Sooooo....this is important: she probably was given the Kennel Cough (bordetella) vaccine and that is where she contracted her URI (upper resp infection).
Bordetella is *not* a core vaccine. The core (necessary) vaccines are rabies, parvo, and distemper. I have never given my dogs bordetella, nor will I.
If I were you, I would not get this vaccine again for your pup. More about vaccine protocol
HERE.
The most important thing now is to be sure that this infection does NOT progress to pneumonia, which is so common in puppies. Watch and treat closely!!!