Scientists believe they may have discovered the cause of an epidemic that struck Mexico’s Aztec population in 1545, killing up to 15 million people.

In a paper published in Nature Ecology & Evolution, they describe how DNA extracted from the teeth of 29 skeletons buried in a cemetery in southern Mexico revealed previously unidentified traces of the salmonella enterica bacterium.

The bacterium is known to cause enteric fever, of which typhoid is an example. According to the study, the symptoms tally with those mentioned in records from the time, which describe victims developing red spots on the skin, vomiting, and bleeding from various body orifices.

The epidemic was one of several to hit the indigenous population soon after the arrival of Europeans in the early 16th century.

"When the Europeans arrived in Mexico, they brought with them lots of different diseases," Ashild Vagene, co-author of the study, told The Independent. "There were dozens of epidemics across the New World and Mexico was particularly hard hit."

"What we're talking about is the devastating decimation of indigenous populations by previously unknown diseases," Dr Caroline Dodds Pennock, lecturer in International History at the University of Sheffield, told The Independent.

"Mortality rates were maybe 80 or 90 per cent by 1600," she said. "Imagine nine out of every 10 people dying - it's almost unimaginable."

The cause of the 1545-1550 epidemic has been debated for more than a century. Measles, pneumonic plague and influenza have all been suggested as possibilities, but historians have never reached a consensus.

The indigenous population gave the outbreak the name “cocoliztli”, a generic term meaning “pestilence” in the Aztec Nahuatl language.

Although estimates vary, the epidemic likely wiped out between five and 15 million people – up to 80 per cent of the population.

It came just two decades after a smallpox epidemic that killed up to eight million people just after the Spanish arrival and is considered one of the most devastating epidemics in human history.

It affected large areas of central Mexico and Guatamala, perhaps extending as far south as Peru.

Ms Vagene and her team analysed the DNA from two sets of skeletons: 24 that were buried in a cemetery that is closely linked with the "cocoliztli" epidemic, and five found in a cemetery that was in use before the Spanish colonisers arrived in 1519.

The DNA was analysed using a new piece of software that allows scientists to screen for any known pathogen.

"This is ground-breaking for our field of ancient DNA," Ms Vagene said. "It allows us to screen for all pathogens that we know today without having to specify a target organism. We can look for the unknown, which is wonderful."

The salmonella strain was found in 10 of the 24 "post-contact" skeletons and none of the "pre-contact" bodies, which Ms Vagene described as a "great finding".

"Ancient DNA doesn't always preserve very well. It breaks down over time," she said. "So to be able to find it in 10 out of 24 is significant."

The fact that traces were found in the teeth is significant too, according to Ms Vagene.

"Salmonella is a disease that you would normally catch through contaminated food or water sources," she said. "It would start in the gut, so finding it in the teeth suggests it had got into the bloodstream. The disease had spread everywhere in their body."

This suggests that these individuals were not simply carriers of the disease - they were victims of it.

More research is needed to determine whether salmonella enterica was the sole cause of the epidemic or whether other viruses and pathogens were also present in these bodies. Ms Vagene also pointed out that her team only studied one group of skeletons from one burial site.

"We just don't know if this pathogen was present in other areas (affected by the outbreak)," she explained.

Whether it was Europeans who introduced salmonella to the indigenous population is also uncertain.

Several factors point towards this conclusion, however. Salmonella enterica existed in Europe well before the Spanish began their conquest of the region, while the "pre-contact" skeletons analysed for this study had no trace of the pathogen.

Furthermore, it is possible for someone to carry the pathogen without presenting any symptoms.

"Seemingly healthy individuals could have travelled from Europe to Mexico without knowing that they had it," said Ms Vagene.

If the infected person's faeces had come into contact with the local water supply, that could have led to a rapid spread of the disease, she explained.

Aztec artefacts: The art of sacrifice Show all 8 1 /8 Aztec artefacts: The art of sacrifice Aztec artefacts: The art of sacrifice 243287.bin Evil eye: a mosaic mask of the Aztec deity Tezcatlipoca The Trustees of the British Museum Aztec artefacts: The art of sacrifice 243288.bin The Codex Moctezuma The Trustees of the British Museum Aztec artefacts: The art of sacrifice 243289.bin A gold, silver and copper pendant, circa 1200 The Trustees of the British Museum Aztec artefacts: The art of sacrifice 243290.bin A pendant showing Xiuhtecuhtli, the god of fire The Trustees of the British Museum Aztec artefacts: The art of sacrifice 243291.bin A stone carving of Quetzalcoat a Mesoamerican deity The Trustees of the British Museum Aztec artefacts: The art of sacrifice 243292.bin The head of an eagle warrior The Trustees of the British Museum Aztec artefacts: The art of sacrifice 243293.bin A sacrificial knife made of wood, mosaic and shell The Trustees of the British Museum Aztec artefacts: The art of sacrifice 243294.bin A double-headed serpent The Trustees of the British Museum

Elizabeth Graham, professor of archaeology at University College London, offered a different interpretation of the findings.

“Salmonella wasn’t necessarily the root cause of the epidemic,” she told The Independent.

People may have been getting sick because of a different disease, which meant that they were less able to look after themselves and each other, increasing the risk of salmonella.

“Everyone was hit at once. No one was able to care for anyone else," she explained. "Salmonella may be a sign of people not being able to care for one another.”

But she welcomed the research and the development of enhanced DNA analysis tools that enabled it.

“Even today, diagnosis of diseases is difficult,” she said. “It’s so much more difficult to try to figure out how people died hundreds of years ago.”

Infectious diseases are particularly difficult to identify, Professor Graham explained, as they usually don’t affect the skeleton.

“Almost no DNA could be detected on skeletons a while ago,” she said. “Detection methods have certainly improved.”

Dr Dodds Pennock also welcomed the study and its measured conclusions.