Sewage was widely believed to be deadly due to its association with "night airs", which the (now disproven) miasma theory of disease held was responsible for many infections. While John Snow demonstrated the epidemiological evidence for contagion (physical contact) as the mechanism for disease transmission in 1857, actual proof that bacteria were the caustative agent in contagious infectious disease only became available in the late 1870s (via the work of, in particular, Robert Koch and Louis Pasteir), and medical opinion (as with public opinion) was slow to adapt to new scientific findings in those days.

More on the miasma theory of disease here: https://en.wikipedia.org/wiki/Miasma_theory