The resistance is not part of the "original" gene code. This is proven by experiment.
New mutations spontaneously appear in the population and sometimes these mutations offer protection against antibiotics.
In the past it was assumed that this is what happened but now, we have the ability to examine all the genes of bacteria and we can find the exact mutation that causes resistance and we know that it was not present previously.
But you are right, we could breed them until doomsday and bacteria will always be bacteria - different kinds of bacteria maybe, but bacteria nonetheless.
A difficult thing to grasp about evolution is that it does not involve cats evolving into dogs or crockoducks. It is about species splitting and becoming different from each other.
If you consider humans and chimps. According to theory, humans did not evolve from chimps. Chimps and humans share a common ancestor which was a primate and even though humans and chimps have evolved in our own direction for six million years we are still primates. We will always be primates.
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