In TOS (for example) you see Kirk, Spock & co. appear to go straight to the transporter, say from the bridge. Should we assume that they go through some sterilization process before being transported but which is not shown for continuity purposes? Or is everything and everybody on the starship in a germ free state?
In the episode "The Apple" the crew beam down to a paradise planet with innocent beings and it would be possible to introduce a disease unknowingly which could wipe them out.
Obviously, in an emergency it may not be possible to have the time but would it be standard procedure?