Hello I am Dr. Joey. Thanks for trusting me to help you and your pet today. I am a licensed veterinarian with over 15 years of experience. I look forward to working with you.
This poor guy! My top recommendation is to use a diluted chlorhexidine solution. Your vet can provide this for you, or you can purchase Hexadene flush (made by virbac) (here is an amazon link: http://www.amazon.com/Hexadene-Flush-12-oz/dp/B000O5HZ4A/ref=sr_1_2?ie=UTF8&qid=1399031308&sr=8-2&keywords=hexadene)
I also want to confirm that since this is not clearing that your vet performed a skin biopsy to ensure that this is just an atypical deep infection, and not an unusual immune-mediated condition that will require an immunosuppressive medication to clear/treat. If this has not been done, then this is recommended. At the time of skin biopsy a culture (deep culture) of tissue can be submitted to the lab to know what antibiotic will resolve this. And to rule out fungal infection.
This needs far more than a swab, given the longevity. It needs a biopsy, which is super easy for your vet to do. He would need some light sedation and then a few samples can be taken. These samples would need to be submitted to a dermatopathologist (not the regular pathologist), but your vet should be aware of this.
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