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A Florida teenager has beaten the odds, surviving an infection by a rare amoeba that kills nearly all of its victims.

Sebastian DeLeon, 16, was on vacation in Orlando when he started feeling sick.

He had a headache on Friday that got worse by Saturday. His parents took him to a local hospital, where doctors found he was infected with an amoeba called Naegleria fowleri.

The deadly amoeba Naegleria fowleri inhabits freshwater according to the Centers for Disease Control and Prevention. CDC

It's a horrifying diagnosis. "I have treated amoeba cases in the past and ... they’ve been fatal," said Dr. Humberto Liriano, who treated Sebastian.

Doctors at Florida Hospital for Children induced a coma, lowered his body temperature to 33 degrees and gave him an anti-parasitic drug called miltefosine.

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“I had to tell them, just say their goodbyes. I had to tell them, 'tell him everything you want to tell your child because I don’t know from the time I put him to sleep to the time I take the tube out will he wake up',” said Liriano.

“I had to tell them, just say their goodbyes."

But the treatment worked.

"We are so thankful that God has given us the miracle through this medical team and this hospital,” Sebastian’s mother, Brunilda Gonzalez, told a news conference.

"I saw him this morning,” Liriano said. “He's ready to go home. I don't know if I want him to leave yet, but he's ready to go home."

Sebastian is just one of four people in the United States who have survived a Naegleria infection in the past 50 years.

Just last June, an amoeba killed an Ohio teenager who was infected at a North Carolina water park.

The protocol for treating patients is based on the case of Arkansas teen Kali Hardig, who survived an infection in 2013. She was 12 at the time and also caught Naegleria while swimming at a water park.

Related: Brain-Eating Amoeba Remains Rare

Naegleria is found in warm, fresh waters all over the world. It’s been seen in hot springs and swimming holes, freshwater lakes and even in neti pots used to clean out sinuses.

"I saw him this morning. He's ready to go home."

It infects through the nose, traveling up the nerve cells that carry smell signals into the brain. Doctors are not sure how or why a very few people are susceptible, but it’s clear that having water forced up into the sinuses, perhaps by dunking or diving, is an important factor.

The Centers for Disease Control and Prevention has worked with the Food and Drug Administration to make miltefosine available directly from CDC for treating amoeba infections in the United States. The drug, sold under the trade names Impavido and Miltex, was approved to treat a different parasitic infection called leishmaniasis.

Sebastian will need several more weeks of medication and rehab, but is expected to make a full recovery.