Flagellated Protozoans Of The Gastrointestinal Tract

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Flagellated Protozoans Of The Gastrointestinal Tract

There are many different flagellated protozoans that live in the gastrointestinal tract of reptiles.

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There are many different flagellated protozoans that live in the gastrointestinal tract of reptiles. Almost all are considered commensal when found at low levels. Some, such as Monocercomonas species and Hexamita species, are considered pathogenic even at low levels. All are considered problematic when the population reaches moderate to high levels or when found in association with illness.


Flagellated protozoans all have a direct life cycle which means they can self-infect a reptile or readily be passed by close contact with another reptile’s feces.


Species At-Risk

More common in reptiles that are wild-collected or exposed to large numbers of other reptiles (e.g., recent imports, purchased at shows or pet shops). However, even reputable breeders may produce infected reptiles.

It is very difficult to make any conclusions about the origin of a flagellated protozoan parasite since many reptiles are asymptomatic carriers of some flagellated protozoans that may cause disease when introduced to reptiles of the same species that come from another population. For example, two breeders of redfoot tortoises each have stable colonies with no outward signs of illness. They exchange specimens. Subsequently each has an outbreak of diarrhea associated with different flagellated protozoan parasites. Each colony had its own unique “signature” of flagellated protozoans that destabilized the gut protozoans of the other colony. Herbivorous reptiles typically show higher concentrations of flagellated protozoans in their feces than omnivorous or carnivorous species.



Diarrhea to soft unformed feces, mucus or blood in the feces, undigested food particles in feces, regurgitation or vomiting in omnivorous or carnivorous species, loss of appetite, dehydration, weakness, sudden death of one or more reptiles.

Predisposing captive conditions and/or other factors

Unsanitary, unhygienic conditions, particularly warm moist environments, allow rapid transmission of flagellated protozoans through a collection. Handling reptiles and their containers at swap-meets without proper hand-washing facilitates transmission. Some flagellated protozoans may encyst and live in dry harsh conditions for months if not properly disinfected.

Diagnostic tests a veterinarian may recommend

An experienced reptile veterinarian should evaluate fresh feces, regurgitated material, or vomitus. In some cases, the veterinarian may perform a cloacal wash or gastric wash in order to get a fresh sample.

Collect the sample with a damp paper towel, place it in an Ziploc bag, seal it, and deliver it to the veterinarian as soon as practical. Keep the sample either at cage-temperature or room temperature to keep the flagellated protozoans alive and mobile.  If the feces, regurgitated material, or vomitus is not fresh, particularly if it has been chilled or allowed to dry out, the flagellated protozoans may encyst making detection and identification impractical even at specialized diagnostic labs. Multiple samples may be needed to detect some protozoan parasites at low levels.


Screening the feces of seemingly unaffected reptiles should be considered.
The motile forms of flagellated protozoans are best detected in a wet mount of very fresh feces. The slides are view at 100x to 400x magnification with the light condenser of the microscope lowered to enhance the contrast in the field of view. The size, shape, and swimming characteristics help discriminate some genera. For example, Hexamita swim in a rapid straight line and quickly disappears from the microscope’s field of view while other flagellated protozoa that bob around slowly in random directions. If flagellated protozoans are detected at concentrations higher than 5 per high power field (i.e., 400x), they are likely contributing to the illness of the reptile. If white blood cells and red blood cells are detected, even low levels of flagellated protozoans should be considered as contributing to the illness of the reptile.

The finding of even a single Hexamita or Monocercomonas in feces is cause for alarm. It may take multiple examinations of different urine and fecal samples in order to detect these parasites. Once Hexamita or Monocercomonas is detected, all reptiles that have been exposed to this reptile should be considered suspect and testing of those reptiles is suggested.

Feces preserved in polyvinyl alcohol may be submitted to specialized diagnostic labs for more thorough identification where needed. Bloodwork and other tests may be needed to better assess your reptile’s health.

Safe Practices / Prevention

 Isolate: Affected reptiles should be isolated. This helps prevent further spread of the disease and may remove them from stressful competition with cagemates.
 If an infection is confirmed, any reptiles that were cagemates or any reptiles that may have otherwise been exposed to the disease isolated. Screening for that particular pathogen is recommended. If the reptiles do not have the infection detected on tests and appear to be healthy and maintaining or gaining weight over the next 45 days, they may be considered at low risk of carrying the infection. Any reptiles that test positive should be treated. Any reptiles that are losing weight or otherwise appear unhealthy should be kept in isolation until an underlying cause is determined.


 Quarantine: All incoming reptiles should be quarantined for at least 30 days to prevent introduction of disease-causing flagellated protozoans.  At least three negative fecal parasite examinations are needed in this time for the new reptile to be considered a low risk addition to the collection.  As a general rule, a reptile should be eating well, maintaining or gaining weight, free from common detectable infectious diseases, and appear healthy for one month before it is released from quarantine or isolation.

 Proper hygiene and sanitation: Move reptile to simple cage with easy to change substrate and nonporous cage furnishing such as plastic, glass, or metal. Ideally, you should have a separate set of tools that you use on the contaminated cage(s). Handle the contaminated reptiles, tools, cage, and other paraphernalia only after you have finished all activities with your healthy reptiles. Remove urates / urine, feces, uneaten food, shed skin, and other wastes from cage daily. Deep clean the cage and all furnishings weekly with warm soapy water, followed by a 15 to 30 min soak in a disinfectant such as diluted household chlorine bleach (1 cup per gallon of water). Rinse well so that no disinfectant remains on any of the items. Clean any tools used in or around the cage and disinfect as above. Handle infected reptiles and cages only after you have completed all tasks required for your healthy reptiles.


Some reptiles may benefit at this time from a quick bath in dilute povidone iodine solution to reduce the level of infective protozoan cysts that may be on the skin and reduce the risk of re-infection.  Soak the reptile in shallow cage-temperature water first so that it drinks and may also defecate or urinate. Dump out this water and refill. Add povidone iodine to shallow cage-temperature water until it is the color of weak tea. Place the reptile in it for 5 minutes. Gently spread the solution over the reptile’s body but take care to keep it out of the eyes of those species with eyelids. Remove from solution and rinse well with water before returning to cage.

Wash your hands with warm soapy water after handling the reptile. Use a disposable paper towel to dry your hands.

To reiterate, never go back and handle a healthy reptile after you have handled a contaminated reptile. A shower and complete change of clothing is needed to reduce the chance of you spreading the infection.

Treatments a veterinarian would likely recommend

A veterinarian may suggest metronidazole, metronidazole and fenbendazole in combination, or ronidazole for many infections.  Supplemental fluids, antibiotics, liquid diets, and other treatments may be needed depending on the seriousness of the infection.  A post-treatment recheck of feces is needed to ensure the reptile was cleared of infection. Periodic fecal examinations are suggested to ensure the reptile remains healthy and is not re-infected.




Good if caught on a routine health screening, fair if caught early in the course of disease. The outlook is poor if an infection is not responding to initial treatment or if reptile is very underweight and showing signs of systemic infection (high white blood cell counts, anemia, elevated kidney enzymes, etc.) Hexamita and Monocercomonas infections carry a guarded prognosis.


Zoonotic Potential

None known.