Leishmania species DNA detection by PCR
General Information
- Lab Name
- Leishmania Species DNA Detection
- Lab Code
- LSHDNA
- Epic Name
- Leishmania Species DNA Detection
- Description
Detection and identification of Leishmania species DNA
Leishmaniasis is a fatal or disfiguring disease caused by a protozoan parasite transmitted by hematophagous sand flies. Globally, 350 million people are estimated to be at risk, resulting in ~1 million cases per year. The disease is an important diagnostic consideration in travelers from Latin America, the Middle East, North or East Africa, and has been reported in the Southern United States. Populations at risk include immunosuppressed persons, immigrants, military and foreign service personnel, and staff or volunteers from non-governmental organizations.Leishmaniasis can manifest in cutaneous, mucosal, and visceral forms. Leishmaniasis can be self-limiting or require treatment, which can be dependent upon the species and disease manifestation. Treatments and medications are toxic and have potential side effects. The multicopy mini-exon gene is present across Leishmania species with differences in length and sequence polymorphisms that can differentiate between Leishmania species or species complexes. This assay in combination with clinical presentation could help guide clinical management of suspected Leishmania infections.
The mini-exon gene is located on chromosome 2, is composed of a semi-conserved spliced-leader region and variable tandem gene repeats with lengths that vary by species group. The mini-exon functions in post-transcriptional processing where the semi-conserved SL region binds to the 5’ end of mRNAs in order to produce mature mRNAs. These primers have shown successful identification of eight different Leishmania species using the spliced-leader sequence and mini-exon gene. The conserved primer binding sites flank length and sequencing variation of Old World, New World, and Leishmania subgenus Viannia species.
- References
- Curtin JM and Aronson NE. 2021. Leishmaniasis in the United States: Emerging Issues in a Region of Low Endemicity. Microorganisms. 9(3):578.
- Aronson N, Herwaldt BL, Libman M, Pearson R, Lopez-Velez R, Weina P, Carvalho E, Ephros M, Jeronimo S, Magill A. 2017. Diagnosis and Treatment of Leishmaniasis: Clinical Practice Guidelines by the Infectious Diseases Society of America (IDSA) and the American Society of Tropical Medicine and Hygiene (ASTMH). Am J Trop Med Hyg. 96:24–45.
- Forms & Requisitions
- Synonyms
- Kinetoplast, Leishmania PCR, Leishmaniasis identification, Leishmaniasis PCR, Leishmaniasis sequencing, Leismania identification, Leismania sequencing, mini-exon PCR, parasite identification, protozoan identification
- Components
-
Interpretation
- Guidelines
- Method
DNA extraction, nucleic acid purification, polymerase chain reaction (PCR), sequencing
- Reference Range
- See individual components
- References
- Curtin JM and Aronson NE. 2021. Leishmaniasis in the United States: Emerging Issues in a Region of Low Endemicity. Microorganisms. 9(3):578.
- Aronson N, Herwaldt BL, Libman M, Pearson R, Lopez-Velez R, Weina P, Carvalho E, Ephros M, Jeronimo S, Magill A. 2017. Diagnosis and Treatment of Leishmaniasis: Clinical Practice Guidelines by the Infectious Diseases Society of America (IDSA) and the American Society of Tropical Medicine and Hygiene (ASTMH). Am J Trop Med Hyg. 96:24–45.
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
- 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.
Conditionally Acceptable Specimens
- Buffy coat with stain positive whole blood: acceptable for Leishmania PCR only
- 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.
- 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
- 87801
- LOINC
- 23159-7
- Interfaced Order Code
- UOW4248