I'd think you'd have to have copies of the same bacteria from prior to nylon to show that the enzyme didn't already exist in some of them doing the job of digesting something else...or having a degree of variability giving it different looks in different individual bacteria.
The enzyme very likely did exist previously to nylon but with another, somewhat related, use. Nylon is a polyamide and amidases are very common in all organisms. I suggest you look up the concept of "enzyme recruitment" and E.C.C. Lin. The enzyme, however, may not have existed in the current bacterium since horizontal gene transfer is quite common in bacteria.
It's not the same bacteria, it digests nylon now. It's evolved.