My vet mentioned that not all antibiotics are safe for rabbits. What antibiotics are safe to give to rabbits? Does the route (oral vs injectable) make a differences? Is there a frequency or duration limit that is different from other animals that can use the same medicine?
There is no such thing as a safe antibiotic. This is true for humans as well as rabbits. But in humans we have a robust immune system that can usually handle the foreign substance and filter it out before it poses a significant threat to us, but after it has had a chance to affect the infection. Rabbits on the other hand are fragile creatures that have evolved a short and high quantity reproduction system to compensate for their relatively weak immune system, and high incidence of mortality.
In nature the adult rabbit's immune and digestive system is a bit more robust because it is exposed to more pathogens and it is forced to deal with a wider variety of food. But in nature annual mortality rates average about 80% per year. So only the most robust rabbits live long enough to breed and the more robust the rabbit the more often they have a chance to breed. This naturally selects for better rabbits in the wild.
In domestic rabbits the selection is most often for appearance. Breeders will go to great lengths to preserve a rabbit that nature would have claimed. Also domestic rabbits are not exposed to the natural pathogens or the diverse diet. Domestic rabbits thrive on a stable diet of hay and pellets, with as little change to the substances in that diet as possible. This makes for a healthy domestic rabbit when all is well but it presents challenges when the rabbit does get sick.
Antibiotics do not just affect the infection, they attack the good bacteria that helps the body digest, keep itself clean, produce oils that protect the fur, and many other functions. The rabbits gut is sensitive and throwing it off can lead to GI Stasis which is often fatal. For this reason the Vet that I talked with recommended never giving antibiotics orally. She recommended using subcutaneous or intravenous injection(depending on the medicine and what it was treating). The only antibiotic she said she regularly prescribes is Pen-G. Any antibiotics besides Pen-G she requires an office visit for the dispensation because of the increased risks.
She also stated that unless it is a serious infection the best medicine is usually a natural solution. For minor eye infections, Vitamin E drops work much better in the long run. Pro-biotics are a more effective treatment for problems with the GI tract.