Actually, kennel cough can't be treated with anti-biotics. It's a virus and doesn't respond to them at all. Antibiotics only work on bacterial infections. When my dogs had it, my vet told me he could give me medication, but it would only be to ease my mind, wouldn't do a thing for my dogs. Kennel cough is a cold and like the human cold, it has to run it's course. The symptoms can be treated. Over the counter cough syrup can be given to dogs. Make sure it has no other ingredients, just a cough suppressant. No pain reliever, decongestant ect.

Frankly, this doesn't sound like kennel cough to me. Kennel cough shouldn't affect her breathing. That sounds like pneumonia to me. I'd strongly suggest you get Muffin to a different vet ASAP!