Drugs only stay in your body for a limited time, and it takes time for them to find their targets. The drugs and the bacteria pretty much have to randomly run into each other in your bloodstream or wherever. So if you took it all at once some of the bacteria would survive no matter how much you took. Taking the meds over a period of time keeps a supply in your body long enough to kill all the bacteria, or to kill enough that your immune system can handle the rest. Good question tho. It makes sense to wonder how this works.
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