Rabbit health and digestion is dependent on bacteria in the gut, disruption of these bacteria from antibiotics can lead to diarrhea and ultimately death of the rabbit. Others can lead to nephrotoxicity or enterotoxemia. Different routes (oral vs injection) can have different impacts. If possible/practical a Culture and Sensitivity is recommenced in conjunction with antibiotic administration.
The following antibiotics have been identified as having higher than average potential for adversely effecting the health of rabbits specifically regardless of route and should be avoided if possible. Cecotrope recolonize or pro-biotic treatment is indicated in conjunction with any antibiotic treatment.
- Amoxicillin/Clavulanic acid
- Penicillin (in general avoid, but indicated in some cases)
- Tilmicosin (some risk of Cardiac issue, with known positive impact in some cases).
Some infections like MRSA are resistant to multiple antibiotics and it may be that using one of the above antibiotics is the only possible treatment. Or there may be other complicating issues requiring the use of one of these; a veterinarian rabbit specialist can address the pro and cons of these with you prior to deciding on a specific course of treatment.
This list above is compiled from the several sources linked in the text of this answer, not all sources mark all as contra-indicated, but each is marked as contra-indicated by at least one source.