It is doubtful that the membranes were damaged inadvertently during installation.  A significant amount of effort would be required to damage RO membranes to the extent that bacteria would easily pass through.  While it’s not impossible for there to be manufacturing imperfections that allow pathogens such as viruses to pass through, bacteria are quite large, so that’s also an unlikely scenario.

In our experience, total coliform counts increase in the permeate almost every time membranes are replaced.  This is because bacteria are introduced to the permeate side components (such as the permeate tube in the membrane and interconnectors), which will cause a high bacterial count in the permeate.  This can be resolved by running the system and sending the permeate to waste for several days (usually 3 days).  Alternately, a peroxide based cleaner or disinfectant can be used (peroxide solution will partially pass to the permeate side under the pressure applied during cleaning; this will disinfect the permeate side).  When disinfecting with hydrogen peroxide or peracetic acid solutions such as AWC D-615, always be sure not to exceed concentrations recommended by the membrane manufacturer.

In order to prevent high coliform counts after membrane loading, good hygiene must be practiced by the contractor’s staff.  They should wash their hands thoroughly.  Disposable gloves should be worn during membrane installation.  All the interconnectors, end-cap adaptors, and other components should be dipped in hydrogen peroxide prior to installation.  Care should be taken not to introduce any type of contamination to the permeate tube of the RO membranes.

We have seen some contractors dip all the permeate-side components in sodium bisulfite solution, but that is never successful.  Bisulfite solution is a good preservative that prevents growth of aerobic microorganisms, but quickly dipping components in bisulfite solution does not result in an instantaneous kill.