For Faerun I generally accept a very advanced level of medical knowledge. Magic can do everything modern science can do (plus a whole lot more) including regenerating limbs, curing any disease (viral or bacterial) and even bringing people back from the dead.

Cities like Sigil and so forth have travelers from all over the planes (including technologically advanced species). There is literally a portal to Stardock in undermountain.

Id presume advanced centers of medical knowledge (Waterdeep) would know about bacteria, viruses and so forth, but have never taken that next step of penicillin etc due to any cleric of 3rd level or higher being able to simply cure all disease via lesser restoration (and a Paladin using 5 points of LoH to do the same).

Got HIV, Malaria, Zeka, a bacterial infection or even cancer? Nothing a rank and file cleric of your local faith cant fix for you.