Authorities have not released the name, age or gender of the infected individual.
The amoeba, called Naegleria fowlerii, lives in warm freshwater. When ingested through the nose, the amoeba travels to the brain causing a rare, but deadly infection.
Out of 133 known cases of the amoeba in the United States from 1962 to 2014, only three people have survived, according to the CDC.
Confirmation of the Florida case comes just four days after 11-year-old Hannah Collins died from the amoeba after swimming in a river in South Carolina.
More articles on infection control:
HHS diverts $81M to fund Zika vaccine research
Florida Zika outbreak could reach Puerto Rico outbreak’s levels, virologist says
Too much of a good thing? Not possible for hand hygiene compliance, study finds
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