If this has you really worried, you could use both filtration and chemicals. So after filtration, something like aqua mira or other formulation of chlorine dioxide. I think I've done this a couple of times tops in a lot of backpacking, but there are a lot of variables at work. It's not enough for someone to say "I've done X and not gotten ill so you'll be fine doing X too" --- just not enough data to really know from something like that.

Still ... I think that as a rule of thumb in the U.S., either (proper) filtration or chemical treatment is likely enough.

One of the tough things here is the incubation period; you generally don't get sick from a waterborne pathogen right away, or rather, you don't experience symptoms. Of those who do get ill, while some might opine that they "know" just what it was that got them sick, I think generally they don't know. And there's always the speculation that they might have gotten sick from other hygiene issues --- most commonly speculated as something like "shared food with someone who didn't clean their hands properly after using the toilet".
Brian Lewis