Yes, there are germs. As for germ theory, most healers, sages, and priesthoods know about cleanliness and infections, and* what they call "contagion" (you can catch things from other afflicted beings).
*=thanks to plagues
For a brief overview, see my EGPEl'sFR book.
#realmslore
Quote
Alexander DeGroot
@SomeYappingDork
@TheEdVerse A bit of a weird question that I need an answer to for a dumb joke in a campaign: Does the Forgotten Realms have Germ Theory? Are there even germs, or does something else cause illness?