This is more confirmation, but it has already been known in the microbiology community for some time.
Many of the genes that contribute to antibiotic resistance are far older than human use of antibiotics.
How can that be? A couple ways. Mom Nature has been playing the antibiotic game for a very long time. Most of our antibiotics come from antibiotic producing organisms in nature (penicillin for example). The countermeasures have long been out there, but only in a small percentage of the bacteria out there, since there is a small cost to maintaining any given gene. When there is a big exposure to a particular antibiotic, the resistance genes spread through the bacterial community and become common, as we often see nowadays.
The other source is that an enzyme that is used for some other purpose may well have some ability to protect against an antibiotic. An example would be a transporter molecule for some substance other than the antibiotic to be pumped out of the cell that is close enough to sometimes pump out the antibiotic. There would then be strong pressure for the bacteria to make more of that transporter protein when the antibiotic is around. Nature is good at using something it already has for a new purpose.
That's one of the reasons antibiotic resistance is such a problem. Mother Nature has been playing this game a very long time and frankly is better at it than we are.