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The CDC says it's found Naegleria fowleri, an almost always deadly amoeba, in a U.S. drinking water supply for the first time. Centers for Disease Control and Prevention

A deadly brain amoeba that’s killed two boys this year has been found in a U.S. drinking water supply system for the first time, officials said Monday -- in a New Orleans-area system.

The Naegleria fowleri parasite killed a 4-year-old Mississippi boy who likely got it playing on a back yard Slip 'N Slide, Centers for Disease Control and Prevention officials say. Tests show it’s present throughout the water supply system in St. Bernard Parish, directly southeast of New Orleans.

“We have never seen Naegleria colonizing a treated water supply before,” said Dr. Michael Beach, head of water safety for the CDC. “From a U.S. perspective this is a unique situation.”

N. fowleri is a heat-loving amoeba that’s usually harmless, unless it gets up someone’s nose. It’s not entirely clear how or why, but in rare instances it can attach to one of the nerves that takes smell signals to the brain. There, the amoeba reproduces and the brain swelling and infection that follows is almost always deadly.

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It killed a Miami-area boy last month -- 12-year-old Zachary Reyna -- and a 12-year-old Arkansas girl, Kali Hardig, is recovering slowly after an unusual experimental treatment.

N. fowleri is usually 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. Incomplete disinfection probably allowed it to thrive in St. Bernard, which has its own independent water system, Beach says.

“The key to this is understanding that this amoeba is kind of a heat-loving bug,” Beach said in a telephone interview. “If water temperatures start going up, you really need to be extremely careful about maintaining the disinfectant. The farther you go from a plant, the more likely you are for the disinfectant levels to get low.”

That’s what apparently happened in St. Bernard, which takes water from the Mississippi River and cleans it up for people to use. “We want all communities … checking the peripheries of their water distribution system,” Beach says.

N. fowleri has only been reported in about 130 people in the U.S. since 1962, making it extremely rare. Kali Hardig is only the third person known to have survived infection. It was formally identified in 1965, in Australia, where it did contaminate drinking water systems for a while, says Beach.

“In Australia, it was basically water being pumped from rivers and overland,” he says. The water got warm over long distances across the desert, and the amoeba thrived. Three children died after being immersed in baths and wading pools. Better disinfection has meant no cases since 1981, Australian health officials say.

Lousiana health department spokesman Ken Pastorick says officials are flushing out and decontaminating the St. Bernard Parish system, a process that may take several weeks.

“They have shocked the water, so to speak,” Pastorick said. “What has caused the problem here is low chlorination.” Pastorick says other Louisiana water systems are safe.

Beach says it’s not necessary to test water systems for the amoeba. Proper chlorination should always take care of it, he says.

And he stresses that water is safe to drink and bathe in even if it’s contaminated. Stomach acid appears to kill the amoeba, and people can protect themselves by not snorting water up their noses, or not allowing it to be forced up the nose.

St. Bernard water customers are being cautioned not to fill kiddie pools with tap water, or to use other water toys such as the sliding game that the 4-year-old boy who died was playing on. Topping up swimming pools with hoses is a bad, idea, too, unless the water first goes through the disinfection system.

“The critical piece is kids in the water,” Pastorick says.