I don't see any list of arguments to choose from.
Personally, I would only point out to the student that the scientific
theory of bacteria, viruses, "germs" and infectious diseases has
been changing constantly for almost 250 years, and has undergone
at least twice as many changes as the theory of the structure and
Physics of atoms.
I would then ask him whether he's had his flu shot this year, and
how useful he feels our current understanding of vaccines and
contagious diseases in general is now, after all the changes.