin from Aspergillus flavus, linked to hepatocellular carcinoma) and mycetism (poisoning from eating toxic mushrooms directly) are distinct mechanisms worth not conflating; and microsporidiosis, caused by organisms once classified as protozoa but now reclassified taxonomically under fungi, causes gastrointestinal, musculoskeletal, and ocular disease.

Hand-drawing notes only (no rendered diagrams)

Four morphological forms of fungi. Draw four small side-by-side sketches: a yeast (single oval cell with one budding daughter about to separate); a yeast-like fungus (a chain of elongated, budded cells still attached, with a visible constriction/waist at each junction — label this constriction explicitly, since it is the one feature distinguishing pseudohyphae from true hyphae); a mold (a branching filament with no constrictions, labelled hypha, gathered into a tangled mass labelled mycelium); and a dimorphic fungus, drawn as two small linked panels — mold form at 25°C on one side, yeast form at 37°C on the other, joined by a temperature arrow — since the defining feature of this group is the switch itself, not either form alone.

Dermatophyte site tropism. A simple three-column table-as-diagram is clearer than a drawing here (already given as a table in notes.md/lnr.md) — Trichophyton infects skin, hair, and nail; Microsporum infects skin and hair only; Epidermophyton infects skin and nail only. Not rendered as a figure since a table already states it precisely.

Not rendered

Classification by sexual spore (Zygomycota/Ascomycota/Basidiomycota/Deuteromycota) and the clinical categories of mycoses (superficial/subcutaneous/systemic/opportunistic) are already fully captured as tables and grouped lists in notes.md/lnr.md — these are classification schemes, not mechanisms or processes, so a rendered diagram would not clarify them beyond what the table already does.

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