A popular treatment for sinus congestion has been linked to a rare brain-eating amoeba, which the FDA has linked to two deaths in the U.S.

The Food and Drug Administration has warned consumers about using tap water in neti pots -- a device with a long spout that is used to rinse nasal passages with a saline solution.

The agency warned that un-filtered tap water can contain bacteria, including amoebas.

While stomach acid is quick to kill the bacteria ingested through the digestive system, the “bugs” could stay alive in the nasal passage and cause serious infections, according to the Centers for Disease Control and Prevention.

A warning on the FDA website posted Thursday states: “Improper use of neti pots may have caused two deaths in 2011 in Louisiana from a rare brain infection that the state health department linked to tap water contaminated with an amoeba called Naegleria fowleri.”

Naegleria fowleri is also referred to as the “brain-eating amoeba.” A 2010 study from Stanford University states that the amoeba can cause primary amebic meningoencephalitis in humans, of which 98 per cent of cases end in death. On average, victims die of the infection only one week after symptoms such as headaches, fever, nausea and vomiting appear, according to the study.

The FDA warning extends to all nasal-rinsing devices, which include bulb syringes and squeeze bottles.

While the devices are generally safe, the agency said they must be used and cleaned properly.

The FDA also warned that some manufacturers’ instructions recommend using tap water in the devices, while others warn against it. Some manufacturers do not provide any instructions or information with the items, the FDA noted. 

It’s recommended to use distilled, sterile or filtered water in any sinus-rinsing product. Consumers can also use boiled tap water that’s been cooled.

 “The nose is like a car filter or home air filter that traps debris. Rinsing the nose with saline solution is similar to using saline eye drops to rinse out pollen,” said the FDA’s Dr. Steven Osborne on the agency’s website.

He said saline enables the water to pass through delicate nasal membranes with little or no burning or irritation.