http://www.digitaljournal.com/tech-and-science/science/contagion-of-the-conquistadors-wiped-out-15-million-people/article/512261

Scientists identify what killed millions in 16th century Mexico

Posted Jan 16, 2018 by Karen Graham
In 1545, an epidemic known as “cocoliztli,” an Aztec Nahuatl word for “pestilence," swept through large areas of Guatemala and Mexico. The disease caused high fevers, headaches, bleeding from the eyes, mouth, and nose, ending in death.
Center for Biofilm Engineering Confocal Scanning Laser Microscopy Lab. Photo by Kelly Gorham  Montan...
Center for Biofilm Engineering Confocal Scanning Laser Microscopy Lab. Photo by Kelly Gorham, Montana State University, 2012
Montana State University/Center for Biofilm Engineering
Looking back in history, the arrival of Europeans in the New World caused a great deal of upheaval with the indigenous populations, not only in North America but in Mexico, Central, and South America.
Besides the deaths resulting from being conquered and brought into submission, the native populations experienced high mortality rates during this early contact period as a result of infectious diseases, many of which were introduced by the Europeans.
Indigenous victims  Florentine Codex (compiled 1540–1585)
Indigenous victims, Florentine Codex (compiled 1540–1585)
en:Bernardino de Sahagún (1499-1590), compiler. Original illustration by unknown 16th-century artis
The time of the pestilence
In 1545, a pestilence struck Mexico's Aztec nation, eventually spreading to Guatemala and even as far as Peru. The disease, often starting with headaches and vomiting, went on to cause bleeding from the eyes, nose, and mouth. Death followed in three to four days. The pestilence went on for five years.
An estimated 15 million people died, 80 percent of the indigenous population before the “cocolitzli" was over. The cocoliztli outbreak is considered by many historians as one of the deadliest epidemics in human history. It comes close to approaching the "Black Death," or bubonic plague that killed almost 25 million people in western Europe in the 14th century.
A second cocoliztli outbreak from 1576 to 1578 killed half the remaining population.
Collapse of population in Mexico during the 16th century  attributed at least in part to repeated co...
Collapse of population in Mexico during the 16th century, attributed at least in part to repeated cocoliztli epidemics.
Acuna-Soto R1, Stahle DW, Cleaveland MK, Therrell MD.
For almost 500 years, the cause of the disease has been in question. Historians believe there were many contagions, from smallpox, chickenpox, influenza, measles, sexually transmitted diseases, and even the common cold that played a part in the decimation of the native populations.
This is because the European colonizers spread germs as they ventured into the Americas. Local populations had never encountered many of these diseases, and therefore had no immunity against them. And this lack of immunity to many diseases is an issue today when isolated indigenous tribes in many regions of the world are encountered for the first time.
Rose spots on abdomen of a patient with typhoid fever due to the bacterium Salmonella typhi.
Rose spots on abdomen of a patient with typhoid fever due to the bacterium Salmonella typhi.
CDC/Armed Forces Institute of Pathology, Charles N. Farmer
Enteric fever caused the cocoliztli
On Monday, January 15, a team of scientists, led by Johannes Krause from the Max Planck Institute, Jena, Germany, along with international colleagues, published a study in Nature Ecology and Evolution, describing how they had isolated the DNA evidence from bones and teeth that points to a specific enteric fever called Salmonella enterica Paratyphi C, that appears to have been the cause of the pestilence.
"In the cities and large towns, big ditches were dug, and from morning to sunset, the priests did nothing else but carry the dead bodies and throw them into the ditches," is how Franciscan historian Fray Juan de Torquemada is cited as chronicling the period.Physicians at that time said the symptoms did not match any known diseases, adding to the mystery.
However, it took two breakthroughs to solve the mystery. First, researchers found an undisturbed cemetery in Oaxaca known as Teposcolula-Yucundaa.
Conquistadors exhort their supporters (1909)
Conquistadors exhort their supporters (1909)
Romance of History, Mexico/ Margaret Duncan Coxhead
The area had become a ghost town after the disease wiped out the surrounding population. The team analyzed DNA extracted from the tooth pulp of 29 skeletons buried in the cemetery and found traces of salmonella enterica bacterium, Paratyphi C.
“Given the historical archaeological context of Teposcolula-Yucundaa, it provided us with a unique opportunity to address the question regarding the unknown microbial causes responsible for this epidemic,” said Ashild Vagene, of the Max Plank Institute for the Science of Human History, one of the first authors.
Use of next-generation sequencing
Secondly, scientists from the Max Planck Institute, as well as Harvard University and the Mexican National Institute of Anthropology and History (INAH) subjected the 500-year-old DNA to a new kind of analysis. Using traditional DNA analysis, scientists screen for a specific germ's DNA within a whole range of genetic information.
But using next-generation sequencing, the DNA was put through a new analytical process called MEGAN alignment tool, or MALT for short. Basically, MALT is a statistical alignment tool that improves on the discovery powers of prior tools like the Basic Local Alignment Search Tool (BLAST), cutting down on the amount of time and power needed to find the answers.
Cortez with stout armored band fights his way back into Tenochtitlan in 1520. Diseases brought in by...
Cortez with stout armored band fights his way back into Tenochtitlan in 1520. Diseases brought in by the Europeans killed an additional 15 million of the native population.
Penelope37
"We tested for all bacterial pathogens and DNA viruses for which genomic data is available," and Salmonella enterica was the only germ detected, co-author Alexander Herbig, also from Tuebingen University, told AFP.
“After we identified traces of Salmonella enterica DNA using our new computational technique, we conducted further experiments and computational analyses that allowed us to study the whole genomes of the Salmonella enterica bacteria identified in the teeth of individuals included in our study,” Vågene said.
In the study, the researchers propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa.
However, the MALT technique is a game-changer because it is opening up new research possibilities for diagnosing diseases of the past and solving centuries-old medical mysteries. According to the research team, “The screening technique used here will be transformative for future work on archaeological disease — it’s no longer necessary to have a candidate pathogen in mind for molecular detection."