I wouldn't worry too much about bacteria, you got so many on you and in you that in general (note) you should be ok. Now with that said, bacteria tend to dislike one of three things: salt, vinegar or sugar. It depends on the type. So if you clean with vinegar there may still be loads of little guys left in there. I know we don't like to use bleach but it is the only really effective way to get rid of all of the bugs. Just rinse and rinse and rinse after cleaning. The good thing about bleach is that it also kills mold, which is much more harmful than the typical bacteria.
So the discussion continues..... As for chemicals in the plastic, yes bisphenol A has been linked to cancer, as have several other organic compounds. Will you get cancer from drinking water from a plastic container/camelback???? Who knows. Personally I try to avoid using any containers that have organic compounds that may leach into the food/water, at least for every day use.