Everyone I know who uses brett in the beer they make will use separate plastic tubing and siphons for their bug beers. Good sanitation can prevent you from having to worry, but I'm not going to take the chance that there's an infection hanging out in there. Like that little rubber piece at the auto siphon... It just seems like a good place to harbor an infection, and it just isn't worth the risk to me.
Plastic tubing is cheap and other than that, there shouldn't be any issues.