Several antibiotics are known to be harmful to hamsters. These include penicillin, cephalosporins, lincomycin, and erythromycin. It is believed that these antibiotics change the balance of micro-flora and allow the proliferation of a harmful bacteria in the gut (known as a bacterial overgrowth). The bacterium involved is believed to be Clostridium Difficile. But other Clostridia may be involved. These bacteria are harmful to the hamster because they produce toxins which cause enterocolitis (an inflammation of the guts).
Other antibiotics may be directly toxic in hamsters, especially the Syrian hamster, these include streptomycin and dihydrostreptomycin.
Antibiotics recommended for hamsters include trimethoprim/sulphadiazine, tylosin, dimetronidazole, chloramphenicol, enrofloxacin, ciprofloxacin, and gentamicin.