Treatment training manual

5. 4 Gut infections: giardia, cryptosporidia, microsporidia

The GI tract (short for gastrointestinal tract) includes and links the internal organs from your mouth, throat, stomach, intestines, bowel, rectum and anus. 

The gut is mainly the middle section of the GI tract, including the stomach and intestines.

Type of gut infections

Giardia, cryptosporidia and microsporidia are tiny parasites (protozoa) that cause stomach upset and severe diarrhoea.

These gut infections are more likely in people with CD4 counts under 300 cells/mm3. The risk increases as the CD4 count falls lower.

Infection is almost always the result of hygiene relating to:

  • Drinking unfiltered water.
  • Swallowing contaminated water when swimming.
  • Eating raw vegetables contaminated by food handlers.
  • Cryptosporidia is also acquired from drinking unpasteurised milk.

Nappies, daycare facilities, pets, farm animals, and other people may be routes of infection.

Main symptoms

  • Persistent diarrhoea that does not resolve within a few weeks.
  • Microsporidia can also cause inflammation in other parts of the body including the lungs, bladder, bowel, sinuses, ears, eyes, brain and pancreas.

Diarrhoea and weight loss are often linked because the body is less able to absorb nutrition from food. Severe diarrhoea can also reduce absorption of medication.

Weight loss (cachexia) in people living with HIV (that is not explained by a change in diet) can be very serious. Any weight loss should be taken seriously

  • Unexplained weight loss of 10% over a year is an AIDS-defining illness.
  • Unexplained weight loss of 5% over 6 months suggests 10% weight loss later.


Laboratory tests of a stool sample can look for causes of diarrhoea. The cause can be difficult to identify.


There are no universally effective treatments for these infections.

Effective HIV treatment (ART) is the most effective treatment as this will increases the CD4 count.

  • Drink plenty of fluids to help prevent dehydration.
  • Anti-diarrhoea medicines like loperamide can help.
  • In people with CD4 counts over 200 the body usually flushes out the parasite without treatment within a few weeks.
  • In people with CD4 counts under 200 this doesn’t always happen and diarrhoea can become chronic.

Microsporidia can be treated using the antibiotic albendazole. Thalidomide has an anti-inflammatory effect but is used more rarely.

Cryptosporidia can be treated with the antiparacitic nitazoxanide, or antibiotics azithromycin and paromomycin, sometimes at high doses.


Ways to minimise risk of these infections for HIV-positive people with low CD4 counts:

  • Wash vegetables in bottled or boiled water and peel them carefully.
  • Cook meat thoroughly.
  • Hygiene (especially washing your hands) is important. This reduces the risk of infection or spreading infection.

Many parasites that cause GI (gastro-intestinal) upset are linked to faeces – hygiene when caring for pets or children is especially important if you are HIV positive.

Other causes of gut inflammation and diarrhoea

Other infections can cause gt and GI problems.

These include bacterial infections, viral infections (including CMV and HSV in the gut) and fungal infections (candida/thrush).

This is why tests are needed to diagnose the cause of gut symptoms.

When the CD4 count is less than 200 cells/mm3 on effective ART, this can include antibiotic, antiviral or antifungal treatment as appropriate.


Last updated: 1 January 2023.