My question was not on how to perform H&E staining, it was more on to how to prepare the mice foodpad for histology without compromising on the kind of staining I want to perform with it.
If you want to do HE or other histological stainings on the food pad, you can fix it in formalin 10 % and then process it normally (ethanol, xylen and paraffin) and then embed it in paraffin and cut it by microtome!
Indeed, in anatomy and histology foot pad contains fat and connective tissue. As I understand you want to work on paw. So decalcifcation is necessary after fixation:)
Anyway, if you want to investigate a special tissue which the bacteria affect on it (for example skin), I suggest to sample just your tissue (skin) for tissue processing (without bone). In this way decalcification is not necessary and your tissue will not damage by the mineral acids during decalcification.