Length of time on antibiotics

I am helping a friend with a now 5 mo qh colt. At roughly 2 1/2 mo old my friend was turning them out (letting baby follow) when he ran the opposite direction and wiped out on macadam. He opened up knee in front (now healed) and opened up his stifle area which left a huge pocket of space filled with gravel below his patella. He was on death's door many times in the last 9 weeks, scariest for me was the 104 temp for 5 days. A month ago the culture revealed 3 types of bacteria, we are down to one, the hole is filling in from the inside out, Since it's not a bandagable area I clean everyday with 2x2's but i can't hardly fit my finger in anymore (used to go up to knuckle) so I'm down to flushing with syringe only. The pus is pretty minimal, his temp is under control. My concern is the lenth of time he's been on Gentamicin. I've been giving him (vet's orders) 9cc intravenously now for 9 weeks, aside from liver damage any other problems to watch for? How about breeding sound?

This is a "talk to a vet" question and not a "petqna.com " type question since we're not vets!

Long term antibiotic use has risks. Nine weeks if IV antibitics is risky in many ways, but it sounds as though the other option (quitting medications) are even riskier! I would consult a really good equine vet. Perhaps have the baby's wound assessed again, including new cultures of the wound.

I would have this little guy on Probiotics immediantely. Antibiotics kills good flora as well as bad, so they can do huge damage to the intestinal flora which can cause weight loss, abd pain, ulcers, colic, etc. You can buy Probiotics specifically for horses, you add a scoop into their daily grain ration.