Maybe your dog is having a problem holding it with all her medical problems. I am no dog expert so hopefully others will chime in. But maybe you can try putting the puppy pee pads somewhere so that she can use that if she has to go and can't wait for you to take her outside.

This is an area rug, correct?

Since you know your dog has a bladder infection, what I would do is to roll up the rug and move it out of the way for now and, as trinigemini says, put down pee pads until her infection has cleared.

If your flooring surface is wood, you might want to lay down a piece of plastic, such as one of those drop cloths you can buy at Home Depot for a couple of bucks, to protect the wood and put the pee pads on top of the plastic. If the flooring surface is ceramic tile or vinyl, I would just use the pads and clean it with floor cleaner as normal.

Once you are sure she is well, remove the pads and see if she goes back to using the great outdoors. If not, you may need to re-house train her. Wait until you see she is no longer going inside before you put the rug back.

Before putting the rug back, I would take it in to a carpet cleaning company for a "deep clean", especially since you paid good $$ for it.

Hope this helps!

If you could expand on the dogs meds and other problems it might make it easier to help. Could me a physical problem which is unresolved, it might be a side effect of a medication and it may be behavior or due to lack of exercise...need more info please.