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Lab has black spots on skin

Dr. Cheng,
My five year old yellow lab has black spots all over her back and I have no idea what it is or how to treat it. The vet has suggested that something may have bitten her, so he gave her a prednisone inj. She has had some allergies to foods and I am careful about what she is fed. I have had her on holistic eagle pack, but just recently put her back on the california natural. The spots are peppered on her back and some are raised up like bumps. she does not seem to be itchy, it just looks miserable. I have her groomed and sheared rather closely to help with the shedding issue and I am wondering if the fresh and clean shampoo they use could be the culprit ? I am just at a loss. Is it food? is it shampoo ? mites? I don't know and I don't think our vet is sure either..any ideas ? your help would be most appreciated. Thank You.
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Have your vet perform a skin scraping, a biopsy, and culture and sensitivity.  This will rule out mites, bacterial or fungal infections, allergies, or something else and you will be able to go from there.  If she was bump free while on the holistic eagle pack I would put her back on that.  If the problem does not resolve put her on a novel protein diet (a protein she has never been exposed to before) for at least 12 weeks.  Most allergic dogs also have enviromental allergies so allergy testing may be a good idea.  Additional options:

Have the groomer use Malaseb shampoo and no cream rinse.
Give your dog Omega 3 fatty acids (DHA and EPA) at 2000mg day.
Give your dog a probiotic, Wobenzyme, and colostrum.
Ask your vet about possibly putting your dog on Temeril-P  and/or Atopica.
Use the flea product Revolution for a hidden scabies infection.

Have your vet treat any secondary bacterial or fungal skin infections at the same time as the other treatments (Atopica, etc.)

If all else fails think about going to a veterinary dermatologist, or holistic vet.
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