Waterborne pathogens die when they dry out.
There is a technique to treating water in, say, a Nalgene bottle. After the treatment cycle (3-4 hours or more, depending on treatment option, water temp, etc.), invert the water bottle, unscrew the cap, and let some water flow (trickle) out. This (I believe) flushes out any pathogens that weren't in the bottle proper, but hanging around on the outside in the thread grooves (where your lips would touch when you take a swig)...