The only method I can think of that would seal it would be to take a large number of bacteria and allow them to found seperate large colonies and then poison them.
I'm sure that this is precisely what was done in the early days of such experiments - this, and the fact that only a tiny fraction of the poisoned bugs typically survive. Nowadays, they can actually identify the specific DNA change, the protein change it causes, and the monkey wrench that that protein change throws into the works of the antibiotic.
I can imagine, too, that the survivors on a Petri dish might be well away from the spot where the great-grandma bacterium was put. That alone would strongly suggest that the resistant strain wasn't there at the point/time of colony start-up.