Think of it like a game of tag. The antibiotic needs to tag all the bacteria to win, but that takes time. You will stop feeling sick when most of the players are gone from the field, but that just means the ones left can figure out how the person who is “it” works. If you don’t eliminate them too, they can join new games of tag on other fields and now they have strategies on how to avoid getting caught.
It’s not a perfect metaphor, but I think it covers all the main points.
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