I started to get a little concerned about that when I used to "go" in King Soopers (City Market, Kroger) wearing slippers. Normally this outfit keeps the men's rest room pretty clean, but I guess you get "shotgunners" testing their patterns at the urinals every once in a while. Can't attest to the ladies' room cleanliness.
I now wear shoes ("sneakers" actually) and decided to rely on molecular wear and tear to dispel the ickies before I got back into my car.
As my mother used to say in that kind of situation, "Don't worry, you'll eat a pound of dirt before you die."
It was just one of the inevitables. You'll probably get exposure and spreading just while removing the booties anyhow.
The other solution-component is to not buy $500 sneakers.
Y' gotta be practical.
Side issue, related, sorta-kinda. There's a photo of a bunch of dignitaries wearing booties as they examined the Trinity Site in 1945:
https://www.gettyimages.com/detail/news-photo/robert-oppenheimer-and-general-leslie-groves-examine-the-news-photo/615305238Terry