Yes. One antibiotic in particular, gentamycin can harm the kidney.
Antibiotics. Certain antibiotics can cause unexpected organ damage. A good example is in some of the more potent antibiotics that kill a significant number of normal colon flora. This leads to overgrowth of clostridial bacteria, producing an exotoxin that leads to c. Difficile colitis., with abdominal pain and diarrhea. This can become so bad that it may require total colon removal or fecal transplant.