I wasn't told specifically it was MSRA, but was told it was a "very serious infection that needed monitoring" which is why he used a Sharpie on my leg.
I'm pretty sure whatever infection came not from the water (which of course smelled like a direct tap from the bleach plant) but from the surrounding decking areas and locker room. I tried to walk in dry areas and keep my shoes on as much as possible in the locker room, but apparently not enough.
I actually worry less about the water, because as you say, they treat the hell out of it and most of it keeps moving to keep it filtered/treated/etc. It's all those wet areas you have to walk through.
Strangely, we've had season passes at the community pool for years and never had a problem, but I also think the water park at the amusement park had a different demographic than the pool we go to, plus I was either in the pool or on a lounge, and otherwise I wore my crocs.