Oh, wait, you say that isn't an option in the cities. Well, cities, yes, well, there's your problem.
Yes, yes it is. Not in the cities, but while living in the cities, via AIWPS. The short explanation is that your shit is pumped into the bottom of ponds with a methane-capturing plastic liner protected from UV damage by virtue of being submerged. Eventually the ponds fill up and they're left to cook momentarily before being sludged out for compost. Heavy metals settle to the bottom and microbes destroy virtually all pathogens and most other contaminants.
Cities are not the problem. Where cities are located is the problem; there's no good reason for them to be in the same place as seaports any longer, for one. And what we choose to do with our technology is a massive problem as well. We have the technologies to solve the problems, but the current "solutions" to these problems are highly profitable. For a tiny slice of the population, of course. And they are maintaining the situation quite aptly.