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

Hamilton, ON, June 16, 2022 – An international team led by researchers from McMaster University, working in collaboration with Université de Paris Cité, has identified and reconstructed the first ancient genome of E. coli, using fragments extracted from the gallstone of a 16^e mummy of the century.

The finding is published online today in the journal Communications Biology.

E. coli is a major public health problem, causing significant death and morbidity, but is not a source of pandemics. It is known as a commensal, a bacterium that resides within us and can act as an opportunistic pathogen infecting its host during times of stress, underlying disease, or immunodeficiency.

Its full evolutionary history remains a mystery, including when it acquired new genes and antibiotic resistance, the researchers say.

Unlike well-documented pandemics such as the Black Death, which persisted for centuries and killed up to 200 million people worldwide, there are no historical records of deaths caused by commensals such as E. coli. , although the impact on human health and mortality was probably enormous.

“A strict focus on pandemic-causing pathogens as the sole narrative of mass mortality in our past misses the heavy burden that arises from opportunistic commensals driven by the stresses of lived life,” says the evolutionary geneticist Hendrik Poinar, director of McMaster’s Ancient DNA Center and principal investigator at the university’s Michael G. DeGroote Institute for Infectious Disease Research.

Modern E. coli is commonly found in the intestines of healthy people and animals. While most forms are harmless, some strains are responsible for outbreaks of food poisoning and serious, sometimes fatal, blood infections. The robust and adaptable bacterium is recognized as particularly resistant to treatment.

Having the genome of a 400-year-old ancestor of modern bacteria provides researchers with a point of comparison to study how it evolved and adapted since then.

The mummified remains used for the new study come from a group of Italian nobles whose well-preserved bodies were found at the Abbey of Saint Domenico Maggiore in Naples in 1983.

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

“When we examined these remains, there was no evidence that this man had E. coli. Unlike an infection like smallpox, there are no physiological indicators. No one knew what it was,” says study lead author George Long, a bioinformatics graduate student at McMaster who conducted the analysis with co-lead author Jennifer Klunk, a former graduate student at university anthropology department.

The technological prowess is particularly remarkable because E. coli is both complex and ubiquitous, living not only in soil but also in our own microbiomes. The researchers had to meticulously isolate fragments of the target bacteria, which had been degraded by environmental contamination from many sources. They used the recovered material to reconstruct the genome.

“It was so moving to be able to type this ancient E. coli and to discover that, although unique, it belonged to a phylogenetic lineage characteristic of human commensals which still causes gallstones today”, explains Erick Denamur, the leader of the French team who was involved in the characterization of the strains.

“We were able to identify what was an opportunistic pathogen, dig down to genome functions, and provide guidelines to help researchers who might be exploring other hidden pathogens,” says Long.

The work was carried out in collaboration with researchers from the University of Pisa and the University of Paris Cité/French Institute for Medical Research (INSERM) and is funded by the Canadian Institute for Advanced Research.