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Overview of Intestinal Protozoan and Microsporidia Infections

By Richard D. Pearson, MD, Emeritus Professor of Medicine, University of Virginia School of Medicine

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The most important intestinal protozoan pathogens are

  • Entamoeba histolytica

  • Giardia duodenalis (G. lamblia, G. intestinalis)

  • Intestinal coccidia: Cryptosporidium sp, Cystoisospora (Isospora) belli, and Cyclospora cayetanensis

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. Nonintestinal protozoan infections are covered in other chapters.

Systemic protozoal diseases include malaria, babesiosis, leishmaniasis, toxoplasmosis, and trypanosomiasis.

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 waterborne outbreaks of intestinal protozoan infection have occurred in the US (eg, the massive waterborne Cryptosporidium outbreak in Milwaukee in 1993). Some GI protozoa are spread sexually, especially with practices involving oral-anal contact, and several protozoan species cause severe opportunistic infections in patients with AIDS.


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

Fecal antigen tests that are sensitive and specific are available for

  • G. intestinalis

  • Cryptosporidium sp

  • E. histolytica

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 PCR-based assays is available for some enteric protozoa and holds promise for the future.