Tough one. Do you know for certain that it's going to be antibiotics for a long long time?
Dogboy is right, urine therapy is not recognise as valid by the medical world. You doctor will very likely tell you not to do it - not on antibiotics and not ever.
I've done a quick search on "antibiotics urine" and it appears antibiotics do filter into urine. Which means that if you drank it, a small proportion of the antibiotic you take would get back into the system. How much, and would that be a significant proportion is anyone's guess.