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Mycobacterium avium complex DNA Detection

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General Information

Lab Name
Mycobacterium avium complex DNA Detection
Lab Code
MAVDNA
Epic Name
Mycobacterium avium complex DNA Detection
Description

Detection of Mycobacterium avium complex DNA

Background

Rapid and accurate identification of pathogenic Mycobacteria is important for correct therapeutic intervention against an infectious disease. Biochemical or phenotypic methods for identification of a Mycobacteria first requires growth of the microorganism in a suitable media. Furthermore, complete identification of organisms can be time consuming in cases where a biochemical reaction needs extended incubation or a phenotype takes a long time to appear on a plate requiring long time viability in the culture media. Identification of pathogenic Mycobacteria by PCR amplification of microbial DNA followed by DNA sequencing or probe can by-pass the requirement for growth of microorganism on a media for slow growing or fastidious organisms and the requirement for extended incubation for scoring biochemical or phenotypic results for many other organisms. Therefore, sequence and probe-based identification of microorganisms offer a faster turn-around time and more accurate result compared to conventional methods based on biochemical and phenotypic tests.

Principle

Fluorescence Resonance Energy Transfer (FRET) methodology, using hybridization probes targeted to species-specific hsp65 sequences, can be used to specifically identify Mycobacterium avium complex and closely related Mycobacterium species DNA by a characteristic melting temperature.

Clinical Indication

  • Clinical suspicion of infection of body fluids (e.g., CSF) or tissues
  • Pathological evidence or clinical suspicion of infectious agents in fixed paraffin embedded tissue specimens
  • Epidemiological or clinical suspicion of contaminated instruments or environmental surfaces

Clinical Utility

  • The rapid identification of bacteria, including cells with fastidious growth properties, dead cells, or an organism not otherwise speciated by morphological/biochemical means
  • The identification of the infectious agent may influence the choice of antibacterial therapy and/or monitoring of effectiveness
  • The confirmation of a diagnosis of bacterial infection vs. other pathological process (e.g., malignancy)
  • The identification of the infectious agent may provide prognostic information important for patient management
  • The detection and monitoring of nosocomial infections

Sensitivity

  • Analytical sensitivities or minimal detection limits are expressed in copies of bacterial or genomic DNA in a single amplification reaction performed on purified DNA. For this assay, analytical sensitivity was estimated to be 5 genome equivalent per PCR reaction with hsp65 amplified probe
  • The sensitivity of detecting microbial DNA from a tissue/fluid sample will vary depending on the organism load in the sample submitted to our lab for testing, pretreatment such as formaldehyde fixation or staining, and any process that introduces exogenous micro-organisms or microbial DNA into the sample submitted for testing
Forms & Requisitions

Molecular Microbiology Order Form

Synonyms
AFB PCR, Atypical Mycobacteria PCR, broad range AFB PCR, broad range Mycobacteria PCR, hsp65, M. avium complex, MAC, MAI PCR, Molecular AFB, Molecular Mycobacteria, Molecular Mycobacterium, MOTT, Mycobacteria avium complex identification, Mycobacterial identification, Mycobacterium avium complex PCR, Mycobacterium identification, universal AFB PCR, universal Mycobacterium PCR
Components
Code Name
MAVRS M avium complex PCR: Detection, hsp65
MAVID M avium complex PCR: hsp65 Identification
MAVSI M avium complex PCR: Specimen Description
MAVSPI M avium complex PCR: External Identifier
MAVSR M avium complex PCR: Special Requests
MAVSC M avium complex PCR: Specimen Comments
MAVNAE M avium complex PCR: Specimen DNA Extraction
MAVREV M avium complex PCR: Pathologist Review
MAVME M avium complex PCR: Method Note

Interpretation

Guidelines
Method

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)
Collection

Acceptable specimens are listed below. Please see Molecular Microbiology Specimen Submission for complete specimen collection and handling instructions.

Shipping/Handling

  • Fresh frozen tissue/fluid specimens should be collected into a DNA free container labeled with at least two identifiers and 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.

Acceptable Specimens

*Mycobacterium avium complex DNA Detection [MAVDNA] can be ordered on sputum

**Fungal PCR reflex NGS [FUNDNA] and Fungal DNA Detection by PCR (without reflex to NGS) [NRFDNA] may have interference due to some lots of eSwabs which have been found to contain Saccharomyces cerevisiae DNA, resulting in false positive detection. Clinical correlation and/or retesting with a different collection method is advised. The detection of S. cerevisiae from eSwab specimens can interfere with our ability to rule out other fungal DNA.

    Unacceptable Specimens

    • Blood, serum, plasma, stool/rectal swabs
    • No citrated or heparinized solutions
    • Tissues floating in formalin
    • Swab/fluid collected in tube containing agar

    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 over scrolls/unstained slides 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.

    Fresh tissue is the optimal specimen of choice, as it reduces the chance of introducing exogenous DNA templates or microorganisms during embedding/fixation. Formalin fixation dramatically reduces the sensitivity of the assays due to reduced template yield and quality.

    Forms & Requisitions

    Molecular Microbiology Order Form

    Handling Instructions

    Please see Molecular Microbiology Specimen Submission for complete specimen collection and handling instructions.

    Quantity
    Requested: See "Collection" for Optimal Quantity
    Minimum: Specimens below optimal quantity are acceptable for testing, however, diagnostic yield is generally proportional to specimen size.

    Processing

    Receiving Instructions

    UWMC/HMC: Store and send fresh tissue/fluid specimens refrigerated, if specimen storage and transport will exceed 8 hours, freeze at -20°C. Freeze all fresh tissue/fluid specimens at -20°C upon arrival in UW Molecular Microbiology.

    Misc Sendout

    Performance

    Lab Department
    Micro Molecular Diag(MMD)
    Frequency
    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?
    No
    Performing Location(s)
    UW-MT Microbiology, Molecular Diagnostics
    206-520-4600

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    Shipping Address

    Attn: Molecular Microbiology
    UW CLSPS
    1601 Lind Ave SW Room 117
    Renton, WA 98057
    Phone: 206-520-4600
    Alternate phone: 206-598-6147

    Performing Lab Address

    Clinical Microbiology Lab, NW177
    University of Washington Medical Center
    1959 NE Pacific Street
    Seattle, WA 98195
    Phone: 206-598-5735
    Alternate phone: 206-598-6147

    Contact Information

    Please e-mail us with any questions or comments you may have. Your inquiry will be answered as soon as possible.

    email: molmicdx@uw.edu

    The Molecular Microbiology lab is open from Monday-Friday, 7am-4pm PDT.

    Billing inquiries and requests for faxed reports can be made to our Client Services Department at (206) 520-4600 or (800) 713-5198.

    For results or other inquiries, we can be reached by phone at the following numbers:

    • Phone: (206) 598-5735
    • Alternate phone: (206) 598-6147
    • FAX: (206) 520-4903

    For assistance during weekends, holidays and after hours, please contact Lab Medicine Resident at (206) 598-6190

    Billing & Coding

    CPT Codes
    87561
    LOINC
    71719-9
    Interfaced Order Code
    UOW4330