Harvey, we seem to be in agreement and posted at the same time. I worked in the water quality field for one year right out of undergrad, so I know just enough to be dangerous. I know enough to know we don't know what's really going on with this situation. The simplest explanations are usually the most accurate.
The tests they do these days for Fecal Indicator Bacteria (FIB) have advanced to where they can detect the source species without DNA testing. The allowable Colony Forming Units (CFU) standards are evolving and generally getting more strict. Oddly, the old standards are based on levels acceptable for a swimming pool and then applied to drinking water, and these standards are still common.
The samples need to be refrigerated and tested quickly. Quality control issues almost always lower the E Coli counts. Yes, the samples are cultured and then counted under a microscope. Testing details are in the link I sent earlier
Lahontan Microbial Study of Eastern Sierra Streams
