Microsporidiosis Workup

Updated: Jul 17, 2019
  • Author: Shirin A Mazumder, MD, FIDSA; Chief Editor: Pranatharthi Haran Chandrasekar, MBBS, MD  more...
  • Print

Laboratory Studies

Body fluid specimens

Microscopic examination of stained stool samples allows the most rapid diagnosis of microsporidiosis, but it does not allow identification of the specific infecting species.

Examine stools for other parasites (ova and parasite examination) and bacteria. Fecal WBCs are usually absent.

The modified trichrome stain (chromotrope 2R) is commonly used to detect microsporidia in urine, stool, and mucus. The microsporidia appear as ovoid, refractile spores with bright red walls. Some spores may have an equatorial beltlike stripe.

The rapid Gram chromotrope method can be performed more quickly (about 11 min) and combines the chromotrope method with a Gram-staining step. The spores stain dark violet, and the equatorial stripe is enhanced. E bieneusi spores measure about 0.9 µm X 1.5 µm; Encephalitozoon species measure about 1.5 µm X 3 µm.

Cytologic and histologic examinations are useful for diagnosis of microsporidiosis. A conjunctival scraping or swab frequently reveals the organism after a Gram stain (organisms usually stain gram-positive) or chromotrope stain. Microsporidial spores can be identified in tissue specimens obtained by biopsy or at autopsy. Stains used to detect microsporidia include the Brown Brenn Gram stain, Warthin-Starry silver stain, Giemsa stain, and trichrome blue stain.

Fluorochrome stains, including calcofluor white and uvitex 2B, have a high affinity for chitin. They can be used to detect microsporidia in urine, stool, mucus, and tissue sections.

Microsporidia stain poorly with hematoxylin-eosin.

Transmission electron microscopy

This is the criterion standard for diagnosis confirmation and allows species identification based on ultrastructure, but it is too costly and time consuming for routine use.

Polymerase chain reaction

This study is available in some research laboratories and can be used to diagnose infection with E bieneusi,V corneae, or Nosema species.

Immunofluorescence assays using monoclonal or polyclonal antibodies

These are available in some research laboratories and can be performed on most specimens, including formalin-fixed tissues. These studies allow visualization of spores and extruded polar tubules.


Routinely examine the urine for spores because disseminated infection with E intestinalis or E hellem frequently involves the kidney.

Liver function tests

Levels of alkaline phosphatase, gamma-glutamyltransferase, and aspartate and alanine aminotransferases are often elevated.

The bilirubin level is usually normal.

Creatine phosphokinase and aldolase

These values may be elevated in patients with myositis.


Patients with disseminated microsporidiosis are usually severely immunocompromised, and the CD4 count is generally below 100/μ L.

D-xylose test and qualitative fecal fat

Patients with prolonged diarrhea can develop malabsorption of fats, vitamins, and other nutrients; therefore, stool studies are required to assess for malabsorption in patients with microsporidiosis of the gastrointestinal tract.


Imaging Studies

CT scanning

CT scanning of the sinuses is used to search for evidence of sinusitis and middle ear involvement in patients with sinus symptoms.

CT scanning of the brain is used to determine if any ring-enhancing lesions are present in patients who present with headache.

Abdominal CT scan is used to assess for intrahepatic and extrahepatic ductal dilatation, gallbladder abnormalities, and liver parenchymal abnormalities in patients with signs of hepatic involvement.


Conduct abdominal ultrasonography in patients with elevated liver function tests to evaluate for cholelithiasis or other abnormalities in the biliary system.


Chest radiography is used to evaluate for pneumonia in patients with respiratory symptoms.


Other Tests


Diarrhea may cause micronutrient deficiency. Vitamin B-12 is the micronutrient that is most commonly deficient in persons with HIV infection; vitamin B-12 deficiency may lead to cognitive dysfunction and anemia.

Depending on symptoms, pay special attention to the levels of micronutrients, especially when a particular deficiency syndrome is detected.

Other assays to consider in patients with microsporidiosis include vitamin B-6 and other B vitamins, fat-soluble vitamins, zinc, and selenium.



Small-bowel endoscopy: The parasite burden is greatest in the proximal jejunum. Obtain biopsy samples from this site whenever possible. Microsporidia spores can often be found in duodenal fluid.

Slit-lamp examination: Keratoconjunctivitis due to microsporidiosis is characterized by diffuse, superficial, punctate keratopathy.

Punch biopsy of skin: Use Gram stain or other staining methods to identify microsporidia.


Histologic Findings

Histologic sections from the small bowel tend to reveal a mild inflammatory infiltrate (primarily lymphocytic) and a patchy distribution of infected enterocytes; therefore, a high index of suspicion is needed. Intestinal biopsy specimens from patients suspected of having microsporidiosis should undergo Gram staining. Villous atrophy and fusion, crypt elongation, and goblet cell depletion are common in affected mucosa.

E intestinalis is more invasive than E bieneusi. E intestinalis can infect enterocytes and cells in the lamina propria, fibroblasts, and macrophages.

Encephalitozoon infections may cause granulomatous lesions in the kidneys and liver.

Foamy histiocytes were observed in the lower dermis of a patient reported to have nodular skin lesions.