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Overview of Intestinal Protozoan and Microsporidia Infections


Richard D. Pearson

, MD, University of Virginia School of Medicine

Last full review/revision Apr 2020| Content last modified Apr 2020
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The most important intestinal protozoan pathogens are

Members of the phylum Microsporidia used to be classified as protozoa but are now, based on DNA studies, thought to be fungi or closely related to them.

Multiple pathogenic parasites and nonpathogenic commensal organisms may be present in the intestine at the same time.

Intestinal protozoa are spread by the fecal-oral route, so infections are widespread in areas with inadequate sanitation and water treatment. They are also common in the US in settings where fecal incontinence and poor hygiene prevail, as may occur in mental institutions and day care centers. Occasionally, large foodborne and waterborne outbreaks of intestinal protozoan infection have occurred in the US (eg, the multi-state outbreak of Cyclospora cayetanensis infection attributed to contaminated fresh vegetable trays in 2018 and the massive waterborne Cryptosporidium outbreak in Milwaukee in 1993). Some gastrointestinal protozoa are spread sexually, especially with practices involving oral-anal contact, and several protozoan species cause severe opportunistic infections in patients with AIDS.

Systemic protozoal diseases are discussed elsewhere and include malaria, babesiosis, toxoplasmosis, leishmaniasis, Chagas disease, and African trypanosomiasis.


Making a diagnosis based on symptoms and physical findings is difficult; stool testing for parasite antigens or DNA and microscopic examination of stool for cysts or organisms are necessary.

Fecal antigen tests that are sensitive and specific are available for

  • Cryptosporidium species

  • E. histolytica

  • G. duodenalis

Microscopic diagnosis may require several samples, concentration methods, and special stains; thus, the laboratory should be notified which pathogen or pathogens are suspected. Some patients require semi-invasive diagnostic techniques such as endoscopic biopsy (see table Collecting and Handling Specimens for Microscopic Diagnosis of Parasitic Infections).

Molecular diagnosis using polymerase chain reaction-based assays is available for many enteric protozoa.

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