In First, Archaeologists Detect Opportunistic Bacteria in a Mummy

Gut bacteria had no business being in the gallbladder of Giovanni d'Avalos, who died in 16th century Naples. Now the bacterial culprit has been sequenced, shedding light on the evolution of our friend E. coli

Ruth Schuster
Ruth Schuster
An external examination of the naturally mummified Giovanni d'Avalos.
An external examination of the naturally mummified Giovanni d'Avalos.Credit: The Division of Paleopathology, University of Pisa.
Ruth Schuster
Ruth Schuster

In 1586, a man named Giovanni d’Avalos died aged just 48 in the seaside city of Naples. His body would be mummified, his name would be misspelled as “Giovani” and his gallstone would make history.

*Whether he died of his chronic cholecystitis – that is, inflammation of the gallbladder – is hard to tell. He definitely had the condition, and left untreated it can be fatal. And it is from one of his gallstones that George Long of McMaster University, Canada, and colleagues managed to do something never done before. They detected an opportunistic infection by bacteria that typically infest our gut, not our sterile innards, and genetically sequenced the microbe, they reported last week in the Nature journal Communications Biology.

Detecting an opportunistic infection in a 436-year-old cadaver is quite the feat. More importantly, this is also the first time that an ancient strain of this bacteria has undergone genetic analysis, shedding light on its evolution and how our habits contribute to its development.

Who’s a good bacteria

The bacterium opportunistically infecting d’Avalos’ innards is Escherichia coli and under normal conditions, you harbor harmless types of it in your intestines.

We need E. coli, which is named after its 1885 discoverer Theodor Escherich, to help digest our food. It may also help protect against less beneficial germs seething within us.

The rub is that there are myriad strains of E. coli (it’s like there are lots of strains of dogs, but they’re all the same species). The E. coli dwelling in our colon helping us digest is a “good bacterium,” but there are “bad” variants that can cause illness, involving symptoms such as stomachache, bloody diarrhea, vomiting and even kidney failure.

If E. coli normally lives within, what does it mean to be “infected” by E. coli? It means that we ate something inhabited by a “bad” strain that sickened us, usually by emitting a toxin that the good strains don’t produce. Many can rebound from “bad E. coli” infection without medical assistance, but “bad” strains have become a public health concern – note the food recalls because of it. Also, antibiotic resistance is developing in some variants of this species too.

But even the good bacteria can stray, and wreak havoc when they do. E. coli being found in the gallbladder constitutes straying.

The snow-capped Vesuvius volcano is seen across the Gulf of Naples and the southern Italian city of Naples.Credit: Cesare Abbate/AP

Something wrong with the mummy

Actually, infection of the gallbladder isn’t rare and the culprit is often E. coli (though other germs can cause it too).

E. coli is among the most thoroughly researched bacteria in the annals of microbiology, but never before had the DNA of an ancient strain been isolated and reconstructed, Long explains.

It bears adding that this isn’t the first time ancient bacteria have been sequenced by any means, but science has tended to focus on the more terrifying of the genre. “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,” the team writes – those being the bacteria causing leprosy, salmonella and the plague (aka “black death”). E. coli has tended to slip under the radar of the paleobacteria set.

As for Giovanni d’Avalos, one may associate mummification more with ancient South America and of course Egypt – which is how we know Pharaoh Amenhotep had been circumcised. But it was also common in medieval and Renaissance Italy, and even as late as the 19th century.

Even children were mummified, though it bears clarifying that many of these were naturally mummified by the environmental conditions of their burial, while a smaller number of the thousands found to date had been artificially preserved. In short, being a mummy, d’Avalos was not an outlier.

Analyzing his remains, the researchers noticed thickened gallbladder walls and a number of intact gallstones. In other words – he had cholecystitis, and chronic bacterial infection is often the cause. Indeed, examination of a gallstone showed the typical brown coloration of bacterial infection, the team explains.

If one’s gallbladder is infected, it is by definition an opportunistic infection. The archaeology of opportunistic infection has been practically nonexistent, until now.

The researchers isolated DNA from a gallstone, identified the invasive miscreant as E. coli (there were other theoretical options) and reconstructed the ancient E. coli genome.

And what did they find? That genetically it was pretty much like its brethren today. It had 4,446 genes, which means nothing much: E. colis have a range of gene counts. So do we.

Mouse work showed that d’Avalos’ opportunistic bacterium was closely related to an avirulent strain existing today.

“The best way to understand this situation is to think of virulence as a continuum and not a binary state,” Long explains. “While there are some strains of E. coli which are beneficial (i.e., our gut microbiome), there are others that are highly pathogenic and responsible for food poisoning outbreaks. Ours falls somewhere in the middle.”

Eat it in a sandwich and this strain shouldn’t cause trouble, he explains (hence the avirulence in the mouse). “But if it’s in an environment that it’s well adapted and it can outcompete other bacteria, then this ancient strain is able to thrive,” Long says. Giovanni d’Avalos’ gallbladder was evidently a lovely environment for this opportunistic germ.

Why is sequencing this ancient bacteria actually helpful? Our understanding of the bacteria’s evolution has been confined largely to germs that lived in the last century. To understand more about its evolution, to understand if things such as our diet are affecting its development, and that of antibiotic resistance – the more we know about ancient variants, the better, Long explains.

For instance, d’Avalos’ E. coli turned out to belong to Phylogroup A. Wow. That is a variant mainly associated with people in relatively nonindustrialized areas, who eat actual food, not the “typical Western diet” (you know what that is), the professor explains. But eating actual food doesn’t seem to have saved d’Avalos from the grim reaper.

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