Escherichia coli, popularly known as E. coli , is a bacteria that is commonly found in the lower intestine of healthy, warm-blooded organisms. Most E. coli bacteria are harmless, but a few have the potential to cause serious food poisoning and digestion trouble. Heavily studied since the 19th century, the evolutionary history of the pathogen has long eluded scientists, but a breakthrough has been made. Canadian scientists have extracted the genetic code of a 436-year-old version of E. Coli from an Italian mummy, and published their results in Communications Biology .
A First-of-Its-Kind E. Coli Genetic Sequencing
What George Long and his colleagues from McMaster University in Hamilton, Canada have achieved is quite remarkable and has never been done before. Taking the mummy of Giovanni d’Avalos, who died in 1586 at the age of 48 in Naples, a first-of-its-kind genetic analysis was performed on the ancient strain of this bacteria. Specifically, they detected the infection in the sterile innards, i.e., the gallstone and were able to isolate and genetically sequence the microbe . This has never been done before!
It remains unclear whether Giovanni d’Avalos had a fatal bout of E. coli. Only further research and study can shed light on this. The bacteria, essential for gut health and digestion can particularly act up during periods of disease or immunodeficiency.
There are several kinds of E. coli. For example, the ones resting in our colon are the good bacterium, helping us digest food, whilst the bad variants can cause stomach aches, bloody diarrhea, vomiting, even kidney failure, reports Haaretz.
Giovanni d’Avalos’ remains come from a group of Italian nobles , whose bodies were recovered from the Abbey of St. Domenico Maggiore in 1983. However, as of now, Giovanni’s e. coli remains a mystery in terms of understanding its full evolutionary history, said the researchers in a press release from McMaster University.
“When we were examining these remains, there was no evidence to say this man had E. coli,” said George Long, a graduate student at McMaster University and lead author of the new study. “No one knew what it was. 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 added.
Helium ion microscopy image showing T4 phage infecting E. coli. Some of the attached phages have contracted tails indicating that they have injected their DNA into the E. coli host. (Terry J. McGenity, Amare Gessesse, John E. Hallsworth, Esther Garcia Cela, et al / CC BY-SA 4.0 )
E. Coli: A Silent Killer
Unlike the COVID-19 pandemic in which thousands of scientists have researched and are still researching the virus’s devastating effects, E. coli has been much less studied by the scientific community.
This is also true of the 14th-century Black Death plague , which evolved from the bacterium Yersinia pestis, killing over 200 million people.
E. coli deaths have not been well documented, even though it has always been a part of the human gut, with a clear correlation with longevity, mortality, and quality of life.
“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,” stated evolutionary geneticist Hendrik Poinar. Poinar is director of McMaster’s Ancient DNA Centre and a principal investigator at the university’s Michael G. DeGroote Institute for Infectious Disease Research.
“Ancient DNA studies typically focus on obligatory pathogens such as M. leprae, Salmonella enterica and Y. pestis that are easily correlated with pathologically distinct, or historically relevant, mortality events,” said the study researchers.
Researchers reconstructed the E. coli genome using fragments from an infected gallstone found in this 16th-century Italian nobleman’s mummy remains. ( University of Pisa’s Paleopathology Department )
Giovanni’s E. Coli: His Gall Bladder and His Diet
In the nobleman’s case, the research team identified thickened gallbladder walls and a number of intact gallstones, implying cholecystitis from a chronic bacterial infection. This was further corroborated by the typical brown discoloration of the gallstone indicating a bacterial infection .
The researchers extracted the DNA from the gallstone and reconstructed the genome of the Italian’s E. coli bacterium.
Long added that this particular strain of E. coli could thrive in an enabling environment and outcompete other bacteria. In this case, the environment was Giovanni’s gallbladder.
This breakthrough research study sheds new light on the evolution of the E. coli bacterium, its role on our diet, and potential antibiotic resistances.
“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, the leader of the French team that was involved in the strain characterization.
Giovanni’s E. coli belonged to the Phylogroup A variant associated with relatively non-industrialized areas, where food is cooked, rather than consumed in uncooked form.
It is still unclear if the gallbladder E. coli is the one responsible for taking Giovanni’s life. Future research focusing on the evolutionary role of the bacteria over time will help scientists understand this unusual E. coli Italian mummy case and others better.
Top image: George Long performing genomic data analysis on the mummy where the E. coli was detected . Source: Georgia Kirkos / McMaster University
By Sahir Pandey