The way he perceived prestidigitation was that it removed the overwhelming majority of solid and liquid mess, but the mess and microbiome can remain in small part. It isn't a fourth dimensional biological sieve, it’s a bulk remover. You still have to kill or remove the remaining spores and whatnot.

Phrased another way, would you be comfortable touching your eye after wiping? You used toilet paper. You can see neither feculence nor pathogens on your hand. It should be safe, right?