Kerala health Secretary Rajeev Sadanandan said all stranded citizens had been rescued and about 196,000 people were sheltered in the 3259 camps across the state.
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The state also had a surplus of antibiotics, which would be ramped up to 100 percent efficiency, Sadanandan added.
Infections such as leptospirosis and chicken pox can spread rapidly, especially in congested habitations such as rescue camps.
While the focus will now shift to rehabilitation, the immediate concern was to provide medication for people dependant on drugs such as insulin and hypertension drugs as prolonged denial of such drugs could lead to further complications.
The government would also check up on patients that were suffering from tuberculosis to continue on its path to complete eradication of the disease in a few years, the health secretary added.