Strains of bacteria that are resistant to medicines become that way because people don't finish the entire course of meds. The more susceptible bacteria are killed, but some hardier ones can live on and reproduce.
All species mutate, and if the mutated ones are more viable that the original, they becomes the dominant ones. They don't develop defenses.

As to which came first, the chicken or the egg, the egg might've been laid by something that wasn't quite a chicken, but if it's a chicken egg, (and barring genetic experimentation) it's definitely going to hatch out a chicken.