I don't know which article you're referencing, but we also had brain parasites found in a man who died about 50 miles from me in Indiana. We've basically been told to avoid freshwater lakes and rivers for now.
Those freshwater incidents sound like protozoa (amoeba) infections with an high mortality rate ("Brain-eating amoeba suspected in Indiana death"). GP is referring to another hazard, also seems to be from nasty water. http://news.ycombinator.com/item?id=4492244. Don't say you weren't warned though !
