That is not how antibiotics work. Well, at least not how all of them do.
If you have a pneumonia (infection of the lungs) you will still get the antibiotics i.v. (intravenous) or p.o. (per os – oral) because the active substances go through the bloodstream to the bacteria.
If you have an infection of the gastrointestinal system you will most likely receive antibiotics p.o., and if you are lucky and your type of bacteria is susceptible to non-absorbable antibiotics than you will get one of those. For example C.Difficile can be treated with Vancomycin which does not get absorbed from your intestines and works only inside the gastrointestinal tract. This will help you not get problems with the bacteria in your skin and mucosa causing mycosis (infections with fungus).
To sum it up: it does not matter how you give the antibiotic (almost never, an exception I have mentioned), it will sadly almost every single time destroy the good bacteria reaching it through the bloodstream.
Side note: there are other options nowadays and we are trying to use local antibiotics. For pneumonia we can also do inhalative therapy. For urinary infections we have some antibiotics that get excreted in urin and for other types of incetions (skin, eyes, ears) we have drops or ointments.
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