Non-issue in normal operation as no fluid leaves the tanks via the tubing. Only a small amount of air, equal to depth
of fluid in tank, is pushed back into the tube. The length of this tiny column of air is normally much shorter than the tube to the manifold so this little column of potentially contaminated air would never come anywhere near the manifold.
If it really worried you then you could probably install a HEPA filter in the tubing. Though it would take some creative use of adaptors unless someone makes a HEPA filter for that size tubing (which is very tiny).