Entamoeba histolytica is an anaerobic, protozoan, intestinal parasite responsible for a disease called amoebiasis. It usually occurs in the large intestine and causes internal inflammation. It belongs to the genus Entamoeba and class Archamoeba. Amongst parasitic diseases, E. histolytica is one of the leading causes of morbidity and mortality in developing countries. E. histolytica is transmitted by ingestion of exit body containing cysts from faecally contaminated food and water or from hands. Due to their protective walls, the cysts can remain viable for several weeks in external environments. Species within this genus are small, single celled organisms with an anterior bulge representing a lobose pseudopod. The E. histolytica trophozoites are oblong and approximately 15-20µM in length, whereas the cysts are spherical and typically 12-15 µM in diameter. Entamoeba cysts are most commonly transmitted by ingestion so must be extremely robust to survive the hostile environment of the stomach. The cysts transform to trophozoites in the small intestine where they multiply by binary fission to then colonise the large intestine. They cause major calcium ion influx to the cells of the large intestine resulting in cell death and ulcer formation. The Trophozoites subsequently form new cysts which are excreted once more in faeces. Infection with E. histolytica generally causes mild symptoms such as abdominal pain, flatulence and diarrhoea, but more severe infections can lead to amoebosis. This is a condition encompassing amoebic dysentery characterized by severe abdominal pain, fever and blood in the faeces and less commonly amoebic liver abscesses.

Spironucleus muris is a flagellated protozoan belonging to the family Hexamitidae which commonly infects laboratory rodents. S.muris is found primarily in the crypts of the duodenum and pyloric glands and infection does not usually show any clinical signs. However, immunedeficient or weanling mice may exhibit diarrhoea, dehydration, weightloss, rough coat, lethargy, abdominal distention, hunched posture and sometimes death. S.muris has a direct development and transmission occurs through contact with infective cysts, most commonly through the faecal-oral route through ingestion of infective cysts. As little as one cyst is enough to cause infection. Prevalence of S.muris in laboratory and wild mouse populations ranges from 4 to 39% and large numbers of S. muris are often an indicator to an underlying disease or infection such as an MHV infection. Additionally, presence of the pinworm may indicate poor biosecurity management. As a result, fast and accurate diagnosis using real-time PCR would greatly aid those keeping and working with laboratory rodents.