The idea is that it kills 99% of them, and then your immune system is up to the task of killing the remaining 1%.
That most virulent 1% then multiplies and infects systemwide... and adds new mutations all the time.
This is true not just for bacteria but also for other living creatures; for example animals that have lots of children have very short average lifespans.
It makes me think that every living species must be at the absolute cutting edge of its capabilities genetically-speaking.