Okay, this caught my attention. I won’t say this is the issue, since it could be something else, but small flies can be a very big problem if they’re not just fruit flies. There are other types of small flies, called Phorid flies, that can do some very, very horrific things. I suggest reading the following:
If the currently symptomatic animal ends up passing, a necropsy would let you know if the flies could be your issue. Otherwise there’s a few other bacteria and things you can test for, has there been any diarrhea or mucus in their feces?