Chlamydiales DNA Detection by PCR

General Information

Lab Name

Chlamydiales DNA Detection by PCR

Lab Code

CLMDNA

Description

Chlamydiales is an order of intracellular bacterial parasites that are responsible for a variety of human diseases. Such organisms can cause acute and chronic respiratory infections (including Chamyida pneumoniae, C. psittaci, and C. abortus), ocular infections (including C. pneumoniae, C. psittaci, C. felis, C. pecorum, C. caviae, C. suis, and C. muridarum), and sexually transmitted infections (including C. trachomatis). Depending on the species and disease entity involved, infection may occur through direct, zoonotic, or environmental exposure.

Although some species within order Chlamydiales are well-described and well-established human pathogens, others remain poorly characterized and are classified as emerging agents of human disease, some of which are being actively investigated through ongoing research efforts. Such emerging pathogens include Waddliaceae chondrophila in adverse pregnancy outcomes, and Parachlamydia acanthamoebae, P. naegleriophila and Simkaniaceae negevensis in respiratory disease.

Diagnosis of infection with bacteria from the order Chlamydiales can be challenging. Because these organisms only replicate within eukaryotic cells, they cannot be recovered or identified by standard microbiological culture. Moreover, the 16s rRNA genes of these bacteria encode an unusual sequence composition that prevents their molecular detection by standard broad-range bacterial PCR assays Bacterial PCR reflex NGS [BCTDNA] and Bacterial DNA Detection by PCR (without reflex to NGS) [NRBDNA]: dedicated molecular testing is required.

Broad-range Chlamydiales DNA detection is conducted using a hybridization probe-based real-time PCR assay to identify organisms from across that taxonomical order. Specimens testing positive for amplification by real-time PCR are subjected to DNA sequencing to determine the identity of the detected organism.

Please note that for the detection of Chlamydia trachomatis from specific specimen types (Endocervical or urethral, Liquid Pap, Vaginal swabs, Throat swabs, Anal or rectal swabs, or fresh urine), ordering Chlamydia trachomatis (CT) Amplified Nucleic Acid Detection [CHLAD] or GC (N. gonorrhoeae) and CT (Chlamydia trachomatis) Amplified Nucleic Acid Detection [GCCTAD] is recommended.

For more information on molecular microbiology testing, please visit Molecular Diagnosis Microbiology Section.

Synonyms

16S PCR, bacteria identification, bacteria PCR, bacteria sequencing, bacterial identification, bacterial PCR, bacterial sequencing, broad range bacteria PCR, broad range bacterial PCR, Chamyida pneumoniae, Chlamydia, Chlamydia abortus, Chlamydia caviae, Chlamydia DNA, Chlamydia felis, Chlamydia identification, Chlamydia PCR, Chlamydia pecorum, Chlamydia psittaci, Chlamydia sequencing, Chlamydia suis Chlamydia muridarum, Chlamydia trachomatis, Chlamydia-like organism, Chlamydiaceae, Chlamydiae, Chlamydiales, molecular bacteria, molecular bacterial, Parachlamydia acanthamoebae, Parachlamydia naegleriophila, Simkaniaceae negevensis, Waddliaceae chondrophila

Components

Code Name
CL16RS Chlamydiales PCR: Detection, 16S rRNA
CL16ID Chlamydiales PCR: Identification, 16S rRNA
CLMSI Chlamydiales PCR: Specimen Description
CLMSPI Chlamydiales PCR: External Identifier
CLMSR Chlamydiales PCR: Special Requests
CLMSC Chlamydiales PCR: Specimen Comments
CLMNAE Chlamydiales PCR: Specimen DNA Extraction
CLMREV Chlamydiales PCR: Pathologist Review
CLMME Chlamydiales PCR: Method Note

Interpretation

Method

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

Reference Range

See individual components

Guidelines

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

    Processing

    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.

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

    Performance

    LIS Dept Code

    Micro Molecular Diag (MMD)

    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

    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

    Billing & Coding

    CPT codes

    87801

    LOINC

    Interfaced Order Code

    UOW6323