Diagnosis: Acanthamoeba spp. encephalitis. This is a subacute disease that occurs mainly in immunocompromised patients, (such as in this case).
Diagnosis can be made from these 2 H&E images by identifying the classic cysts and trophozoites of Acanthamoeba spp. They are typically found clustered around blood vessels, consistent with the hematogenous route of entry to the brain. Note that these double-walled cysts are classic for Acanthamoeba spp., with a wrinkled or stellate outer cyst wall and smooth to slightly irregular inner cyst wall.
Your primary differential diagnosis in this case is infection with Balamuthia mandrillaris. Like Acanthamoeba spp., this ameba causes subacute meningoencephalitis in immunocompromised patients and results in cysts and trophozoites in the brain around blood vessels. However, the cysts have a much thicker outer cell wall than those of Acanthamoeba spp.
Finally, the ameba Naegleria fowleri can also cause human disease. Unlike the 2 amebae mentioned previously, N. fowleri causes fulminant and often fatal meningitis in previously healthy individuals. The 'typical' patient is a child who had recent contact with warm fresh water lakes. The route to the brain is not hematogenous; instead, amebae enter the nose with contaminated water and directly penetrate the cribiform plate. Cysts are NOT seen with Naegleria fowleri infection; instead, only trophozoite are seen in the leptomeninges.