Mepron and malarone are almost the same. They both contain atovaquone but malarone contains a second drug. Proguanil(another antimalarial).
You get far more atovaquone from 2-3 teaspoons mepron per day versus the lower dose of you get from 2-4 pills of malarone( and i'm talking about a lot more). You can't go much high with the malarone because it contains proguanil. You can't go very high with proguanil(minimum safe levels). Honestly though. I'm sick of seeing LLMD's prescribe malarone. It was designed solely as a preventative drug to be taken before you enter a zone with possible malaria. Such as on vacation or what not. It is a replacement for Doxycycline. Doxy used to be the malaria prentative drug of choice before going into a malaria known region.
That doesn't mean i'll let mepron off the hook. Both of them have the ability to make babesia go away, 9 times out of 10, it is only temporary. But it almost always(i'm not saying in all cases) comes creeping back. Plus you will piss off your insurance company, it costs about $600-800 per bottle. Not saying that insurance companies shouldn't pay for anything you need. But when you keep going through tons of mepron and they start to get the bill. They might look further into things and possibly cut you off or report your lyme dr. Who knows what the jerks might do after they read the IDSA guidelines. However, very little is known about babesia so they usually don't question it. Also, just because babesia is similar to malaria, it does not mean the popular malaria eradication drugs will work against babs.
If you have the prescription, i'd say go with it. It will help out a lot but don't count on malarone or mepron to bring you victory over babesia.
Also, be 100% sure you eat something with a natural fat such as cheese or milk with the mepron. Long story but if you don't, you will have very small amounts of atovaquone making it into your bloodstream. 85% or more would just end up in the toilet. Atovaquone dissolves in the fat and the fat crosses through the stomach and intestinal cells carrying the atovaquone with it.