It sounds like your dog might have either kennel cough
www.marvistavet.com/html/body_kennel_cough.html
or canine influenza
www.marvistavet.com/html/body_canine_influenza.html
You can ask your vet (just call and ask) if some Robitussin DM will help the dog breathe better and control the cough. Read here about cautions and dose info
http://www.petplace.com/drug-library/dextromethorphan-robitussin-dm/page1.aspx
As you are on your second round of antibiotics this may be the canine flu. It takes 2-3 weeks or more of care to get a dog over that.
I believe your puppy was sick at the time of purchase. Depending on where you live, the breeder or pet store may be liable for some of the care costs.
www.malteseonly.com/lemon.html
Hope this helps you!
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