It is not possible to tell the 2 subspecies of Trypanosoms brucei apart microscopically, but the origin of the patient (Sudan) would be consistent with East African trypanosomiasis due to T. b. rhodesiense.
The flagellated form of T. brucei (called trypomastigotes) are typically seen in peripheral blood, and in late stage disease, in CSF. They can be differentiated from the similar-appearing T. cruzi trypomastigotes by the small size of their kinetoplast (arrows, below).
Occasionally, trypomastigotes of other zoonotic organisms such as T. rangeli can be transiently present in the blood of humans, although they are not usually associated with disease. These trypomastigotes can be differentiated from human pathogens by their morphologic features (e.g. position of the kinetoplast) and geographic location of acquisition.
During the meningoencephalic stage, tissue biopsy typically shows a lymphoplasmacytic perivascular infiltrate containing plasma cells engorged with immunoglobulin. These engorged plasma cells are called "Mott" or "morula" cells. Although they are often seen with meningoencephalitic trypanosomiasis, they are not definitive for this disease and can be seen in other conditions.
Thanks to everyone who wrote in about this interesting case!