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Hello and thanks for trusting me to help you and your pet today. I am a licensed veterinarian with over 25 years experience and would be happy work with you.
If you are noting dark spots and itching in a dog with seasonal allergies, it should definitely be evaluated by your vet. Even though the apoquel seemed to help some, there may be a reason why she still continues to experience some degree of itching. It may be that the apoquel dose needs to be adjusted as can commonly occur. Or even more common is the occurrence of a secondary infection with bacteria or yeast on the skin surface. This can be evaluated by taking a small sample or the surface cell in the areas she is scratching or that are pigmented and looking at the cells under the microscope. If bacteria or yeast are present, they will need to be treated separately with either an oral or topical product as the apoquel has no effect on that.
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My posted replies are for general education only and not meant as a diagnosis. Only after a thorough veterinary examination can a diagnosis for your pet be made and specific treatments be advised or medications be prescribed.
Yes, benedryl would only be expected to possibly help if the problem was allergy only and not due to secondary infections. My bet is that they will find bacteria or yeast. In the meantime, bathing followed up by a moisturizer for dogs to help repair the skin's defective barrier (that occurs in dogs with seasonal allergies) may provide some relief.