You could use a foam Filter hooked to a air pump. That way when your hospital tank has nothing, then there is no bacterias, so throw the foam in your main tank to maintain the bacteria until you ready to use it. Be sure after using it to get all the medicine and chemicals out before putting it in the main tank.
One more thing about the aquaclear mini is you can run just the foam if you are doin a treatment then add charcoal to remove the meds and the foam will still be colonized with good bacteria.