Answer: Granulomatous amebic encephalitis due to Acanthamoeba species/Balamuthia mandrillaris
The characteristic features of this case include predominance of organisms around blood vessels (reflecting its hematogenous route of dissemination) and presence of both characteristic cysts and trophozoites.
It is not possible to differentiate Acanthamoeba species from B. mandrillaris, and therefore additional testing was performed. This cases tested positive for Balamuthia mandrillaris by both our in-house and CDC's real-time PCR assay for free-living amebae. Dr. Ali at the CDC also confirmed the findings using an indirect immunofluorescence assay. Note how the trophozoites beautifully light up using B. mandrillaris-specific fluorescent-labelled antibodies.