No, bacteria is onmipresent, i.e. everywhere on everything. Of course not all bacteria is harmful. Bacteria are 'large' compared to virus , being visible in a hobby microscope whereas viruses generally require electron microscope power to visualize. I try to get filters that realistically get down to 5 microns and also use bleach or other chemicals to kill organismsI have a few of the Sawyer system filters. Their website says the Sawyer MINI Water Filter is rated to 0.1 micron absolute. If that is true, then based on what you said above, they should clog quickly. I have tested two of the ones I currently own and they worked pretty well without clogging, granted I started with a relatively safe water source to begin with (one was well water on a farm, the other was out at Loch Raven). Would it be safe to assume the water did not have a lot of bacteria to begin with? There was not a lot of visible particulate matter to begin with (at least with my tired eyes).