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Hi, this is Dr. Hill. It is very frustrating to deal with chronic disease. I am concerned about him being on Apoquel and the possibility of infection. Apoquel has been a miraculous drug for allergies, but it is not without complications. Apoquel is a drug that suppresses the immune system and should not be used if there is an infection.
First and foremost, chronic lesions on the feet should be biopsied and samples sent to a dermatohistopathologist, not a regular pathologist. I assume they suspect he has allergies, but did anyone talk about immune mediated diseases? A biopsy would show if it is immune mediated and the treatment would be different.
If he does have allergies then it is usually a mix of environmental (inhalant) and food. Have you ever tried a prescription diet for allergies (Ultamino, science diet Z/D)? It can take several months to find out what works best. I strongly encourage you to consider a punch biopsy first and then look at doing a food trial (10-12 weeks of prescription diet only with no people food or treats). Feel free to ask additional questions. Take care.