It doesn’t. The antibiotics go through your entire body. Most antibiotics work by penetrating the cell wall of the bacteria that is causing the infection. You take a pill (or sometimes and IV infusion) and the antibiotics get into your blood stream. When they come across the bacteria, a chemical reaction occurs that kills the bacteria. But it does not “know where to go.” It just goes everywhere. This is why stomach problems are a common side effect of antibiotics. Your gut relies on a robust variety of bacteria living inside of it to help you digest food. Antibiotics inherently weaken those bacteria colonies and some people get sick as a result of it. The goal on developing antibiotics is to develop kinds that tend to work really well on the infectious microbes and not very well on the good bacteria in your body.
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