Bring your own cup to drink coffee from roadstops. At restaurants, eat only cooked food. Yeah, those salads and seafood dishes look tempting but they are nothing but trouble. The African forms of sleeping sickness do not exist in Madagascar as there is no tsetse vector. There is the Trypanosome organism that only affects chameleons.
Cerebal malaria is a problem for humans.
Other than immunizations, there are protective measures that you can take to decrease your risks from becoming infected with malaria and other insect-borne diseases. Another way to prevent diseases such as malaria is to dress appropiately. Use tiger balm or calamine lotion to reduce itching if bitten. The foregoing hints on eating will help. Another tip is that you order your meat to be cooked well-done.