Scientists reconstructed the genome of ancient E. coli from an Italian mummy

Scientists reconstruct the genome of centuries-old E. coli using fragments extracted from an Italian mummy.


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Despite the fact that E. coli is a major public health concern that causes significant death and morbidity, it is not a cause of pandemics. Also known as a commensal, a bacteria that lives inside us and can behave as an opportunistic pathogen, infecting its host when stressed, has an underlying disease, or is immunodeficiency.

According to scientists, its whole evolutionary history is unknown, including when it acquired unique genes and antibiotic resistance. 

Having the genome of a 400-year-old ancestor to the modern bacterium offered scientists an opportunity to study- how it evolved and adapted.

In collaboration with the University of Paris Cité, Université Paris Cité /French Institute of Medical Research (INSERM), scientists at McMaster University have identified and reconstructed the first ancient genome of E. coli. They obtained fragments from the gallstone of a 16th-century mummy.

The mummified remains come from a group of Italian nobles whose well-preserved bodies were recovered from the Abbey of Saint Domenico Maggiore in Naples in 1983.

For the study, scientists conducted a detailed analysis of one of the individuals, Giovani d’Avalos. A Neapolitan noble from the Renaissance period, he was 48 when he died in 1586 and is thought to have suffered from chronic inflammation of the gallbladder due to gallstones.

George Long, a lead author of the study, said, “When we examined these remains, there was no evidence to say this man had E. coli. Unlike an infection like smallpox, there are no physiological indicators. No one knew what it was.”

Scientists meticulously isolated the fragments of the target bacterium, which had been degraded by environmental contamination from many sources. They used the recovered material to reconstruct the genome.

Erick Denamur, the leader of the French team involved in the strain characterization, said, “It was so stirring to be able to type this ancient E. coli and find that while unique, it fell within a phylogenetic lineage characteristic of human commensals that are today still causing gallstones.”

Long said“We were able to identify what was an opportunistic pathogen, dig down to the functions of the genome, and provide guidelines to aid researchers who may be exploring other, hidden pathogens.”

Journal Reference:

  1. Long, G.S., Klunk, J., Duggan, A.T. et al. A 16th century Escherichia coli draft genome associated with an opportunistic bile infection. Commun Biol 5, 599 (2022). DOI: 10.1038/s42003-022-03527-1


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