Before microscopes, the notion of tiny invisible organisms causing disease was entirely counter-intuitive.
Up until the 19th century, even as medical knowledge improved, the connection between diseases and unseen bacteria was not made. The germ theory of disease was not initially convincing; even physician/scientists as late as the 18th century continued to believe in the miasma theory, for example. Sporadic observations contributed to a gradual association: cholera and polluted water in the 1800s, the observation of microbes in microscope studies. Only as hygienic procedures were introduced was the relationship between unseen bacteria and disease emphatically acknowledged.