Fungal DNA Detection by PCR

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General Information

Lab Name
Fungal DNA Detection by PCR
Lab Code
Epic Ordering
Fungal DNA detection by PCR

In many specimens, fungal elements can be seen by microscopy of tissue sections but are very difficult to grow due to their fastidious nature, or are not viable as a result of antifungal therapy.

Some specimens may never reveal the presence of a fungal pathogen because of low abundance and/or lack of viability. Often, fungal elements are seen on paraffin embedded tissue when a fresh tissue specimen is no longer available.

The use of PCR technology to detect fungal DNA within the total DNA extracted directly from clinical specimens facilitates the identification of these pathogens. Using both fungal 28S and Internal Transcribed Spacer sequence (ITS) DNA as targets we have set up PCR assays to detect fungal pathogens. Sequences of amplified DNA are analyzed to identify the fungal pathogen present in the specimen.

REFLEXIVE TESTING: When suspected pathogen microorganisms are detected, identification procedures are performed, as appropriate for the organism and specimen.

Coccidioides DNA detection by PCR [COCDNA]

Cryptococcus DNA detection by PCR [CRYDNA]

Mucorales DNA detection by PCR [MUCDNA]

Histoplasma DNA detection by PCR [HISDNA]

Pneumocystis DNA detection by PCR [PNEDNA]

Incidental Finding Reflexes:

Acanthamoeba and Balamuthia species PCR [AMBPCR]

Leishmania species DNA detection by PCR [LSHDNA]

Toxoplasma DNA detection by PCR [TOXDNA]

Multiple Template Reflexes, if requested by ordering physician:

Fungal DNA Detection by ITS Next Gen Seq [NGSITS] (Fungal detection by ITS NGS)

For more information on this test, to download a requisition form, and for a list of acceptable and unacceptable specimens, please refer to: Molecular Diagnosis Microbiology Section Website

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DNA extraction, nucleic acid purification, polymerase chain reaction (PCR), sequencing

Reference Range
See individual components

Ordering & Collection

Specimen Type
Tissue (Fresh frozen or paraffin-embedded), Fluid (see Acceptable Specimens for details)

Acceptable specimens are listed below. Please see this page for complete specimen collection and handling instructions.

Specimens should be collected into a DNA free container labeled with at least two identifiers.

Acceptable Specimens

  • Fresh frozen tissue
  • Fresh frozen fluid: any body fluid is acceptable if it is not listed under Unacceptable Specimens. See common examples below.
  • Formalin Fixed Paraffin-embedded tissues (FFPE, PET): blocks, scrolls, and unstained slides are acceptable
  • eSwabs* and UTM (universal transport media)
  • Sodium polyanethol sulfonate (SPS, Wampole Isolator Tubes) acceptable with disclaimer

*Some lots of eSwabs have been found to contain Saccharomyces cerevisiae DNA, resulting in false postive detection. The detection of S. cerevisiae from eSwab specimens can interfere with our ability to rule out other fungal DNA. Clinical corrrelation and/or retesting with a different collection method will be advised.

Common acceptable body fluid examples: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.

Unacceptable Specimens

  • Sputum, blood, serum, plasma, stool
  • No citrated or heparinized solutions
  • Tissues floating in formalin
  • Swab/fluid collected in tube containing agar
Handling Instructions

Fresh frozen tissue/fluid specimens should be submitted and maintained on dry ice.

Formalin Fixed Paraffin-embedded tissues (FFPE, PET) can be sent ambient or with ice packs during warmer summer months to prevent melting.

Optimal Quantity:

  • Fresh Tissue: 0.3-1.0 cm^3
  • Fluid: 0.2-1 mL
  • Formalin Fixed Paraffin-embedded Tissue (FFPE/PET): blocks are preferred and will be sent back to client upon completion of testing
  • Scrolls/unstained slides: cross-sectional area >1cm^2 send 10 sections of 10µm thickness, if <1cm^2 send 20 sections if available

Please note: We do not need a separate specimen aliquot for each test ordered. Only a single specimen aliquot or block of optimal quantity is necessary for performing multiple tests. If multiple aliquots or blocks of optimal quantity are sent, up to 2 will be pooled.

requested: See Optimal Quantity above
minimum: Specimens below optimal quantity are acceptable for testing, however, diagnostic yield is generally proportional to specimen size.



UWMC/HMC – store and send specimen refrigerated and freeze specimens at -20°C upon arrival in UW-ML Microbiology. If specimen storage and transport will exceed 8 hours, freeze at -20°C.

Freeze specimens at -20°C upon arrival

Outside Laboratories: Freeze specimens in sterile containers at -20°C. Transport all specimens on dry ice.


LIS Dept Code
Micro Molecular Diag (MMD)
Performing Location(s)
UW-MT Microbiology, Molecular Diagnostics

Clinical Lab, Room # NW177,
University of Washington Medical Center,
1959 NE Pacific street, Seattle, WA 98195

Fresh frozen tissues/fluids result in 2-3 business days after receipt of specimen. Formalin Fixed Paraffin-embedded tissues result in 3-4 business days after receipt of specimen.
Available STAT?

Billing & Coding

CPT codes
Interfaced Order Code