One of my buddies used to work with imported snakes, where mouth rot is a common problem. He found that flagellate protozoans were often present in the mouth and digestive tract along with the mouth rot bacteria. So it might be worth having the vet do a microscope check for them. Those protozoans die fairly soon after leaving the snake, so they may have died before laboratory worked on the samples. Especially if the lab only cultured for bacteria.
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