There are many bacteria and micro-organisms that can make your dog sick. Fighting these infections with a proper antibiotic is the way to go. Antibiotics should only be used after being instructed to do so by a veterinarian. The antibiotic you should use to treat your dog will depend on which organism is causing your dog's infection and how the medication works in your dog's body. As with all prescription medication, there are side effects, which your veterinarian will discuss with you.