There is a use for cleanliness, but as the saying goes "for every reaction, there is an equal and opposite reaction."
In India, where antibiotics are (also) overused, there are new strains of TB not cureable.
Staph and strep are fast becoming ultra-resistant as well.
We live amoungst...and are made of...bacteria and virii:
Humans are a cocktail of bacteria and human cells
Early exposure to germs has lasting benefits : Nature News & Comment
Provirus - Wikipedia, the free encyclopedia
"It is thought that proviruses may account for approximately 8% of the human genome in the form of inherited endogenous retroviruses."