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You are absolutely right, most odors are due to yeast overgrowth. It's good that you are working so diligently to control the problem, but I am suspicious that she still may have some in difficult to treat areas such as the nail fold.
Your vet can check for ongoing yeast problems using a tape prep on her skin, and also scraping along the nail fold. Both can then be examined on a glass slide on a microscope.
If we continue to find yeast in spite of the topical regimen, I would strongly consider using an oral antifungal (ketoconazole). This is available by prescription only, and it is not without potential for side effects. I would not use it without first confirming that there is ongoing yeast growth.
Aside from that, I would switch your shampoo to a chlorhexidine and antifungal product such as Douxo Chlorhexidine PS.
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