I am not at all an authority on this but I think they use UV light to kill it during one of the treatment steps.
But it's not really necessary most of the time.
It's often done more for political reasons than technical ones, because it's easier for the public to understand and trust UV disinfection than the other, much more complex processes that are typically used.
Cobb County GA is an example of a plant that has large scale UV treatment right before discharge into the Chattahoochee River. But it's effluent is cleaner than the water getting pumped into their water supply.