The Great Plague of London occurred in 1665, before the advent of the germ theory of disease. Nonetheless, people back then had some general notion that the disease could be spread through social contact, and for that reason quarantines were (quite correctly) imposed on incoming travellers and infected individuals. But many other possible routes of transmission were also mooted, including cats, dogs, and "bad air" (the miasma theory), and on the basis of these theories further control measures were put in place. These latter measures were at best ineffective and at worst harmful, since we are now confident that the plague was transmitted by fleas, which were in turn spread mostly by rats.
I am wondering whether anyone in 1665 (or thereabout) identified rats or fleas as being responsible for spreading the plague. Obviously if they did, the idea never gained any traction in society in general. But given the multiplicity of explanations and cures for the plague that people were advancing (admittedly in desperation and without the benefit of modern-day medical knowledge), I am curious as to whether anyone was lucky enough to accidentally hit upon the correct mode of transmission. Can anyone point me to a contemporary source for someone blaming fleas or rats for the plague?
EDIT: I have since discovered two relevant pieces of information:
First, in their book The Great Plague (Johns Hopkins University Press, 2004, p. 280), A. L. Moote and D. C. Moote write of rats' link to the plague that "rats were virtually unmentioned in 1665". This wording implies that rats were mentioned, albeit rarely, so I would be interested in learning what those mentions are.
Second, in his Journal of the Plague Year, Great Plague contemporary Daniel Defoe describes the mass culling of dogs and cats ordered by the Lord Mayor, but then goes on to say that
Endeavours were us'd also to destroy the Mice and Rats, especially the latter; by laying Rats Bane, and other Poisons for them, and a prodigious multitude of them were also destroy'd.
So it seems that there was indeed a concerted city-wide effort to eliminate rats from the city, though it is not clear from Defoe's text whether this action was taken because people assumed that there was some link between rats and the plague, or merely because they understood that the rats would become even more of a nuisance once all the cats and dogs had been killed. It is probably safe at least to say that if there was an order to kill rats, it did not come from the Lord Mayor; his order discusses only the removal, impounding, or culling of "Hogs, Dogs, or Cats, or tame Pigeons, or Conies".