Have a look at Chapter 38 in my Grey book, where most of the nasty
things that can infect Drosophila are at least mentioned - including
Hamp's microsporidia (which are now fungi rather than protozoa).
Entomophagous fungi are welll known and there has been some work on
them, but I have never seen them be a lab problem, tho, like Hamp
I have seen them (but rarely) in wild caught flies.