Despite the fact that E. coli is a major public health concern that causes significant death and morbidity, it is not a cause of epidemics. Also known as a commensal, a bacterium that lives inside us and can behave as an opportunistic pathogen, can infect its host when it is stressed, has an underlying disease, or has immunodeficiency.
According to scientists, its full evolutionary history is unknown, including when it acquired unique genes and antibiotic resistance.
Having the genome of a 400-year-old ancestor of the modern bacterium gave scientists the opportunity to study how it evolved and adapted.
In collaboration with the University of Paris City, Université Paris City/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 gallstones of a 16th-century mummy.
The mummified remains come from a group of Italian nobles whose well-preserved bodies were recovered in 1983 from the Abbey of St. Domenico Maggiore in Naples.
For the study, the scientists conducted a detailed analysis of one of the individuals, Giovanni de Avalos. A Neapolitan nobleman of the Renaissance period, he was 48 years old when he died in 1586 and is believed to have suffered from chronic inflammation of the gallbladder due to gallstones.
Study lead author George Long said, “When we examined these remains, there was no evidence to say that this man had E. coli. Unlike an infection like smallpox, there are no physical indicators. No one knew what it was.”
The scientists carefully isolated fragments of the target bacterium, which had been spoiled by environmental pollution from multiple sources. They used the recovered material to reconstruct the genome.
Eric Denmoor, the leader of the French team involved in the stress characterization, said, “It was very encouraging 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 is still causing gallstones today.”
Long said, “We were able to identify an opportunistic pathogen, dig into the genome’s functions, and provide guidelines to aid researchers who may discover other, hidden pathogens.”
- Long, G. S., Clunk, J., Duggan, A. T. et al. A 16th-century Escherichia coli draft genome associated with an opportunistic gall infection. Commune Biol 5, 599 (2022). DOI: 10.1038/s42003-022-03527-1