Separate teams of scientists studying the origins of Europe’s historical plagues confirmed in a study published last week that the plagues were caused by bacterium Yersinia pestis.
Europe experienced three great plagues in its history, the Justinian Plague in the 6th century, the Black Death from 1347 to 1349, and the Great Plague of London from 1665 to 1666. Amongst the three, the Black Death was the deadliest and is estimated to have killed 30%-60% of Europe’s population. The Great Plague of London killed an estimated 100,000 people (~20% of London’s population), and the Justinian plague, which was the first great plague, struck the Byzantine Empire from 541 to 542 AD, killing around 100 million people.
The three plagues were caused by three different strains of the bacterium Yersinia pestis. By comparing the genetic makeup of the bacteria from mass burial grounds across Europe in which the dead were interred to the genetic variations in living strains of Yersinia pestis, scientists conclude that the three strains shared a common ancestor and most likely originated from China. However, the killing of humans by Yersinia pestis is likely an "accident" as scientists believe that the natural hosts of the bacterium are various species of rodents, and that it has no interest in people.
This map shows how the bacterium might have spread from China to the rest of the world
New York Times Article on the Great Plagues