The rare condition is not contagious, but it is usually fatal, said Dr. Jaime Carrizosa, an infectious disease specialist at the hospital.
"We're doing everything we can for him, but this is a very serious infection," Carrizosa said. "Once inside the body, these amoebas just divide and divide, and you will have an overwhelming infection very quickly."
Although the state has counted only 19 cases since 1962, the infectious amoebas are common in Florida's freshwater lakes and rivers. Doctors say they get into the brain after the swimmer takes them into his or her nostrils.
The amobebas live in the material on the bottoms of freshwater lakes, rivers and hot springs, and have also been found in swimming pools which have not been chlorinated.
The boy, who has not been identified, apparently picked up the infection at either Long Lake Park in Oveido or in the Conway Chain of Lakes in Orange County where he has been swimming recently.
Health officials said it did not make much sense to close a lake because of the amoebas, because so many bodies of water are infected. A 1999 study found that 46 percent of the lakes sampled contained the organism.
"If we wanted to avoid all potential exposures to this organism, we would have to close all bodies of water in the state of Florida," said Dr. Steven Wiersma of the Florida Department of Health.
Headaches and nausea are the first symptoms, followed by seizures and coma.
Doctors said little is known why one person will become infected and another will not. One theory is that it takes a lot of water jammed into the nasal passages, perhaps by falling off water skis or jumping into the water.