There are many things which can cause lameness and it sounds like your vet might need to do more tests or just try a few things to see what works. Basically MRSA is a normal bacteria carried by some people and animals. It usually only causes a problem if it gets from the skin into the blood stream or other tissues through wounds or surgery. It can’t have lain dormant in the joint for this time but if your dog is a natural carrier and had a small wound which went unnoticed it could have got back into his body from the skin. I’m sure your vet wants to be on the safe side and rule out possible causes of lameness like infection which could get severe if left. You may find he wants to do a joint tap at some point to see if any infection or other causes are present. It can be very difficult to find the cause of lameness because sometimes you concentrate on one joint which seems obvious and it turns out to be something else altogether. Make sure your vet also knows if you’ve been abroad with your dog in the last few years because some of the more exotic diseases like Lyme’s disease (which is also present in this country) can present as lameness. Good luck and let us know what happens if you get time.