Archeologists have uncovered 3,500 skeletons of victims of the Great Plague of London 1665-1666. The skeletons where in a burial site that was discovered when building an underground railway line across London (Crossrail). The bodies had been neatly buried indicating respect for the deceased despite the gravity of the situation and the dire circumstances.
Testing on the skeletons confirmed the presence of DNA from the Yersinia pestis bacterium which caused the bubonic plague. It was long believed to be the cause but this confirmed it.
The Yersinia pestis bacterium at that time was found in the rat flea (primarily the brown rat). The flea would have bitten humans and transmitted the disease to people. A quarter of London’s population died. The population of London at that time was around 400,000.
When the flea feeds on a host the bacterium is regurgitated into the wound causing the infection. Humans would have passed on the disease to others through coughing and vomiting if their symptoms had progressed to the pneumonic form.
At the time the cause was unknown. Experts speculated and guessed. There was an effort to kill all cats in London (I suppose domestic, stray and feral) and dogs by order of the City Corporation. This would have made matters worse and lengthened the duration of the plague as some cats would have preyed on rodents including brown rats.
Antibiotics cure the disease today.