If you click here you will get to a BBC report on the causes of the 1665 plague outbreak. It states that;
“DNA testing has for the first time confirmed the identity of the bacteria behind London’s Great Plague. The plague of 1665-1666 was the last major outbreak of bubonic plague in Britain, killing nearly a quarter of London’s population. It’s taken a year to confirm initial findings from a suspected Great Plague burial pit during excavation work on the Crossrail site at Liverpool Street. About 3,500 burials have been uncovered during excavation of the site. Testing in Germany confirmed the presence of DNA from the Yersinia pestisbacterium – the agent that causes bubonic plague – rather than another pathogen. Some authors have previously questioned the identity of pathogens behind historical outbreaks attributed to plague.”
This might not be as conclusive as it first seems however. Some diseases then were not as deadly as today. Smallpox, which Queen Elizabeth contracted in 1562, for example was not the killer it later became. Thus, some historians accept that the dead had come into contact with the bubonic plague, but still argue that there was another killer.
If you want to know more, then you might like to read Susan Scott’s “The return of the Black Death as a good starter.