Fleas certainly can be a concern, and they can sometimes be difficult to find. Isolating your pet to a crate with a white towel/sheet and giving an oral Capstar tablet from your vet and watching for any signs of fleas over the next 4 hrs can be a simple test your veterinarian can do for you in the office or you can do at home with your veterinarians assistance.
Provided it's not fleas (it's good you treat him monthly (hopefully it's from your veterinarian to ensure it's actually effective)), your veterinarian can help him with atopica or some other products to help give him some relief.
With the shot (long acting steroids, I assume?), the fat lip can go away on it's own, but it may not be enough. Please visit your veterinarian for more suggestions to help get your cat some more relief. A specialized hydrolyzed protein prescription diet may also be a key factor in helping your cat.
Fish may or may not be the culprit. Don't make assumptions, but feel free to avoid fish if you wish. Seeing a veterinary dermatologist may also be of some help for more specific targeting answers.
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Itchy skin, sores, and the fat lip (likely an eosinophilic granuloma) are indeed all allergy related. The fat lip also is commonly secondarily infected with bacteria, so I would recommend a 2-3 week course of antibiotics if not already done. The three types of allergies are parasite (fleas, mites), food allergy, and pollen/dust allergies. If your cat is already on a good flea control such as Advantage or Revolution, then parasites are less likely. Options to treat allergies are to continue to treat symptoms with medications (okay if symptoms only occur occasionally and your cat only needs 1-2 steroid injections per year), or to identify and treat the underlying cause. There is no accurate skin or blood test for food allergy in pets, the test and treatment are the hypoallergenic diet trial (rabbit/pea, duck/pea, venison/pea, z/d are all good options, whatever he'll eat) and nothing else for 8 weeks. If the symptoms go away and stay away, then its food allergy and the hypoallergenic diet is continued lifelong. If the itch comes back despite the hypoallergenic diet, then the reason/diagnosis would be pollen/dust allergies (Atopy) and referral to a veterinary dermatologist for allergy skin testing and desensitization injections (just like allergy shots in kids) would be warranted to reduce the steroid need. Additionally, some allergic cats will respond to Atopica (oral cyclosporin) which would be less toxic long term compared to frequent steroid injections, and you can ask your veterinarian about Atopica if your cat's symptoms persist despite steroids and antibiotics.
Kimberly Coyner DVM
Diplomate American College of Veterinary Dermatology