supposedly, in between plagues the bacteria merely infected rodents: which is why we get occasional cases in the Navajo area each year.
But is the plague still alive in European rodents?
"We don't know why the Great Plague of London was the last major outbreak of plague in the UK and whether there were genetic differences in the past, those strains that were circulating in Europe to those circulating today; these are all things we're trying to address by assembling more genetic information from ancient organisms."
The rumor is that the massacres and famine deaths from Genghis Khan's army conquering the Middle East were the source of the Plague, but this hasn't been proven.
longer post on this moved to my medical blog.