Naegleria is a free-living amoeba which can enter the brain through the nasal passages. Once established, it is 100% fatal and usually kills within weeks.
The good news is that it is rare, requires very warm water, must be inhaled into the nose (and even then, infections are uncommon) and is easily killed by chlorination.
In the northern part of the country, Naegleria deaths are very,very rare and typically occur in over heated and under-chlorinated pools (the two often go hand in hand, in that over heating tends to drive off the chlorine).
This year has seen more deaths than average in the south, but the disease is still extremely unusual. Like hanta virus and plague in the Southwest, sporadic cases of amoebic encephalitis occur from time to time, but brain amoebiasis is not a major public health concern. Like rabies and plague, it is a dramatic and lethal illness that garners more media attention than the general risk it poses deserves.
The key is to be sure to keep hot tubs and heated pools properly chlorinated (it is wise never to immerse your head in a hot tub at all). The risk from very warm freshwater bodies of water is harder to assess and impossible to eliminate, but that risk is still quite low.
A good friend of mind, recently diseased, was one of the world's leading experts on this infection.
