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.
Natl Geographic, March, 2020 Why Plague Doctors Wore Those Beaked Masks (https://www.nationalgeographic.com/history/reference/european-history/plague-doctors-beaked-masks/?cmpid=org=ngp::mc=crm-email::src=ngp::cmp=editorial::add=History_20200316&rid=555EE595E2E27C47F3DEE1879DCE3A3F)