If I have understood the ...

If I have understood the question correctly the problem is to control the increase in microbial counts in ETP treated water (presumably disinfected) and RO permeate. The development of colonies is a natural process that will occur as long as there is a source of the organisms accessing the water and nutrient in the water for them. The question that needs to be asked is are they a problem that we need to do something about? If so then either some disinfection process with a residual such as chlorine or chloramine for longer effect is needed or UV radiation at the point of use.