There are a variety of reasons for recurrent superficial pyoderma (the medical term for repeating skin infections). Sometimes I see many puppies that have recurrent skin infections that just go away when they get older. Other possibilites may be food allergies, environmental allergies, immune mediated, mites (one skin scrape makes it unlikely but not impossible), other parasites, etc...
How long of a course is he on for antibiotics? Sometimes a longer course of antibiotics is necessary. Some patient need 4-6 weeks of antibiotics or more. Is the skin 'totally normal' for several days before the medication has finished? If we are concerned that the skin infection is the same bacteria coming back again, a culture of the bacteria where it is grown and tested against several different antibiotics in order to find out sensitivity can help out.
To work up the other problems... a food trial might be the place to start since your vet has already skin scraped. Food trials can help evaluate for food allergies. If a pet is allergic to food, they are usually allergic to more than one protein in the food. Thus food based off of novel protein sources (protein the pet has never been exposed to) or better still (hydrolyzed protein which means the protein molecules have been reduced in size to avoid immune response) are needed. The protein complexes stay in the pet's system for 6-8 weeks. Therefore a minumum of 8 and usually of 12 weeks is needed on the food in order to assess response. It is important that during that time, nothing else if fed to the pet. Ask your vet as to which food they recommend if you are interested (there are both commercial and home cooked diets available).
The other problems are often best sorted out by a dermatologist. Ask your veterinarian for other tests that they can do. Blood testing, etc...
And fatty acids supplements are great! I recommend them for all mammals.
I hope this answers some of your questions....
