A 10-year-old girl has died in hospital in the US after contracting a rare "brain-eating" amoeba while swimming in a river.

Key points: The amoeba is present in fresh water across Texas but officials say deadly cases are rare

The amoeba is present in fresh water across Texas but officials say deadly cases are rare Lily Mae came down with a headache and fever before her condition deteriorated

Lily Mae came down with a headache and fever before her condition deteriorated She died roughly a week after she started experiencing symptoms

Lily Mae Avant swam in a river and lake in Texas over the US Labor Day holiday weekend then came down with a headache and a fever a week later, on September 8.

A Facebook group called #Lilystrong was created on Thursday to update family, friends and wellwishers on the 10-year-old's condition.

"After hearing what they thought were sounds of Lily having a nightmare in her sleep, [Lily Mae's mother] quickly realized Lily was beginning the fight of her life," one post said.

"She was incoherent, unresponsive and was quickly swept up and taken to the [emergency room].

"Her spinal tap revealed that she actually contracted a very rare amoeba that is aggressive with a high fatality rate."

Her health quickly deteriorated, and she was taken to a local hospital before being transferred to Cook Children's Hospital in Fort Worth.

By Monday, the infection had killed her, a statement from her family said.

The 10-year-old's symptoms began two weeks ago and her condition declined rapidly. ( Facebook: Dustin Yadon )

The Texas Department of State Health Services told local media Lily Mae had contracted primary amoebic meningoencephalitis, a brain infection caused by the so-called brain-eating amoeba Naegleria fowleri.

The first symptoms of the infection typically appear about a week after the amoeba enters the nose.

"The amoeba is present in freshwater across Texas and elsewhere in the US, and there's no particular body of water that would present a greater risk," agency spokesman Chris Van Deusen told television station KWTX.

"Cases are extremely rare, despite the millions of people who swim in lakes and rivers every year."

The family wrote on Facebook Lily Mae was now "in the arms of Jesus".

"Words cannot begin to express how overwhelming this past week has been for our family," the family said.

"We have been flooded by your love and support and feel incredibly humbled by how many lives have been impacted by our sweet and sassy Lily Mae."

AFP