I don't think you always know when there is reason to suspect. When I used this approach, I got giardia twice, about a month the first time, but three years the second time because the symptoms and history didn't mesh with what the doctor was looking for. Pretty awful.
So I'm not willing to rely on my intuition or deductive powers. All water, unless boiled snow, gets pumped through a Sweetwater Walk-About, @10 oz. in a bag about the size of a pint bottle. That is one of the few concessions to weight that I'm willing to make. The second case of giardia ended with treatment in 2001. Nothing since.
Also note that with a pump filter, the potentially contaminated water does not get into or on any bottles or other gear. The only contamination that stays with me is on the inlet hose and prefilter, that are wrapped around the filter and kept separate from the outlet hose in the carry bag. Logically, some bacteria could migrate on the inside of the carry bag to the outlet hose, but this hasn't been a problem. So far, so good.