Usually, after secondary treatment, the wastewater is released into the environment. A distant dream. Due to high cost, this is not widely done. Tertiary treatment methods purify the wastewater further until it is drinkable. Activated charcoal binds non-specifically to many of the dissolved organics and remaining particulates, removing them from the water.
Selective precipitation removes phosphate from solution as insoluble salts.
These precipitates, which also carry along most remaining microorganisms, are allowed to settle and are then removed. Chlorination kills any remaining microorganisms. Many enterics fit these criteria, including E. coli and Salmonella sp. Coliforms are used to indicate if the water contains fecal contamination. Although not necessarily pathogens, coliforms are useful as indicators of true pathogens present in feces that we might not have an assay for.