If you own a rabbit, or you wish to care for one that appears to be ill, be cautious if your vet wants to prescribe antibiotics as a treatment. A lot of antibiotics have been found to be harmful to rabbits, particularly in the form of enteritis. High doses of ampicillin, clindamycin, lincomycin, and penicillin can causes up to 100% fatal enteritis. Amoxicillin, cephalexin, erythromycin, spectinomycin, and tylosin can cause diarrhea, minocycline reduces growth rate, and spiramycin causes nervousness.
Enteritis is a common disease which you might recognise in humans, caused by pathogenic bacteria such as salmonella, and campylobacter, often called stomach flu, although it can often be tackled by our bodies, it can cause death especially in the old and the young. Antibiotics act by killing bacteria in a relatively non specific manor, such as ampicillin which acts by preventing cell wall synthesis, which prevents bacterial growth. This can kill the good bacteria in our stomach, which have a role in preventing the bad bacteria from causing infection.
Rabbits have a unique digestive system, which is inhabited by a variety of good microorganisms which help the rabbit to digest its food. It appears that antibiotic treatment in rabbits has the same type of effect, and kills the good bacteria in the cecum and the intestines, significantly increasing susceptibility to pathogenic infections, such as Clostridiumspp, which can produce dangerous toxins. The antibiotics can also cause death through toxicity, such as vancomycin which has been shown to cause 100% mortality, it should be noted that these toxins can take up to 10 days to have an effect. The treated rabbit can appear to be normal up to two days before you notice reduced appetite, and activity, with watery diarrhoea, and ultimately death within two days.
Bacterial infections can occur in many places in the body, and it can sometimes be difficult for a vet to determine where a particular infection is situated, or what type of bacteria is responsible, different antibiotics can be more effective at tackling specific bacterial infections, so if possible you should get your vet to try and determine what bacteria you are dealing with before you allow administration of antibiotics. You should work with your vet to determine what the best action might be, and remember that some antibiotics can be used with a higher level of safety, especially when administered via injection, rather than orally, an example are Cephalosporins.
References
T. H. Morris: Antibiotic Therapeutics in Laboratory Animals. Laboratory Animals 29: 16-36.
Rabbit Medicine by Frances Harcourt-Brown.