I run the water hose as Peggie suggests -- been criticized for wasting water if I just let it run so I use it to rinse the decks first, and start with a little dab of liquid soap in my hand to wash the hose-end and threaded fitting. Then I never insert it or rest it against the inside of the fill hole. Instead I hold it above the fitting while it fills.

Does that stop contamination? I'm sure it doesn't -- but it probably reduces it and that's what antibodies are for. Also, since I'm in the US the water is chlorinated and I figure that will kill most of the bugs in the tank. We cook and drink from gallon jugs of spring water but use the unfiltered tank water for washing dishes and ourselves (and rinsing the tooth brush) and haven't had a problem so far. Been doing this for years. I "shock" the fresh water system with bleach every spring.