The greatest challenge the colony has to endure is the "happy valley fever", or malaria, outbreak. Many important characters die from malaria, and May-may loses her baby.
Malaria was a devastating disease in the tropics. Until the discovery and wide use of quinine (cinchona, in the book), malaria was devastating. They didn't realize that malaria was caused by a parasite till the 1880s, and that mosquitos are the source till 1897. Scientists who forwarded the treatment of Malaria won many Nobel Prizes.
There are a lot of tense moments in the book, as we're waiting to see whether the priest will arrive with the cinchona bark in time to save May-may's life, and then to see whether the cinchona will actually cure malaria.
We're most familiar today with quinine as tonic water - that amazingly bitter-sweet mixer often combined with gin. Tonic water by itself is an acquired taste, but one that's hard to break.