An international study led by a team of Canadian researchers has identified and reconstructed what is believed to be the first ancient genome of E. coli using fragments from a 16th-century Italian mummy.
Researchers at McMaster University, in collaboration with the University of Paris Cite, were able to rebuild the ancient bacterium using gallstone extractions from the remains of a Neapolitan noble of the Renaissance period.
Researchers say having a genome of the "400-year-old ancestor" to modern-day E. coli offers scientists a comparison for studying how the bacterium has evolved and adapted over time.
The discovery was published Thursday in peer-reviewed journal Communications Biology and was funded by the Canadian Institute of Advanced Research.
Escherichia coli (E. coli) is a commensal bacterium that lives in the intestines of both healthy people and animals. Although most strains of E. coli are harmless, others can cause serious illnesses, including sometimes fatal food poisoning outbreaks and bloodstream infections.
The bacterium is known as an "opportunistic pathogen," causing infections when a person experiences stress, underlying disease or immunodeficiency. It also is known to be resistant to antibiotics and treatments.
E. coli is a major public health concern, but it is not a source of pandemics. Yet researchers note that its evolution has remained much of a mystery.
There are no historical records of death caused by E. coli, however, McMaster evolutionary geneticist Hendrik Poinar says its impact on health and mortality was likely significant.
"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 commensals driven by the stress of lives lived," Poinar said in a press release.
According to the study, the mummified remains are of Giovani d'Avalos, a 48-year-old noble who died in 1586. Researchers say he was thought to have suffered from chronic gallbladder inflammation due to gallstones. His remains were recovered with a group of Italian nobles from the Abbey of Saint Domenico Maggiore in Naples in 1983.
"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," said lead study author and McMaster graduate student George Long in the release.
According to researchers, isolating E. coli fragments from remains is complex as the bacterium lives in human microbiomes, but can also be found in soil. The study's author's say the gallbladder fragments from the mummy were decayed by environmental contamination and they had to work carefully to recover the DNA material to then reconstruct the genome.
Researchers say the reconstructed E. coli was found to be a unique strain, but still fell within a phylogenetic lineage characteristic of human commensals that presently still causes gallstones.
The study's authors say the ancient E. coli helps to "paint a more complete picture of the burden of opportunistic infections of the past."
"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," Long said in the release.
