It is well known that when Europeans arrived in the New World they brought with them appalling diseases to which the indigenous population, having never been exposed to them before, were particularly susceptible. Very large numbers died of from illnesses including smallpox, measles, mumps and influenza.

These acknowledged killers, however, were comparatively late arrivals in Europe’s brutal colonisation.

In Mexico, at least, another disease laid waste to the locals, starting in 1545, very soon after the invaders landed. And with the next disease came a new word, growing out of the local tongue: cocoliztli, meaning pestilence, or epidemic.

Between 1545 and 1550, a disease roared through the indigenous Mexican population, killing an estimated 800,000. And while there is plenty of evidence to support the fact that the epidemic took place, until now there has been precious little to identify the pathogenic culprit.

Researchers led by Ashlid Vagene of the Max Planck Institute for the Science of Human History in Jena, Germany, have now unmasked the killer. To do so they extracted biological material from between the teeth of 24 corpses interred in a cocoliztli cemetery in the town of Teposcolula-Yucundaa in the Oaxaca region of Mexico.

The burials were known to be those of people who died during the 1545-1550 epidemic. As controls, the team also excavated remains from five nearby corpses known to have been buried before European arrival.{%recommended 6220%}

The extracted genetic material was subjected to a metagenomic analysis using a device called a Meta Genome Analyser Alignment Tool (MALT), with which microbial DNA was extracted, and from which genomes were reconstructed.

Writing in the journal Nature Ecology and Evolution, Vagene and his colleagues reveal the killer disease: Salmonella enterica, a bacteria these days commonly linked with food poisoning.

The use of the MALT to recover definitive DNA evidence has solved a long-standing mystery for archaeologists and historical epidemiologists. Until now, tentative diagnosis of the epidemic had been based necessarily only on reports of symptoms, which included high fever, headache, jaundice, abdominal pain, and bleeding from the nose, ears and mouth.

The time from symptom onset until death was estimated to be three to four days. Whatever the pathogen involved, it did not inhabit its victims long enough to damage or deform hard tissues – which might have allowed its early identification – and nor, of course, did it leave behind any lasting remains of its own.

In a 2000 study in the American Journal of Tropical Diseases, a team of Mexican investigators headed by Rodolfo Acuna-Soto concluded that the cause of the epidemic was some type of viral haemorrhagic fever.

Other suggested causes have included measles and pneumonic plague. Salmonella was never considered a possibility.

Vagene and his colleagues say the MALT technique provides fast and accurate results. They suggest it will be useful in future investigations of ancient diseases, as well as modern outbreaks for which the cause is unknown.