By all means you should let your vet know. Be sure to include the information that she seemed better briefly. Respiratory infections can be caused by several organisms, mostly viruses and bacteria and often a combination of both. Antibiotics have no effect on viruses and no one antibiotic is always effective in eliminating bacteria. We sometimes have to continue antibiotic therapy for several weeks in order to eliminate all bacterial growth. It is also sometimes necessary to change antibiotics to finally resolve the infection. The most important thing to realize is that as long as your puppy eats well and feels good she will get well. Treatment should continue until at least 5-7 days after the cough is gone. Kennel cough is a term that has become kind of a catch all phrase for coughing puppies. We can identify the underlying causes of an infection through diagnostic tests but this many times would not change our course of therapy and they can be expensive.