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A 15-year-old native of nearby Panavalli was infected with the disease called primary amoebic meningoencephalitis, it said.
Additional information regarding the patient was not made available by the government.
The disease was earlier reported in the Alappuzha municipality area in 2017, the health officials said.
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Considering the severe nature of the disease, the district health officials have advised people to avoid taking bath in contaminated water. The main symptoms of the disease are fever, headache, vomiting, and seizures.