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Microbiology

Major Pathogens

This section covers the major fungal pathogens encountered in clinical microbiology, focusing on their associated disease states, key laboratory procedures for identification, and important considerations

Yeasts

  • Key Genera: Candida, Cryptococcus, Malassezia
  • Disease States
    • Candida: Mucocutaneous candidiasis (thrush, vaginitis), invasive candidiasis (candidemia)
    • Cryptococcus: Meningitis, pneumonia
    • Malassezia: Pityriasis versicolor, folliculitis
  • Lab Procedures
    • Microscopy: Gram stain, KOH prep (visualization of budding yeast cells, pseudohyphae)
    • Culture: SDA, chromogenic agar (colony morphology, color)
    • Identification: Germ tube test (C. albicans), biochemical tests, MALDI-TOF MS
    • Antigen Detection: Cryptococcal antigen (CrAg) test
  • Considerations: Candida species identification is crucial for antifungal selection; Cryptococcus requires prompt diagnosis due to its severity; Malassezia requires lipid supplementation in culture media

Dimorphic Fungi

  • Key Genera: Histoplasma, Blastomyces, Coccidioides, Sporothrix
  • Disease States
    • Histoplasma: Histoplasmosis (pulmonary, disseminated)
    • Blastomyces: Blastomycosis (pulmonary, cutaneous, disseminated)
    • Coccidioides: Coccidioidomycosis (Valley Fever - pulmonary, disseminated)
    • Sporothrix: Sporotrichosis (cutaneous, lymphocutaneous)
  • Lab Procedures
    • Microscopy: GMS, PAS stain (visualization of tissue form - yeast or spherules)
    • Culture: SDA, BHI agar (mold and yeast/tissue form)
    • Identification: Microscopic morphology of mold form (conidia), exoantigen testing, MALDI-TOF MS
    • Serology: Antibody detection (EIA, complement fixation), antigen detection (Histoplasma, Blastomyces)
  • Considerations: Dimorphism is key for identification; geographic location is critical; Coccidioides cultures are highly infectious (BSL-3)

Dermatophytes

  • Key Genera: Trichophyton, Microsporum, Epidermophyton
  • Disease States: Tinea infections (pedis, cruris, corporis, capitis, unguium)
  • Lab Procedures
    • Microscopy: KOH prep (visualization of hyphae and arthroconidia)
    • Culture: SDA, DTM (colony morphology, color change on DTM)
    • Identification: Microscopic morphology (macroconidia, microconidia), Wood’s lamp examination (Microsporum)
  • Considerations: Proper specimen collection is essential; microscopic morphology is key for identification; DTM color change is presumptive

Mucorales (Zygomycetes)

  • Key Genera: Rhizopus, Mucor, Lichtheimia
  • Disease States: Mucormycosis (rhino-orbito-cerebral, pulmonary, cutaneous, disseminated)
  • Lab Procedures
    • Microscopy: GMS, PAS stain (visualization of broad, non-septate hyphae)
    • Culture: SDA, rapid growth (cottony colonies)
    • Identification: Microscopic morphology (sporangia, rhizoids), MALDI-TOF MS
  • Considerations: Rapid growth and invasive nature require prompt diagnosis; hyphal morphology is distinctive; Rhizopus has rhizoids

Hyaline Molds

  • Key Genera: Aspergillus, Fusarium, Penicillium, Scedosporium
  • Disease States
    • Aspergillus: Invasive aspergillosis, aspergilloma, allergic bronchopulmonary aspergillosis (ABPA)
    • Fusarium: Keratitis, onychomycosis, disseminated infections
    • Penicillium: Rare infections, penicilliosis (P. marneffei)
    • Scedosporium: Mycetoma, sinusitis, disseminated infections
  • Lab Procedures
    • Microscopy: GMS, PAS stain (visualization of septate hyphae)
    • Culture: SDA, rapid growth (various colony colors and textures)
    • Identification: Microscopic morphology (conidiophores, conidia), MALDI-TOF MS
    • Antigen Detection: Galactomannan (Aspergillus)
  • Considerations: Aspergillus has dichotomous branching; Fusarium has sickle-shaped macroconidia; Scedosporium is often drug-resistant

Dematiaceous Molds

  • Key Genera: Alternaria, Cladosporium, Fonsecaea
  • Disease States
    • Alternaria: Skin infections, sinusitis, allergic reactions
    • Cladosporium: Skin infections, sinusitis, allergic reactions, chromoblastomycosis
    • Fonsecaea: Chromoblastomycosis
  • Lab Procedures
    • Microscopy: KOH prep, GMS, PAS stain (visualization of dark-pigmented hyphae)
    • Culture: SDA, slow to moderate growth (dark colonies)
    • Identification: Microscopic morphology (conidiophores, conidia), MALDI-TOF MS
  • Considerations: Dark pigmentation is key; Fonsecaea causes chromoblastomycosis with sclerotic bodies

Pneumocystis jirovecii

  • Disease State: Pneumocystis pneumonia (PCP)
  • Lab Procedures
    • Specimen: Induced sputum or bronchoalveolar lavage (BAL)
    • Microscopy: GMS, Giemsa, DFA stain (visualization of cysts and trophozoites)
    • Molecular Detection: PCR
  • Considerations: Atypical fungus; GMS stains cysts, Giemsa stains trophozoites; PCR is highly sensitive

Microsporidium spp.

  • Disease States: Microsporidiosis (intestinal, keratoconjunctivitis, disseminated)
  • Lab Procedures
    • Specimen: Stool, urine, corneal scrapings
    • Microscopy: Modified trichrome stain, calcofluor white (visualization of small spores)
    • Molecular Detection: PCR
  • Considerations: Very small spores require careful examination; modified trichrome stains spores pink-red; PCR is useful for species identification