If you are careful not to cross-contaminate your filtered water with unfiltered water, a Sawyer Mini should reliably remove bacteria, even when it is numerous enough that unfiltered water could cause you problems.
If there are likely to be cattle grazing upstream from where you pull your water, then bacteria might be plentiful. In the high mountains where snowmelt is the primary source of water, I would not worry much about bacteria at all. Large volumes of water will tend to dilute bacteria in any event. Natural springs, a few feet from their source, provide much the safest water out there.
In the high mountain west, I'd try to be aware of any potential problems with polluted runoff from old mining tailings. A filter won't really solve that for you. The Rockies and the Sierra have many old mines. The Cascades, being volcanic, have very few old mines to worry about.