The last thing you want to do when your rabbit is sick is make them feel worse. Unfortunately, rabbits try to hide signs of illness as long as possible. You don't want to give antibiotics that aren't needed. But, once you have a sick bun on your hands, they're way less likely to get better without medical treatment than we are. Rabbits have especially sensitive digestive systems that are easily thrown out of wack by antibiotics. Antibiotics can eliminate some of the "good" bacteria in the gut, allowing for an overgrowth of harmful bacteria. Some antibiotics are safer than others, but all carry some risk of causing problems.
Even vets with the best intentions can prescribe drugs that are harmful to rabbits. Common broad-spectrum antibiotics like amoxicillin are commonly and safely given to cats, dogs, and even rats all the time. For these species, it is safe and effective, which is great ... for them. However, because of this medicine popularity, they're too often prescribed for rabbits, guinea pigs, even hamsters.
These little guys have a different gut flora that's easily imbalanced by certain antibiotics. Antibiotics in the penicillin family (including amoxicillin), ampicillin, lincomycin, vancomycin, and clindamycin are most likely to cause digestive upset and have the highest rate of causing a fatal reaction. These medicines are known for causing an overgrowth of the bacteria Clostridia. Clostridial species of bacteria in turn create potentially life-threatening toxins that are absorbed by the GI tract (enterotoxaemia).
It is recommended all rabbit owners keep handy a list of safe and unsafe antibiotics. Check at the vet, and double check before giving that first dose. Unfortunately, once an antibiotic is given, there are no take-backs. Antibiotic-induced gastroenteritis as a result of a dangerous antibiotic doesn't always show up right away. Your rabbit may even seem to get better, then 2, 3, even 5 or more days pass and he begins to develop diarrhea and stops eating. Profuse, watery diarrhea accompanied by lethargy is always an extreme emergency in rabbits. Probiotics, fluids, lots of high-fiber hay, and syringe feeds can be given as supportive care. However, the prognosis will depend on the amount and strain of the harmful bacteria that may have multiplied in the gut.
Luckily, there are plenty of antibiotics that rabbits are more likely to tolerate. Commonly prescribed antibiotics include enrofloxacin (brand name Baytril), trimethoprim sulfamethoxazole, chloramphenicol, metronidazole. Other safe oral antibiotics like doxycycline, azithromycin, or ciprofloxacin are sometimes given instead. Not every antibiotic will treat every ailment in every rabbit. It's always okay to ask the vet why they chose the drug they did and how they arrived at the prescribed dosage.
It's ideal to take a sample of the infected tissue to decide which antibiotic will work best. For example, the vet might take a culture of an abscess, urine for a suspected UTI, or nasal discharge for respiratory infections. Results can take up to a few days to come back. Because rabbits aren't ones to complain, by the time they admit to being sick there's likely not too much time to waste. Your vet may prescribe a safe, broad-spectrum antibiotic immediately while waiting on results. If another medicine turns out to be a better choice or your rabbit doesn't improve in 48 hours, your vet should advise you how to switch medications safely.
Lessening Side Effects
In cases of severe infections or rare diseases (e.g. rabbit syphilis), sometimes there is no choice but to turn to the "last resort" antibiotics. In this case, there are some antibiotics that can be safely injected or given subcutaneously at home. While it doesn't completely eliminate risk from those pesky penicillins, avoiding oral dosing can help by bypassing the digestive system.
No matter what antibiotic is being used, it's a good idea to give probiotics an hour or two after every dose of antibiotics. Replenishing this "good" bacteria that are wiped out by the antibiotic can keep the ratio of "bad" bacteria in check. Unfortunately, there isn't a wide selection of probiotics formulated, especially for herbivores (YET). Regardless, probiotics won't hurt and can't be overdosed. If you choose to use a capsule made for humans in a pinch, make sure it's a vegan formula.
Monitor your rabbit closely when on antibiotics. If his original symptoms aren't improving in a few days, he gets worse, or develops new symptoms, he could be intolerant to the antibiotic or need a different type. Make sure your rabbit keeps eating and drinking, isn't losing weight, doesn't develop soft stool or diarrhea, or become lethargic and depressed. If you're concerned she is having a bad reaction to antibiotics, don't hesitate to call your vet.