Hello I am Dr. Joey. Thanks for trusting me to help you and your pet today. I am a licensed veterinarian with over 16 years of experience. I look forward to working with you.
I am sorry to hear your dog has created new spot. These can recur for a variety of reasons, and I am sure you have discussed possible underlying reasons with your vet. As far as treatment the topical muporicin is excellent as you mentioned. You are welcome to try it, but if you feel it is that deep, then it probably is going to require an oral (or injectable) antibiotic to aid in clearing. If the would is through the skin into muscle then some techniques to encourage rapid wound repair that your vet can do are probably also in order.
In the meantime, until you can have this examined keeping it covered but not tightly bandaged to prevent him from licking is important. If you can get away with only using a cone and feel it will not get too contaminated while outdoors then this would be best to allow it to air dry. But if he is able to get to the area even with the cone, as may dogs are often able to when it comes to paws, then keeping the bootie on is a good idea.
I am at a point I need to know what questions you have. I hope that the information I provided has been helpful.
Please let me know if for any reason you need further clarification, have more questions, or were expecting a different type of answer.
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