This answer is actually pretty simple in most cases: it doesn’t.
The medicine you take by mouth will get digested and then enter the blood steam where it circulates throughout your whole body (but maybe not your brain… It’s hard to get medicine into the brain).
If you have a throat infection, you might see the buildup of bacteria on your throat, but they aren’t just on the outside of you, they are inside of you, too. By circulation of antibacterial medicine throughout your whole system, you kill off that bacteria (and other bacteria) everywhere.
Notice I said and other bacteria, as well… This is why most antibiotic medication will have a warning to take it with food, because it typically causes an upset stomach. That upset stomach is caused by multiple factors, but one of them is the antibiotic medication killing the microbiota in your digestive tract.
Everything that I just said above, for the most part, is specifically for oral medication (stuff you take by mouth).
The rules change a little bit when you’re talking about topical ointments, eye drops, or injectables. It gets even crazier when you start talking about some types of anti-cancer drugs, that are designed to essentially build up in tumor tissue, but not stick around in the rest of your body. I’m going to skip those explanations for the moment, because doing that in an ELI 5 fashion is going to be tricky.
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