A 16th-century mummy helped scientists rebuild the DNA of an E.coli cell

An international collaboration of researchers has successfully reconstructed the genome of an E.coli from the remains of gall bladder stones of an Italian noble, mummified in the 16th century, a press release said. 

Escherichia coli (E.coli) was originally thought to be a commensal - a microscopic organism that resides within the host body without offering any benefit but not causing any harm either. Over the years, scientists have found out that inside the human gut, E.coli helps us digest our food, protecting us from other infections, while also helping in the production of vitamin K and B12.

But E.coli also has a mean side. When the host body is undergoing stress or has low immunity, E.coli assumes the role of an opportunistic pathogen that can launch a full-blown attack on the host if they manage to enter the bloodstream, urinary tract, or kidneys. Some strains of the organism can also result in serious and sometimes even fatal food poisoning outbreaks and infections.

A silent killer within us?

While E.coli has often been associated with sporadic outbreaks, it has never been looked at as a pandemic-capable organism, even though it is highly resistant to treatments. Hendrik Poinar, an evolutionary geneticist at the McMaster University in Canada, who was involved in the research said, "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 [such as E.coli]."

The researchers argue that although we do not have historical records of deaths caused by organisms like E.coli their impact on human health and mortality has likely been tremendous. To understand the evolutionary history of the organism, such as where it acquired its novel genes or antibiotic resistance, the researchers needed the genome of its ancestor, and 16th-century mummified remains were a good opportunity to achieve this. 

The mummified Italian noble

Well-preserved mummified remains used in this study were found way back in 1983 at the Abbey of Saint Domenico Maggiore in the city of Naples, Italy. One of the remains was confirmed to be of Giovani d’Avalos, a Neapolitan noble from the Renaissance period. In 1586, d'Avalos died at the age of 48, from what is thought to be chronic inflammation of the gallbladder due to gallstones, the press release said. 

Unlike infections like smallpox, the nobleman had no visible signs of infection so there wasn't any evidence to say that he had E.coli infection as well. The research team, working in Tyvek suits and masks in a clean room put the gallstones from the remains under multiple demineralization digests.

In an email to Interesting Engineering, George Long, a bioinformatics student at McMaster University and the lead author of the study compared this to the peeling of an onion. The researchers hoped that the deeper they went with each demineralization step, the better preserved the DNA would be. 

The team worked meticulously to isolate sample fragments while protecting them from environmental contamination and the recovered material was sequenced to map genes of E.coli that were present in these gallstones. This would give the researchers a better idea of the role the organism played inside the gut of the nobleman. From there, the research team then reconstructed the genome of the E.coli, which was then compared to modern-day versions. 

Narrowing down on E.coli infection

Although they had taken all possible precautions, the researchers found that the handling and processing of the sample introduced some other organisms, which were detected during sequencing.  Compared to that, the gallstone samples, had an overwhelming presence of E.coli, reaching as much as 60 percent levels in some cases. "We'd only expect to see that in a clear infection of the gallstone," Long told Interesting Engineering. 

Another evidence that the E.coli detected was indeed ancient is the antimicrobial resistance (AMR) profile that the researchers obtained for these samples. Bacteria are continuously adapting to their environment and pass on antimicrobial resistance genes between themselves if they are likely to confer a survival advantage. "We can say that our ancient strain was part of a relatively rare sequence type and it contained an AMR profile similar to one seen in modern strains not subjected to antibiotics," Long clarified in the email.  

The research team had also tested the nobleman's lungs, bladder, and small intestine in a similar way but did find anything significant there.  

“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 today are still causing gallstones,” said Erick Denamur, Professor of Biochemistry and Molecular Biology at the Université Paris Cité, who was also involved in the study.

The findings of the study were published today in the journal Communications Biology. 

Abstract

Escherichia coli – one of the most characterized bacteria and a major public health concern – remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16^th century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past.