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The best thing would be to put him on some antibiotics and not have to mess with them locally. If that's not an option, then you can try to make up a warm water/ soap foot bath and let him soak in that for a few minutes a couple times daily. This can sometimes be more tolerated than trying to rub anything on the feet.
If he won't let you do a foot bath either, then I think you're stuck and you'll have to run him in and get some antibiotics started.
I hope this helps, let me know if you have any other questions.