Genes associated with antibiotic resistance have been found in an 11th-century mummy’s colon and feces, long before antibiotics were introduced.

The find suggests that gene mutations responsible for antibiotic resistance occurred naturally in 1,000-year-old bacteria and are not necessarily linked to the overuse of antibiotics.

The research, published in the online issue of PlosOne, began as an international team of scientists analyzed the microbiome of the remains that were mummified naturally in the cold climate of the Andes Mountains.

Photos: Mummy Had Antibiotic-Resistant Genes

Found in Cuzco, the ancient capital of the Inca empire, the mummy was brought to Italy in the second half of the 19th century by professor Ernesto Mazzei. It was then donated to the Museum of Anthropology and Ethnology of the University of Florence, Italy, where it is currently stored with 11 other mummies.

“The mummy lay in a basket made of fibers which contained two drapes covering the body entirely. Only the skeletonized head and part of the hands were visible,” Gino Fornaciari, professor of history of medicine and paleopathology at the University of Pisa, told Discovery News.

Fornaciari explained that the mummy was prepared according to funerary customs which required that the bodies, sometime treated with smoking, be arranged in a fetal position and wrapped in baskets. Such baskets had opening so that faces of the dead could be seen. The baskets had also handles for hanging in family tombs.

“The cold and dry climate of the Andes produced a natural mummification,” he added.

Fornaciari and colleagues unwrapped the mummy from her basket and carried out an autopsy.

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They found the mummy arranged in the fetal position, with ropes tied around the wrist, ankles and hips. The researchers estimated the body belonged to a woman who had died between 18 and 23 years of age.

The mummified heart, esophagus and colon (containing an enormous amount of feces) were abnormally enlarged, suggesting a symptom of a chronic case of Chagas’ disease.

This is a potentially life-threatening condition caused by the protozoan parasite Trypanosoma cruzi (T. cruzi). It is spread by bloodsucking insects known as Triatominae or kissing bugs.

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About 6 to 7 million people are estimated to be infected worldwide, mostly in Latin America.

A team of international researchers from California, Puerto Rico and Italy directed by Raul Cano, a professor at the California Polytechnic State University, was able to fully sequence the bacteria DNA in the mummy’s colon and feces.

The researchers found abundant DNA belonging to Trypanosoma cruzi, confirming the Chagas disease’s diagnosis already made by Fornaciari in 1992 by other methods.

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“It is very likely that Chagas’s disease was the cause of death for the young woman,” Fornaciari said.

The woman survived for some time, despite having advanced heart disease, megacolon and megaesophagus, suggesting that she was probably treated with drugs, possibly coca leaves.

“Toxicological analyses are underway on a 50 cm (19.6-inch)-long braid. The hair’s length corresponds to 5 years of life and should tell us about use of phychoactive substances,” Fornaciari said.

Analysis of the mummy’s microbiome also revealed the presence of other disease caused by bacteria, such as Clostridium difficile, from which C. difficile infection that causes diarrhea and colitis originates, and some types of human papilloma virus (HPV), a sexually transmitted virus which causes cervical cancer.

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While the recovered T. cruzi appeared more primitive than modern forms of the modern parasite, it was 98 to 99 percent similar to today’s virus.

“This shows that while T. cruzi had to adapt to new conditions in the human guest, HPV was already accustomed to the human body since remote times,” Fornaciari said.

Most interestingly, the researchers identified many antibiotic-resistant genes that would have made treatment with modern broad-spectrum antibiotics -- such as fosfomycin, chloramphenicol, tetracycline, quinolones and vancomycin -- ineffective.

“In particular, vancomycin was discovered more than 50 years ago, and vancomycin-resistant genes have been mainly implicated with the increased use of this antibiotic,” the researchers wrote.

The gut microbiome of the basket mummy from Cuzco reveals a different picture, showing that antibiotic- resistant genes predate therapeutic use of these compounds.

“The finding has practical implications in modern medicine and helps understand the evolution of pathogens,” Fornaciari said.