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Mridul died at 11.20 pm on Wednesday, Kerala State Health Department said on Thursday.
This is the third case of fatal infection reported in the State since May. The first instance was the death of a five-year-old girl from Malappuram on May 21 and the second a 13-year-old girl from Kannur who died on June 25.
According to the health department sources, the child had taken a dip at a small pond here and preventive measures were being taken.
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The health authorities have advised people to exercise caution against amoebic meningoencephalitis.
The disease was earlier reported in coastal Alappuzha district in the state in 2023 and 2017.