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Heracles has allergies or auto-immune thing?

I had noticed that Heracles, my Australian Shepherd, had been scratching himself a lot, and figured that it might be fleas. I applied a once a month treatment to all 4 pets last Sunday, but it seemed like Heracles was still scratching. I then got a really good look at his face and front region, and he had rather a lot of scratches, fur being thin and just in general looking like he was tweaked out on meth. I felt awful for not having caught it earlier. (Well, the way his fur and coloring are, it didn't really stand out at first.)

So, I was able to get him in to the vet's today. I got the rather cute male vet that he has seen before. (The same vet was the one who treated Morgaine.) The good news is that we were able to eliminate mites, fleas and infestations as the cause.

THe vet said that it was a rather odd area. He was wondering if it was allergies (hmm, no new food or anything else in his environment, that I can recall) or maybe an auto-immune thing. So we have him on some meds that will hopefully help.

It might be a bit, and I really hope that he is all better soon. He is a wonderfully loyal and affectionate dog. When we were waiting in the vet's office, I was trying to keep him from getting too wound up about the other pets. He's a medium size dog, but he does like lying in my lap, sort of like carrying a baby. Right now, he is resting on the floor quietly.