The first ancient genome of Escherichia coli (E. coli) has been identified and reconstructed from a 16th-century Italian mummy, by a research team from McMaster University and the University of Paris Cité. The work has been published in Communications Biology.
Even in today’s world, E. coli is a public health concern and can cause death. E. coli is a bacteria that is often found in the intestines, is normally harmless, and can keep the digestive tract heathy. However, some strains of this bacteria can make people very sick by causing diarrhea, pneumonia, respiratory illness, and other illnesses. It is also an opportunistic pathogen that can infect a host during immunodeficiency, stress, or underlying disease.
The actual evolutionary history is still not well understood. Some mysteries are unknown, such as when it required antibiotic resistance and novel genes. It is thought that E. coli has had a tremendous impact on the health of humanity, but there are not many historical documents on this, unlike other diseases such as the Black Death – which killed around 200 million people globally.
“A strict focus on pandemic-causing pathogens as the sole narrative of mass mortality in our past misses the large burden that stems from opportunistic commmensals driven by the stress of lives lived,” Hendrik Poinar, the director of McMaster’s Ancient DNA Centre and a principal investigator at the Michael G. DeGroote Institute for Infectious Disease Research, said in a statement.
The researchers used the mummified remains of a group of Italian nobles. These mummies were recovered in 1983 from the Abbey of Saint Domenico Maggiore in Naples. The researchers focused on one individual – Giovani d’Avalos – a Neapolitan noble who died in 1586, aged 48. He was thought to have suffered from chronic inflammation of the gallbladder because of gallstones.
The research team isolated fragments of the target bacterium from d’Avalos's gallstone and reconstructed the E. coli genome. This 400-year-old E. coli ancestor could then provide researchers with a direct comparison to analyze how the bacteria have adapted and evolved over time.
“When we were examining 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,” explained George Long, co-lead author of the study.
This study was a technological feat, as the bacteria is very complex and can live in the soil as well as human microbiomes.
“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 is today still causing gallstones,” said Erick Denamur, one of the authors of the paper.
“We were able to identify what was an opportunistic pathogen, dig down to the functions of the genome, and to provide guidelines to aid researchers who may be exploring other, hidden pathogens,” added Long.
The research is providing insight into the burden of E. coli infection in the past.