16th century Italian mummy reveals ancient presence of E. coli

An international team of Canadian, Italian and French researchers including Professor Eric Dynamore, a specialist in population genetics of E. coli and Director of Unit 1137 Infection, Antimicrobials, Modeling and Evolution (Paris City University, Sorbonne University Paris Nord, Enserm), has reconstructed the first ancient genome of E. coli, using fragments extracted from a gallstone from a 16th-century Italian mummy.

While that. coli is a public health problem today, causing significant mortality and morbidity, until now there was no physical evidence of its existence prior to the 19th century, and very little is known about its expansive history.

In contrast to well-documented epidemics of pathogens such as the Black Plague, which lasted for centuries and killed up to 200 million people worldwide, there is no historical record of deaths caused by opportunistic pathogens such as E. coli, despite their impact on humans. The health and mortality may have been enormous.

Escherichia coli is a commensal that resides in the intestines of healthy people and animals. While most forms are harmless, some strains are responsible for food poisoning and serious, sometimes fatal blood infections. These bacteria, adaptable to many different lifestyles, are becoming increasingly resistant to antibiotics. The manner in which they evolved remains to be elucidated, with the acquisition of new genes isolated or aggregated on plasmids conferring resistance to antibiotics and pathogens.

In 1983, a team of Italian archaeologists from the University of Pisa discovered the mummified remains of several Italian nobles found in the monastery of San Domenico Maggiore in Naples (Italy). A careful pathological and histological examination was made of one of the individuals, a nobleman of Naples who died in 1586 at the age of 48. This examination revealed, among other things, the presence of several intact gallstones indicating that this person may have chronic cholecystitis. Professor Hendrik Poinar, an evolutionary geneticist, director of the Center for Ancient DNA at McMaster University and principal investigator at the university’s Michael J. DeGroot Institute for Infectious Disease Research, discovered the presence of the bacterium E. coli five centuries ago.

A specialist in population genetics for E. coli, Professor Eric Dynamore (PU-PH Université Paris Cité) has joined the international team of researchers to reconstruct and analyze the first ancient genome of E. coli. “It was very moving to write this ancient E. coli and discover that it was almost unique but was part of a lineage characteristic distinct to the human symbionts that today causes cholecystitis,” says Eric Dynamore.

The technological prowess is more than remarkable because the ubiquitous Escherichia coli lives not only in the soil but also in our microbiomes. The researchers had to meticulously isolate fragments of the targeted bacteria, which were degraded by environmental pollution from many sources. The recovered material allowed them to reconstruct the genome.

Having the genome of a modern, 500-year-old bacterium provides researchers with a comparative point to study its evolution and adaptation since that time. This dive into the past could also help predict its future developments in terms of virulence, resistance and possibly also those of other opportunistic pathogens.

Reference: 16th century Escherichia coli genome project associated with opportunistic bile infection –
George S Long, Jennifer Klink, Anna T Duggan, Madeleine Tabson, Valentina Giuffra, Lavinia Jazz, Antonio
Fornaciari, Sebastien Duchenne, Gino Fornaciari, Olivier Claremont, Eric Dinamore, J. Brian Golding 1 and Hendrick
Poinar (https://doi.org/10.1038/s42003-022-03527-1)

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