First there has to be bacteria in the municipal water. The city does a pretty good job there,
Second there has to be organic matter for the bacteria to grow. Again, cities are good with that.
But even if you have bacteria in your water, a good RO system's pores should be smaller than a virus (really smaller than a prion) or it won't be able to remove metallic ions.
But let's assume after two years these assumptions fail because the filters get old. Replace the filters and flush the system with bleach.
My fear with RO are bad filters. I once had a Zero pitcher and it tasted bad, acidic. A few weeks later there was a recall that the RO membrane was leaking ionomers.
Moral of the story- trust your senses. If municipal water tastes bad, it's bad. If bottled water tastes bad, it's bad. If RO water tastes bad, it's bad.