I use single-use sponges that I sterilize by boiling between uses.  I try to sponge a base under all brushwork when possible.  I rinse out brushes thoroughly between uses.  For lips I use Q-tips. I avoid all broken skin and rashes.  If anyone looks in the least questionable, I use disposable sponges and Q-tips for line work.  I use professional quality paints that are inherently anti-bacterial.  I don't paint anyone who is coughing, sneezing, or has any indication of any contagious condition.  I've sometimes used a peroxide rinse for my brushes (did this during flu season). 

So far, no apparent problems. 

Where are you at?  I may know a face painter in your neck of the woods that you could get together with to ask some questions in person. 

You can contact me off list at artist at chameleonfaces dot com