When using filters, only treated water comes in contact with the water container. When using chemical treatment, shaking up the bottle with loosened threads exposes all relevant areas to the chemical, and those areas are in contact with the chemical for just as long as the rest of the water, so they should be treated as effectively. When using boiling water, decontamination is unnecessary, since the bottle is never exposed to untreated water(and even if it is, boiling water could be used to sterilize the whole container).

I did notice after I made that post that the prefilter could be used to keep the threads clean, but that is adding additional complexity, and doesn't change the fact that without the prefilter, the SteriPen is ineffective it preventing consumption of contaminated water, for the reason stated in my previous post. It is also seems very unlikely that the part of the prefilter that contacts the nalgene threads can be kept isolated from the parts of the prefilter that contact contaminated water. Even if you meticulously rinse the prefilter with treated water after each use, the rinsing process would expose the clean parts to contanimated water.

As far as sealing the mouth with the SteriPen, inverting it, and agitating it, that would still leave the outside threads and probably the cap contaminated with untreated water. And again, sealing the SteriPen to the bottle requires the prefilter, if using a standard wide-mouth bottle. This also can't be done using a cup(and if the drinking water in a restaurant or public place is questionable, then the water used to wash dishes probably is also).

I'm not trying to be belligerant, but I beleive this is a major flaw which seems to defeat the purpose and pose a health risk by providing a false sense of security when used according to it's instructions. If the prefilter was included as standard equipment and the instructions made it's use mandatory, then it would be a different story. As it currently stands, only a warning among many in the back of the manual warns of the danger of the areas which remain contaminated in the normal use of the product. I find this very irresponsible.

It would be great if someone did some real world testing(Doug, you listeneing?) of water treatment systems, including filters, chemicals, SteriPen, Miox, etc. I'm thinking a small, contained outdoor fountain or body of water deliberately contaminated with high concentrations of some kind of bacteria or virus known to cause a minor illness, along with the ground or rocks around that area. Then have inexperienced volunteers use the various systems repeatedly over several days from that same water source. Either they can drink the water and see if someone gets sick, or more likely, have water samples and samples from the threads taken regularly and analyzed.