British red squirrels are infected with two different strains of the bacterium that causes leprosy, according to a study.
Leprosy was thought to have died out in the UK in medieval times, but these recent discoveries confirm that red squirrels carry the disease.
Despite this, researchers are keen to stress that the squirrel infection poses little, if any, threat to humans.
The research is published in the journal, Science.
In 2014 scientists studying red squirrel populations in Scotland noticed that some of the animals had abnormal growths on their ears, snout and limbs.
"We found that they were suffering from a form of leprosy," Prof Anna Meredith from the University of Edinburgh told the BBC's Science in Action.
The red squirrel is an endangered species found across Eurasia.
UK populations are especially under threat due to habitat loss, as well as through direct competition and the deadly effects of squirrel poxvirus following the introduction of the grey squirrel from North America.
The scientists do not think that it is having a negative impact on overall population size, although they are not sure of its effects on individual infected animals.
There are two species of bacterium that cause leprosy: Mycobacterium leprae, which is often referred to as "human leprosy", and a recently described species that also infects humans, called Mycobacterium lepromatosis.
The Scottish squirrels were infected with the more recently discovered form of the bacterium.
Following this initial report of the disease, the public alerted the Edinburgh-based researchers to cases of lesions that looked suspiciously like leprosy in other populations of red squirrels across the UK.
One of these reports focussed on animals living on an isolated island in Dorset in the south of England, which Prof Meredith was keen to follow up.
"We took samples from those squirrels, investigated further and we found that the squirrels on Brownsea Island were also infected with leprosy, and it's the human form of the disease," she said.
So squirrels living in different parts of the UK were infected with different species of leprosy.
"It's still quite puzzling as to why some [squirrels] have one species and not the other and why this differs in different sites," observed Dr Rachael Tarlinton from the University of Nottingham, who was not involved in the research.
"This may be sampling size problems - it's hard to get lots of samples from endangered species."
Digging up the past
Having shown that infection was widespread they were keen to find out where the infection had come from.
To do this the researchers analysed the DNA sequences of the squirrel leprosy genomes and used this data to generate a leprosy family tree.
Related bacteria branch together, and the Brownsea Island leprosy bug's closest relatives were bacteria circulating in humans in medieval Europe.
One of these was obtained from the skeleton of a leprosy victim who died and was buried in Winchester more than 700 years ago.
Winchester is only 70km from Brownsea Island.
Surprised by their findings Prof Meredith is now trying to get to the bottom of this "chicken and egg" bacterial conundrum.
"What we're trying to tease out now is did the squirrels get leprosy from people and have just been carrying it ever since, or in fact does it work the other way round - were humans originally infected from squirrels?"
Irrespective of which came first, the research raises the possibility that animals might serve as an important reservoir for leprosy.
Although Prof Meredith doesn't think that the squirrels pose a threat to humans, the possible spillover of bacteria from animals into humans in other parts of the world where human contact with infected animals might be more common is still a possibility.
The World Health Organization reports thousands of new cases of human leprosy every year.
That's one of the reasons why researchers are keen to study other populations of red squirrel and rodents from other parts of the world.
The first step will be to determine whether red squirrels in the rest of Eurasia might be infected, so Prof Meredith is keen for people to email her with details of any other populations of red squirrels that appear to be affected by leprosy.
Signs to look out for include abnormal growths on the ear and snout.