Flagellates (Giardia muris, Hexamita muris, Trichomonas)
In laboratory animal facilities, parasitic infections are highly prevalent, with intestinal flagellates being the most common. It is estimated that up to 33% of non-research-related deaths in animals are linked to chronic, recurrent enteritis, often manifesting as symptoms such as diarrhea, weight loss, dehydration, and stunted growth. National standards also explicitly require that SPF-grade mice and rats be free from this flagellate pathogen.

Data source: Suzhou Xishan Biotechnology Co., Ltd.

Pathogens and Epidemiology
Among flagellates, the three that have received the most attention are Giardia lamblia, Hexamita muris, and Trichomonas. Giardia lamblia is commonly found in the anterior section of the small intestine and features a short median body located near the middle of its axial filament. It exists in two distinct forms—trophozoites and cysts—and can switch between these two stages. When an animal excretes its feces, the cysts become infectious. If a host ingests water or food contaminated with these infectious cysts, it will become infected. Once inside the host, the cysts release trophozoites, which then migrate to the large intestine before transforming back into cysts, ultimately being expelled along with the host's feces to initiate the next cycle of infection. Hexamita muris is also predominantly found in the anterior portion of the small intestine; it possesses five anterior flagella and one posterior flagellum, along with a conspicuous oral groove, a distinctive shield-like structure, and a prominent parabasal body. Axial filaments are clearly visible and extend outward from the cell. As for Trichomonas species, there are several types, including Trichomonas muris, Trichomonas hominis, and Trichomonas tenax. Both Giardia lamblia and Hexamita muris spread primarily through direct contact with infectious cysts or pseudocysts during their respective transmission stages.

Trichomonas under a 40x microscope

A six-flagellated mouse trichomonad under a 40x microscope

40x Magnification of Mouse Giardia

Laboratory diagnostics
In laboratory diagnostics, stool or intestinal contents are typically used for smear testing, where diagnostic identification is made by examining the concentrated cysts or trophozoites present in the stool or intestinal samples. Alternatively, polymerase chain reaction (PCR) amplification can also be employed for diagnosis.

Prevention and Removal
In recent years, parasitic infestations in animal facilities remain a widespread issue. Facility managers should conduct regular screenings of animals, and newly introduced animals must undergo quarantine and health checks before being allowed into the facility. Strict adherence to facility rules and regulations is essential to prevent wild animals from entering and causing unnecessary losses. If flagellate infections occur within the colony, it is recommended to carry out thorough environmental disinfection—removing all fecal matter from the premises—and follow up with chlorine-based disinfectants. For infected animals, appropriate purification measures should be implemented; for valuable specimens, medications such as metronidazole can be used for treatment.
References
Fu Jie, Liu Xiongwei, Lu Guoping, Gao Cheng. Light and Electron Microscopic Observations of Flagellates in the Rat Intestine. Shanghai Journal of Laboratory Animal Science, 1998, 18(3,4): 150–152
Laboratory Animal Epidemiology
Gao Cheng, Fu Jie, Wang Shengchang. Species and Identification of Intestinal Flagellates in Laboratory Rats and Mice. Acta Parasitologica et Entomologica Medica 1999, No. 3
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