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Microsporidiosis Workup

  • Author: Valda M Chijide, MD; Chief Editor: Pranatharthi Haran Chandrasekar, MBBS, MD  more...
Updated: Oct 05, 2015

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.

Contributor Information and Disclosures

Valda M Chijide, MD Clinical Professor, Department of Medicine, University of Saskatchewan; Consultant in Infectious Diseases, Regina, Saskatchewan, Canada

Valda M Chijide, MD is a member of the following medical societies: American College of Physicians, HIV Medicine Association, Infectious Diseases Society of America

Disclosure: Nothing to disclose.

Specialty Editor Board

Francisco Talavera, PharmD, PhD Adjunct Assistant Professor, University of Nebraska Medical Center College of Pharmacy; Editor-in-Chief, Medscape Drug Reference

Disclosure: Received salary from Medscape for employment. for: Medscape.

John W King, MD Professor of Medicine, Chief, Section of Infectious Diseases, Director, Viral Therapeutics Clinics for Hepatitis, Louisiana State University Health Sciences Center; Consultant in Infectious Diseases, Overton Brooks Veterans Affairs Medical Center

John W King, MD is a member of the following medical societies: American Association for the Advancement of Science, American College of Physicians, American Federation for Medical Research, Association of Subspecialty Professors, American Society for Microbiology, Infectious Diseases Society of America, Sigma Xi

Disclosure: Nothing to disclose.

Chief Editor

Pranatharthi Haran Chandrasekar, MBBS, MD Professor, Chief of Infectious Disease, Program Director of Infectious Disease Fellowship, Department of Internal Medicine, Wayne State University School of Medicine

Pranatharthi Haran Chandrasekar, MBBS, MD is a member of the following medical societies: American College of Physicians, American Society for Microbiology, International Immunocompromised Host Society, Infectious Diseases Society of America

Disclosure: Nothing to disclose.

Additional Contributors

Joseph R Masci, MD, FACP, FCCP Professor of Medicine, Professor of Preventive Medicine, Icahn School of Medicine at Mount Sinai; Director of Medicine, Elmhurst Hospital Center

Joseph R Masci, MD, FACP, FCCP is a member of the following medical societies: American Association for the Advancement of Science, American College of Chest Physicians, American College of Physicians, American Medical Association, American Society for Microbiology, American Society of Tropical Medicine and Hygiene, Infectious Diseases Society of America, International AIDS Society, International Society for Infectious Diseases, New York Academy of Medicine, New York Academy of Sciences, Physicians for Social Responsibility, Royal Society of Medicine, Association of Program Directors in Internal Medicine, Physicians for Human Rights, Association of Professors of Medicine, HIV Medicine Association, American Academy of HIV Medicine, Association of Specialty Professors, International Association of Providers of AIDS Care, Federation of American Scientists, American Society of Tropical Medicine and Hygiene

Disclosure: Nothing to disclose.


The author would like to thank Deidrea Parker, BS, and the Medical College of Georgia Department of Pharmacy for assistance in the literature review of the drug therapy for microsporidiosis.

  1. Loignon M, Labrecque LG, Bard C, Robitaille Y, Toma E. Cerebral microsporidiosis manifesting as progressive multifocal leukoencephalopathy in an HIV-infected individual - a case report. AIDS Res Ther. 2014. 11:20. [Medline]. [Full Text].

  2. Ladapo TA, Nourse P, Pillay K, Frean J, Birkhead M, Poonsamy B, et al. Microsporidiosis in pediatric renal transplant patients in Cape Town, South Africa: Two case reports. Pediatr Transplant. 2014 Nov. 18(7):E220-6. [Medline].

  3. Hocevar SN, Paddock CD, Spak CW, Rosenblatt R, Diaz-Luna H, Castillo I, et al. Microsporidiosis acquired through solid organ transplantation: a public health investigation. Ann Intern Med. 2014 Feb 18. 160(4):213-20. [Medline].

  4. Coyle CM, Weiss LM, Rhodes LV, et al. Fatal myositis due to the microsporidian Brachiola algerae, a mosquito pathogen. N Engl J Med. 2004 Jul 1. 351(1):42-7. [Medline].

  5. Aikawa NE, Twardowsky Ade O, Carvalho JF, Silva CA, Silva IL, Ribeiro AC, et al. Intestinal microsporidiosis: a hidden risk in rheumatic disease patients undergoing anti-tumor necrosis factor therapy combined with disease-modifying anti-rheumatic drugs?. Clinics (Sao Paulo). 2011. 66(7):1171-5. [Medline]. [Full Text].

  6. Didier ES, Weiss LM. Microsporidiosis: not just in AIDS patients. Curr Opin Infect Dis. 2011 Oct. 24(5):490-5. [Medline].

  7. Chan CM, Theng JT, Li L, et al. Microsporidial keratoconjunctivitis in healthy individuals: a case series. Ophthalmology. 2003 Jul. 110(7):1420-5. [Medline].

  8. Font RL, Su GW, Matoba AY. Microsporidial stromal keratitis. Arch Ophthalmol. 2003 Jul. 121(7):1045-7. [Medline].

  9. Anane S, Attouchi H. Microsporidiosis: epidemiology, clinical data and therapy. Gastroenterol Clin Biol. 2010 Sep. 34(8-9):450-64. [Medline].

  10. Bartlett JG, Belitsos PC, Sears CL. AIDS enteropathy. Clin Infect Dis. 1992 Oct. 15(4):726-35. [Medline].

  11. Bach AC, Babayan VK. Medium-chain triglycerides: an update. Am J Clin Nutr. 1982 Nov. 36(5):950-62. [Medline].

  12. Wanke CA, Pleskow D, Degirolami PC, et al. A medium chain triglyceride-based diet in patients with HIV and chronic diarrhea reduces diarrhea and malabsorption: a prospective, controlled trial. Nutrition. 1996 Nov-Dec. 12(11-12):766-71. [Medline].

  13. Sharpstone D, Rowbottom A, Francis N, et al. Thalidomide: a novel therapy for microsporidiosis. Gastroenterology. 1997 Jun. 112(6):1823-9. [Medline].

  14. Ott M, Fischer H, Polat H, et al. Bioelectrical impedance analysis as a predictor of survival in patients with human immunodeficiency virus infection. J Acquir Immune Defic Syndr Hum Retrovirol. 1995 May 1. 9(1):20-5. [Medline].

  15. Carr A, Marriott D, Field A, et al. Treatment of HIV-1-associated microsporidiosis and cryptosporidiosis with combination antiretroviral therapy. Lancet. 1998 Jan 24. 351(9098):256-61. [Medline].

  16. Conteas CN, Berlin OG, Ash LR, et al. Therapy for human gastrointestinal microsporidiosis. Am J Trop Med Hyg. 2000 Sep-Oct. 63(3-4):121-7. [Medline].

  17. Cunningham E. Ocular Complications of HIV Infection. The Medical Management of AIDS. Philadelphia, Pa: WB Saunders, Co; 1999. 171-84.

  18. DeGirolami PC, Ezratty CR, Desai G, et al. Diagnosis of intestinal microsporidiosis by examination of stool and duodenal aspirate with Weber's modified trichrome and Uvitex 2B strains. J Clin Microbiol. 1995 Apr. 33(4):805-10. [Medline].

  19. Didier ES. Microsporidiosis. Clin Infect Dis. 1998 Jul. 27(1):1-7; quiz 8. [Medline].

  20. Didier ES. Microsporidiosis: an emerging and opportunistic infection in humans and animals. Acta Trop. 2005 Apr. 94(1):61-76. [Medline].

  21. Diesenhouse MC, Wilson LA, Corrent GF, et al. Treatment of microsporidial keratoconjunctivitis with topical fumagillin. Am J Ophthalmol. 1993 Mar 15. 115(3):293-8. [Medline].

  22. Dore GJ, Marriott DJ, Hing MC, et al. Disseminated microsporidiosis due to Septata intestinalis in nine patients infected with the human immunodeficiency virus: response to therapy with albendazole. Clin Infect Dis. 1995 Jul. 21(1):70-6. [Medline].

  23. Dunand VA, Hammer SM, Rossi R, et al. Parasitic sinusitis and otitis in patients infected with human immunodeficiency virus: report of five cases and review. Clin Infect Dis. 1997 Aug. 25(2):267-72. [Medline].

  24. Dunn JP, Holland GN. Human immunodeficiency virus and opportunistic ocular infections. Infect Dis Clin North Am. 1992 Dec. 6(4):909-23. [Medline].

  25. Eeftinck Schattenkerk JK, van Gool T, et al. Clinical significance of small-intestinal microsporidiosis in HIV-1-infected individuals. Lancet. 1991 Apr 13. 337(8746):895-8. [Medline].

  26. Garcia L, Bruckner D. Intestinal Protozoa (Coccidia, Microsporidia) and Algae. Diagnostic Medical Parasitology. 3rd ed. Washington, DC: ASM Press; 1997. 54-89.

  27. Gunnarsson G, Hurlbut D, DeGirolami PC, et al. Multiorgan microsporidiosis: report of five cases and review. Clin Infect Dis. 1995 Jul. 21(1):37-44. [Medline].

  28. Infectious Diseases Society of America. 1999 USPHS/IDSA guidelines for the prevention of opportunistic infections in persons infected with Human Immunodeficiency Virus. USPHS/IDSA Prevention of Opportunistic Infections Working Group. Infectious Diseases Society of American. Ann Intern Med. 1999 Dec 7. 131(11):873-908. [Medline].

  29. Kartalija M, Sande MA. Diarrhea and AIDS in the era of highly active antiretroviral therapy. Clin Infect Dis. 1999 Apr. 28(4):701-5; quiz 706-7. [Medline].

  30. Kester KE, Turiansky GW, McEvoy PL. Nodular cutaneous microsporidiosis in a patient with AIDS and successful treatment with long-term oral clindamycin therapy. Ann Intern Med. 1998 Jun 1. 128(11):911-4. [Medline].

  31. Kotler DP. Malnutrition in HIV infection and AIDS. AIDS. 1989. 3 Suppl 1:S175-80. [Medline].

  32. Kotler DP. Nutrition and Wasting in HIV Infection. MEDSCAPE HIV Clinical Management Series. 1999. 8:1-33. [Full Text].

  33. Lew EA, Poles MA, Dieterich DT. Diarrheal diseases associated with HIV infection. Gastroenterol Clin North Am. 1997 Jun. 26(2):259-90. [Medline].

  34. Lowder CY, McMahon JT, Meisler DM, et al. Microsporidial keratoconjunctivitis caused by Septata intestinalis in a patient with acquired immunodeficiency syndrome. Am J Ophthalmol. 1996 Jun. 121(6):715-7. [Medline].

  35. Markell E. Lumen-Dwelling Protozoa. Markell and Voge's Medical Parasitology. 8th ed. Philadelphia, Pa: WB Saunders, Co; 1999. 24-89.

  36. Medical letter on drugs and therapeutics. Drugs for parasitic infections. Med Lett Drugs Ther. 1998 Jan 2. 40(1017):1-12. [Medline].

  37. Micromedex. Albendazole. Available at: 2000. [Full Text].

  38. Micromedex. Fumagillin. Available at: 2000. [Full Text].

  39. Molina JM, Tourneur M, Sarfati C, et al. Fumagillin treatment of intestinal microsporidiosis. N Engl J Med. 2002 Jun 20. 346(25):1963-9. [Medline].

  40. Moon TD, Oberhelman RA. Antiparasitic therapy in children. Pediatr Clin North Am. 2005 Jun. 52(3):917-48, viii. [Medline].

  41. Patel R. Infections in recipients of kidney transplants. Infect Dis Clin North Am. 2001 Sep. 15(3):901-52, xi. [Medline].

  42. PDR. Physicians' Desk Reference. Montvale, NJ: Medical Economics Company, Inc; 2000.

  43. Raynaud L, Delbac F, Broussolle V, et al. Identification of Encephalitozoon intestinalis in travelers with chronic diarrhea by specific PCR amplification. J Clin Microbiol. 1998 Jan. 36(1):37-40. [Medline].

  44. Rosenblatt JE. Antiparasitic agents. Mayo Clin Proc. 1999 Nov. 74(11):1161-75. [Medline].

  45. Sandfort J, Hannemann A, Gelderblom H, et al. Enterocytozoon bieneusi infection in an immunocompetent patient who had acute diarrhea and who was not infected with the human immunodeficiency virus. Clin Infect Dis. 1994 Sep. 19(3):514-6. [Medline].

  46. Schwartz DA, Visvesvara GS, Diesenhouse MC, et al. Pathologic features and immunofluorescent antibody demonstration of ocular microsporidiosis (Encephalitozoon hellem) in seven patients with acquired immunodeficiency syndrome. Am J Ophthalmol. 1993 Mar 15. 115(3):285-92. [Medline].

  47. Strano A, Cali A, Neafie R. Microsporidiosis. Pathology of Tropical and Extraordinary Diseases. Washington, DC: Armed Forces Institute of Pathology; 1976. Vol 1: 336-9.

  48. Talal A, Dieterich D. Gastrointestinal and Hepatic Manifestations of HIV Infection. The Medical Management of AIDS. 6th ed. Philadelphia, Pa: WB Saunders, Co; 1999. 195-216.

  49. Thomson MICROMEDEX. Albendazole. MICROMEDEX Healthcare Series. 2007. 131:

  50. Weber R, Bryan RT. Microsporidial infections in immunodeficient and immunocompetent patients. Clin Infect Dis. 1994 Sep. 19(3):517-21. [Medline].

  51. Weber R, Schwartz D, Bryan R. Microsporidia. Mandell, Douglas, and Bennett's Principles and Practice of Infectious Disease. Philadelphia, Pa: Churchill Livingstone; 2000. 2920-29.

  52. Weiss L. Microsporidiosis. Mandell, Bennett, and Dolin's Principles and Practice of Infectious Diseases. 2005. 2: 3237-54.

  53. Weller, Peter. Protozoal and Intestinal Infections and Trichomoniasis. Harrison' Principles of Internal Medicine. 17th. 2008. 1314/208.

  54. Wittner M, Tanowitz HB, Weiss LM. Parasitic infections in AIDS patients. Cryptosporidiosis, isosporiasis, microsporidiosis, cyclosporiasis. Infect Dis Clin North Am. 1993 Sep. 7(3):569-86. [Medline].

Electron micrograph (X30,000) of Nosema connori in diaphragm showing a coiled polar filament (arrow). Courtesy of the Armed Forces Institute of Pathology (AFIP 71-11521-4).
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