Archaeological discoveries

An ancient strain of Escherichia coli extracted from a mummy

The oldest genome of the bacterium Escherichia coli could be reconstructed from 400-year-old fragments. An opportunity to better understand the history of this pathogen responsible for food poisoning.

E.coli bacteria seen in electron microscopy.

Unlike well-documented pandemics like the Black Death, which persisted for almost half a millennium and decimated half of Europe's population, there are no historical records to study the impact caused by bacteria responsible for much more limited epidemics. Thus, it is unclear how many deaths are caused by pathogens such as Escherichia coli , Pseudomonas aeruginosa or Staphylococcus aureus , although they are probably linked to several million deaths in history.

A commensal bacterium

One of the reasons explaining this anomaly is that most of these germs are commensal, that is to say that they live in harmony with their host, in this case the human. E.coli is, for example, present in the intestine of all mammals and many vertebrates, again without causing damage, most of the time. Nevertheless, certain strains of this bacterium are responsible for sometimes severe food poisoning that can progress to sepsis; they particularly affect the most fragile people:the elderly, immunocompromised or young children. Recent news has again reported this with the Buitoni pizza scandal. Part of the seriousness of E.coli infections is due to the ability of this bacterium to resist common treatments, the famous "antibiotic resistance". Understanding how this or rather these resistances were acquired would allow doctors to better target treatments and therefore treat patients. Hence the interest in having old strains dating from before the time of Alexander Fleming, the discoverer of penicillin.

A 16th century Italian mummy from which E.coli DNA fragments were extracted. Credit:Division of Paleopathology of the University of Pisa.

Mummified nobles

It is such a strain, 400 years old, that has been identified in an Italian mummy. She belongs to a group of Italian nobles whose well-preserved bodies were found at the Abbey of Saint Domenico Maggiore, Naples, in 1983. For the study, researchers from McMaster University, Canada, and the Paris Cité University conducted a detailed analysis of one of the individuals, Giovani d'Avalos. A Neapolitan Renaissance nobleman, he was 48 when he died in 1586. The individual suffered from chronic cholecystitis, an inflammation of the gallbladder (in the liver), caused by stones. These small pebbles, which cause severe pain, were analyzed by Erick Denamur, a specialist in the genetics of E.coli populations. And the researcher found fragments of the bacterium there, more than 400 years old. "It was so moving to type this ancient E. coli and discover that it was almost unique but that it was part of a phylogenetic lineage characteristic of the human commensals that today cause cholecystitis “, he says in a press release.

Analyzes and reconstruction of the genome of this ancestral bacterium show that its 4,446 genes belong to phylogroup A and to an exceptionally rare type 4995 sequence. It does not have a specific virulence factor or acquired resistance to antibiotics. On the other hand, some of the genes that can induce this resistance are already present in this strain, indicates the study published in the journal Communications Biology . Phylogroup A is usually present in the gut of individuals living in rural areas or sparsely urbanized communities. It is also frequently found in cases of biliary infections. According to the researchers, it is therefore an opportunistic germ that affected the liver of this noble Italian, taking advantage of an unsolved immune circumstance.

This is not the only bacterium found:fragments of Klebsiella aerogenes were also identified. The two germs would even have exchanged genes during their cohabitation in the bile ducts of Giovani d'Avalos. "Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections in the past", explain the researchers. But this research also provides a point of comparison for the study of the evolution of the genomes of the different strains of E. coli and perhaps even to predict their future evolution "in terms of virulence and resistance and possibly also those of other opportunistic pathogens “, conclude the authors.