Treponema pallidum DNA detection by NAAT
General Information
- Lab Name
- Treponema Pallidum DNA detection by NAAT
- Lab Code
- TPLDNA
- Epic Name
- Treponema pallidum DNA detection by NAAT
- Description
Detection of Treponema pallidum DNA
The rapid and continued growth in syphilis cases, caused by the spirochete bacterium T. pallidum subsp. pallidum, in the United States is associated with significant maternal-fetal mortality and health disparities for racial/ethnic minorities and men who have sex with men (CDC 2021). Improvements in speed and accuracy of laboratory diagnosis are critical to disrupt this cycle of worsening infections by supporting prompt treatment decision-making. Serologic Syphilis Screen [SYPHSC] is the current mainstay of clinical syphilis testing, but require confirmation by stepwise, algorithmic testing for treponemal and non-treponemal antibodies, increasing turnaround time (TAT). Additionally, testing algorithms may be falsely negative in early/incubating syphilis and, confirmation of results by overburdened Public Health Laboratories can take weeks to result. Rapid molecular identification can help resolve ambiguous serologic results and speed pathogen identification to clinicians.
This test detects Treponema pallidum, the etiologic agent of syphilis and endemic treponematoses (e.g., yaws and pinta). It can be ordered as a primary diagnostic when syphilis is suspected and is also available reflexively when Bacterial PCR reflex NGS [BCTDNA] or Bacterial DNA Detection by PCR (without reflex to NGS) [NRBDNA] suggests the presence of T. pallidum below the reporting threshold.Please note that this assay does NOT distinguish subspecies of T. pallidum.
- Forms & Requisitions
- Synonyms
- 23S LAMP, 23S PCR, chancre, darkfield microscopy, FTA-ABS, meningovascular, neurosyphilis, RPR, spirochete, Syphilis, tabes dorsalis, TP-PA, TPPA, Treponema, Treponema pallidum, treponeme, VDRL
- Components
-
Interpretation
- Guidelines
- Method
DNA extraction, nucleic acid purification, Loop Mediated Isothermal Amplification
- Reference Range
- See individual components
Ordering & Collection
- Specimen Type
- Tissue (Fresh frozen or paraffin-embedded), Fluid (see Acceptable Specimens for details), Whole blood (EDTA-anticoagulated whole blood is an acceptable validated specimen type but requires director approval due to logistical & specimen batching considerations)
- 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
- Fresh frozen tissue
- Fresh frozen fluid: any body fluid is acceptable if it is not listed under Unacceptable Specimens.
- Common examples include: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.
- Formalin Fixed Paraffin-embedded tissues (FFPE, PET): blocks, scrolls, and unstained slides. Note that fresh tissue is considered the optimal specimen of choice, as it reduces the chance of introducing exogenous DNA templates or microorganisms during embedding/fixation, and because formalin fixation dramatically reduces the sensitivity of molecular assays due to reduced template yield and quality.
- Sputum: acceptable - except for Bacterial PCR reflex NGS [BCTDNA]/Bacterial DNA Detection by PCR (without reflex to NGS) [NRBDNA], Fungal PCR reflex NGS [FUNDNA]/Fungal DNA Detection by PCR (without reflex to NGS) [NRFDNA], and Nontuberculous Mycobacteria DNA Detection [NTMDNA]* assays
- eSwabs**, UTM (universal transport media), body fluid/bone marrow in EDTA (not including blood)
- Sodium polyanethol sulfonate (SPS, Wampole Isolator Tubes) acceptable with disclaimer
*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.
[TEMPORARILY UNAVAILABLE] Conditionally Acceptable Specimens
Director approval is required for submission of blood samples due to logistical & specimen batching considerations.- Whole blood/cord blood: acceptable for Treponema PCR only, submit in a lavender/purple top EDTA tube
- Forms & Requisitions
- 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. Whole blood is batched and currently performed 1 – 2 times per week.
- Available STAT?
- No
- Performing Location(s)
-
UW-MT Microbiology, Molecular Diagnostics
206-520-4600----------------------------------------
Shipping Address
Attn: Molecular Microbiology
UW CLSPS
1601 Lind Ave SW Room 117
Renton, WA 98057
Phone: 206-520-4600
Alternate phone: 206-598-6147Performing Lab Address
Clinical Microbiology Lab, NW177
University of Washington Medical Center
1959 NE Pacific Street
Seattle, WA 98195
Phone: 206-598-5735
Alternate phone: 206-598-6147Contact 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
- 87798
- LOINC
- 41163-7
- Interfaced Order Code
- UOW4596