I'm inclined to think it's more of a very slow shift towards an unhealthy balance. And then once it gets to a certain point, the baddies start producing enough toxins that kill the good ones even further and they finally rule the environment.
Also, consider that you might take Antibiotics oral or with a shot to knock out an ear infection so it clearly is transported via blood vessels, so, the Antibiotic circulates everywhere and kills whatever specific class/type of bacteria it finds - so most Antibiotic are systemic.