MERSA is pretty uncommon unless you’ve already got it and don’t know it or you’re hanging out in hospitals or prisons a lot. Regular old staph infections would make sense though.
It also occurred to me that while CDDA is supposed to be set in New England, there are a few other disease-carrying critters that could be interesting: Squirrels (black plague, in the American South at least) and Armadillos, which often have leprosy.
On the subject of whether or not diseases add something to the game- I’d say they do, as long as they’re implemented properly. I agree that arbitrarily coming down with something that kills or incapacitates your character is no fun, so all of these should be preventable, relatively minor, or treatable with some doing. (even if treating leprosy just means replacing stuff with bionics… hmmm…) For instance- it should be relatively hard to catch tetanus from stepping on things if you’re wearing combat boots (or any other footgear with the “tough” descriptor)