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Microsporidia species, Molecular Detection, PCR

Useful For

Detection of Enterocytozoon bieneusi and Encephalitozoon species in stool and urine specimens to support the clinical diagnosis of microsporidiosis

Testing Algorithm

The following algorithms are available in Special Instructions:

-Parasitic Investigation of Stool Specimens Algorithm

-Laboratory Testing for Infectious Causes of Diarrhea

Reporting Name

Microsporidia PCR
Seattle Children's Hospital Note:

Clinical System Name: Miscellaneous Test

Specimen Type


Necessary Information

Specimen source is required.

Specimen Required

Submit only 1 of the following specimens:



Specimen Type: Unpreserved stool

Supplies: Stool container, Small (Random), 4 oz (T288); Stool Collection Kit, Random (T635)

Container/Tube: Stool container (T288)

Specimen Volume: 5 g

Specimen Stability Information: Refrigerated 7 days (preferred)/Frozen 7 days


Specimen Type: Preserved stool          

Supplies: ECOFIX Stool Transport Vial (Kit) (T219); Stool Collection Kit, Random (T635)


Preferred: ECOFIX preservative (T219)

Specimen Volume: 5 g

Specimen Stability Information: Ambient 7 days (preferred)/Refrigerated 7 days/Frozen 7 days


Specimen Type: Urine

Container/Tube: Sterile container

Specimen Volume: 5 mL

Collection Instructions: Mid-stream, clean-catch, suprapubic aspirates and catheterization collections are acceptable. Please submit in a clean, sterile container free from preservatives. The first portion of the voided urine (first void) is also acceptable.

Specimen Stability Information: Refrigerated 7 days (preferred)/Frozen 7 days

Specimen Minimum Volume

Stool: 1 g; Urine: 0.5 mL

Specimen Stability Information

Specimen Type Temperature Time
Varies Refrigerated (preferred) 7 days
  Ambient  7 days
  Frozen  7 days

Reject Due To








Urine containing preservatives

Prostate secretions and samples

Stool in preservatives other than ECOFIX

Reference Values


Method Description

Nucleic acid is extracted from stool and urine using the automated MagNA Pure bead-based system (Roche Molecular Systems). The extract is then transferred to individual self-contained capillary cuvettes for amplification. The LightCycler is a self-contained automated instrument that amplifies and monitors the development of target nucleic acid (amplicon) after each cycle of PCR.


The DNA target for PCR assay is the 18S rRNA gene of Enterocytozoon bieneusi, Encephalitozoon intestinalis, Encephalitozoon hellem, and Encephalitozoon cuniculi.


This assay utilizes 2 primers and 2 probes, which are specific for E bieneusi and 3 primers and 2 probes specific for Encephalitozoon species. The specific base pair DNA target sequence is first amplified by PCR using the target-specific primers. Amplicon is then detected during melting curve analysis using fluorescence resonance energy transfer (FRET) probes, which utilizes one hybridization probe with a donor fluorophore, fluorescein, at the 3' end and a second hybridization probe with an acceptor fluorophore, at the 5' end. Fluorescence is produced when the 2 probes anneal to the target sequence in close proximity to one another. The LC-Red 670 emits a measurable and quantifiable light signal at a specific wavelength when E bieneusi is present and the LC-Red 610 emits a measurable and quantifiable light signal in the presence of Encephalitozoon species.(Cockerill FR, Uhl FR: Applications and challenges of real-time PCR for the clinical microbiology laboratory. In Rapid Cycle Real-Time PCR. Edited by U Reischl, C Wittwer, F Cockerill. Springer, NY 2002)

Day(s) and Time(s) Performed

Monday through Saturday; 6 a.m.

Performing Laboratory

Mayo Medical Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information


LOINC Code Information

Test ID Test Order Name Order LOINC Value
LCMSP Microsporidia PCR In Process


Result ID Test Result Name Result LOINC Value
MSPS Specimen Source 31208-2
36744 Encephalitozoon species In Process
36745 Enterocytozoon bieneusi 41443-3

Method Name

Real-Time Polymerase Chain Reaction (PCR)/DNA Probe Hybridization


If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:

Microbiology Test Request Form (T244) (

Gastroenterology and Hepatology Test Request Form (T728) (