If bacteria exist in cow dung, it is considered impure. As per scriptures, it cannot be considered clean for more than three days.
Cow dung was used in the olden days on mud floors for prevention from insects. It was used to clean floors and certain vessels; it shall not be used to cleanse the hands, feet, or other items so that there is no chance for bacteria to stick to them.
Moreover, after using cow dung, the floor should be cleansed well with a cloth by sprinkling water. There should not be a trace of the smell of cow dung. Then only it can be considered clean per shastram.