I remember hearing somewhere that many gastrointestinal illnesses while backpacking are not caused by water but by poor hygiene; not washing hands or cookware. I finally read an actual research paper on this topic that confirms what I had heard.

Conclusions: Lack of hygiene, specifically handwashing and cleaning of cookware, should be recognized as a significant contributor to wilderness gastrointestinal illness. Hikers should routinely disinfect water and avoid untreated surface water.

I am kind of obsessive about using hand sanitizer while backpacking and I guess it is definately worth it as I have never been sick. I'm also careful about not reaching my hand into bag of trail food if I can pour it out instead when I'm on a group trip. Little things probably ake the difference.