The family of a Florida boy left brain dead by a water-borne parasite said they believe that "God will step in."

It's been two weeks since doctors diagnosed 12-year-old Zachary Reyna with primary amoebic meningoencephalitis, a rare and almost-always-fatal form of meningitis caused by the amoeba Naegleria fowleri.

Only two people in North America are known to have survived the infection, according to the U.S. Centers for Disease Control and Prevention. A 12-year-old girl from Arkansas, Kali Hardig, is set to be the third survivor after showing signs of recovery last week, and Zachary's family still hopes he will be the fourth.

"We respect the doctors protocol but we continue with our faith and believe God will step in on his time irregardless of what has been said," the family wrote Sunday on the Facebook page "Pray4Number4." "We ask that you continue to pray and believe along with us."

Warm Weather Stirs Up Amoeba Warning

The plea for prayers came one day after the Reyna family announced that Zachary's "battle is over" in a Facebook post.

"At 1:54 today there was a crack of a bat heard. Zac took it deep. My boy hit his homerun. One that I'll never forget. I'm so proud of him. He left it all on the field and I can't ask for more," the post from Saturday reads. "He did so well that he'll be the starting 2nd baseman for The Lords team."

The family invited friends and family to visit Zachary Sunday at Miami Children's Hospital, where was being kept alive by a ventilator so that his organs can be donated.

"Even though Zac has passed, he will still be saving many lives," a Facebook post reads.

It's unclear whether Zachary is still connected to the ventilator.

Read more about Zachary's battle with Naegleria fowleri.

Naegleria fowleri thrives in warm, standing freshwater and the sediment of rivers and lakes. And while it's usually harmless, it can cause fatal brain swelling if inhaled through the nose.

Zachary is thought to have contracted the brain-eating amoeba while knee-boarding in a ditch near his family's home in LaBelle, Fla., ABC affiliate WZVN-TV reported. The Glades County Health Department confirmed the diagnosis Aug. 12.

"This is a very rare occurrence," county health department spokeswoman Brenda Barnes told ABCNews.com. "This amoeba is out there. It could be anywhere in any warm, fresh water."

Early symptoms of a Naegleria infection include a severe frontal headache, fever, nausea and vomiting, according to the CDC. But those can swiftly give way to a stiff neck, seizures, confusion and hallucinations as the amoeba makes its way up through the nasal cavity into the brain.

"After the start of symptoms, the disease progresses rapidly and usually causes death within about five days," the CDC's website reads. "People should seek medical care immediately whenever they develop a sudden onset of fever, headache, stiff neck and vomiting, particularly if they have been in warm freshwater recently."

Read about Kali Hardig's first words after contracting Naegleria.

Zachary's family initially thought the boy had a virus, according to his brother, Brandon Villarreal.

"I wish I could just touch him and it would transfer over," Villarreal told WZVN. "It don't work like that."

Rachel Perry, a spokeswoman from Miami Children's Hospital, told ABCNews.com she was not authorized to comment on Zachary's condition.

"Miami Children's Hospital expresses heartfelt condolences to this devoted family," the hospital said in a statement. "We respect the family's wishes and honor their privacy at this time."

Zachary Reyna, 12, was diagnosed with primary amoebic meningoencephalitis. (ABC News)

ABC News' Alexis Shaw and Sydney Lupkin contributed to this story.