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. Sporadic observations contributed to a gradual association: cholera and polluted water, for example. Another example was the sudden drop in deaths of women and their newly delivered infants when attending physicians washed their hands before the delivery.
The germ theory of disease was not initially convincing. Only as hygienic procedures were introduced was the relationship between unseen bacteria and disease acknowledged.