Are they confirmed E coli or ...

Are they confirmed E coli or coliforms or presumptive?  There are certain gram positive sporing rods, which can grow on the media used to detect coli providing false positive results.  I would expect these bacteria to be present at high levels in a WWT plant.  Chlorination kills the vegetative part of the cell leaving the resistant spore behind.  This then germinates on contact with the growth media.  As long as the water is clear and has no organic demand, 1 ppm of free chlorine at a pH of 7.2 will kill E coli and coliforms very quickly.  If the pH rises to 8.2, 1 ppm free chlorine has the equivalent kill rate of 0.1-0.2 ppm free chlorine.  The kill rate starts dropping dramatically above 7.5, so good pH control is important.  If there is ammonia present, chlorine reacts with the ammonia and  chloramines develop.  These are volatile and are rapidly lost from water, but even in water their bacterial effectiveness is much lower than chlorine.  I hope this is some help.