Bees like water with a bit of smell to it, and will often prefer water containing chlorine or sewage over "pure" sources. My bees get their water out of the runoff creek from the water treatment plant up the street. Well, that's what I tell myself, but I bet they get it from the settling ponds too. Ugh.
The bees themselves either have the intestinal fortitude to withstand whatever pathogens are in the water, or in many cases, have "intestines" that are not targeted by the bugs that would make us sick. I'm sure my girls pick up plenty of e.coli, but e.coli only selects warm blooded animals for hosts and does not colonize the bee gut, so no symptoms.
As for the honey, it is so acidic and hygroscopic that few microbes can survive in it and even fewer can reproduce. So say a bee lands by the sewage plant and steps in e. coli-contaminated water. It tracks some of those bacteria into the hive, and maybe a few end up in a cell of honey.....and they die right there because honey is a deadly environment for bacteria. If you licked the comb, or accidentally ingested contaminated water along with the honey like you did with your cutout, then you might get sick, but the honey by itself is very nearly sterile.