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Test ID: LCMSP Microsporidia species, Molecular Detection, PCR, Varies

Useful For

Detection of Enterocytozoon bieneusi and Encephalitozoon species in fecal 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

Specimen Type


Advisory Information

For specimens other than feces or urine, MTBS / Microsporidia Stain, Varies should be ordered since it will detect other microsporidia that are not targeted by this assay.

Necessary Information

Specimen source is required.

Specimen Required

Submit only 1 of the following specimens:



Specimen Type: Unpreserved feces

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

Container/Tube: Fecal container (T288)

Specimen Volume: 5 g


Specimen Type: Preserved feces

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

Container/Tube: ECOFIX preservative

Specimen Volume: 5 g


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 Minimum Volume

Feces: 1 g
Urine: 0.5 mL

Specimen Stability Information

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

Clinical Information

Microsporidia are highly specialized fungi that cause a wide variety of clinical syndromes in humans. The most common microsporidia are Enterocytozoon bieneusi and Encephalitozoon intestinalis, which infect the gastrointestinal tract and cause a diarrheal illness, and Encephalitozoon cuniculi and Encephalitozoon hellem that can infect the conjunctiva, respiratory tract, and genitourinary system. Human infections have been reported most frequently in patients with AIDS, but also can occur in other immunocompromised patients, including solid organ allograft recipients and, sporadically, immunocompetent hosts. Less commonly, other microsporidia such as Vittaforma corneae and Brachiola species can cause disseminated or organ-specific disease. This assay detects only the most common microsporidia, Enterocytozoon bieneusi and Encephalitozoon species, and not microsporidiosis due to other species.


See Parasitic Investigation of Stool Specimens Algorithm and Laboratory Testing for Infectious Causes of Diarrhea in Special Instructions for other diagnostic tests that may be of value in evaluating patients with diarrhea.

Reference Values



A positive result indicates the presence of Enterocytozoon bieneusi and Encephalitozoon species DNA and is consistent with an active or recent infection. Since microsporidia DNA may be present in feces or urine in the absence of clinical symptoms, results should be correlated with clinical presentation.


A negative result indicates absence of detectable DNA from Enterocytozoon bieneusi and Encephalitozoon species in the specimen, but does not always rule out ongoing microsporidiosis since the organism may be present at very low levels or may be sporadic.


Other tests to consider in the evaluation of a patient presenting with acute or chronic watery diarrhea include cultures or specific assays for bacterial, viral, and parasitic pathogens.

Clinical Reference

1. Didier ES, Weiss LM: Microsporidiosis: Not just in AIDS patients. Curr Opin Infect Dis 2011;24 (5):490-495

2. Nagpal A, Pritt BS, Lorenz EC, et al: Disseminated microsporidiosis in a renal transplant recipient: case report and review of the literature. Transpl Infect Dis. 2013 Oct;15(5):526-532

3. Verweij JJ, Stensvold CR: Molecular Testing for Clinical Diagnosis and Epidemiological Investigations of Intestinal Parasitic Infections. Clin.Microbiol. Rev. April 2014;27:371-418

4. Wolk DM, Schneider SK, Wengenack NL, et al: Real-time PCR method for detection of Encephalitozoon intestinalis from stool specimens. J Clin Microbiol 2002 Nov;40(11):3922-3928

Day(s) and Time(s) Performed

Tuesday through Friday; 6 a.m.

Analytic Time

2 days

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 94332-4


Result ID Test Result Name Result LOINC Value
MSPS Specimen Source 31208-2
36744 Encephalitozoon species 94333-2
36745 Enterocytozoon bieneusi 94334-0

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 (T244)

-Gastroenterology and Hepatology Client Test Request (T728)

Mayo Clinic Laboratories | Gastroenterology Catalog Additional Information:

mml-gi-id, mml-gi-intestinal-infections, mml-gi-intestinal-infections-pathogens