As summer nears, Australian rural healthcare workers are being advised to be on alert for a deadly brain disease after the death of a baby boy in Townsville.

Doctors are urged to be on alert this summer for a very rare but deadly brain disease in children that is contracted by swimming in lakes and rivers.

The warning follows the death of a 12 month-old boy at Townsville Hospital, Australia's latest victim of primary amoebic meningoencephalitis (PAM).

From a nearby West Queensland cattle-farming area, the baby boy was unable to breathe on his own within 18 hours of leaving home with a persistent high fever and lethargy, and died in 2015.

PAM is caused by Naegleria fowleri, a brain-eating amoeba - a type of organism - found in warm fresh water, such as ponds, lakes, rivers, hot springs and poorly maintained municipal water supplies.

Rural and remote communities are particularly at risk, where hot bore water and long surface pipelines promote the growth of large concentrations of Naegleria fowleri.

Infection occurs when water enters the nose and attacks the central nervous system.

The first confirmed case of PAM at the hospital was an 18-month-old girl from a rural location in North Queensland who presented with fever, seizures and an altered level of consciousness. She died within 72 hours of being admitted.

Tragically her older sibling, who died several years prior, was retrospectively diagnosed with PAM.

PAM is rare, but it is fatal in 95 per cent of cases. It is also very difficult for doctors to diagnose as the symptoms are identical to those of bacterial meningitis, including high fever, confusion and seizures.

Research presented at the International Congress for Tropical Medicine and Malaria and published in the Medical Journal of Australia highlights a need for greater awareness of PAM among doctors, says Dr Claire Nicholls.

Dr Nicholls, who works as emergency registrar at the Townsville Hospital, hopes better education will lead to more medical practitioners testing for the rare disease.

With summer approaching, it's vitally important that doctors and communities be aware of PAM and respond immediately, says the president of the Australasian Society for Infectious Diseases, Professor Cheryl Jones.

"Any acutely unwell child with a history of bore water exposure and signs of meningitis or encephalitis should be considered for PAM as a potentially life-threatening diagnosis," said Prof Jones.

"Families should avoid swimming or diving into warm fresh water or to hold their nose if this can't be avoided," she said.