Bacterial testament – the DNA of historical pathogens


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Bacterial testament – the DNA of historical pathogens

Learning from past mistakes

Exploring fossils, mummies, or deep geological formations has always been a huge interest of scientists worldwide. That is because they tell us a lot about the past, and help us to predict the future. For example, the bones of the Vesuvius volcano eruption victims found in Herculaneum tell us not to hide in closed boathouses… Unless we want to get baked like a pizza at the extreme temperature of 500 °C.

Skeletons of Herculaneum boathouses.
Photo credit: Marta Matuszewska (author)

Bones have a story to tell… written in DNA

Learning from the past became even more exciting when scientists realized they could look into history on the molecular biology level. Ancient DNA (aDNA) is the genetic material isolated from ancient biological specimens. A notable example of aDNA is the 50,000 year old DNA of a female Neanderthal, isolated from her phalanx bone and sequenced by the research group led by Svante Pääbo in 2013. Obtaining aDNA is complicated, and things get even more difficult when we want to read its sequence. Typically, DNA degrades when it is not sustained by a living cell. In ancient remains, the usually long DNA strands are fragmented and crosslinked, which makes them particularly hard to sequence and put together. Bonus problem: contamination with contemporary DNA is almost unavoidable – the first sequence of Neanderthal mitochondrial DNA contained ~11% of modern human DNA

Geneticist at the Max Planck Institute for Evolutionary Anthropology extracting ancient DNA from a bone (2005).
Photo credit: National Institutes of Health (U.S.A.) 

But bacteria have no bones!

As we’ve learned, isolating aDNA is very difficult, even from well-preserved skeletal remains. But scientists can go even further! Think about bacterial pathogens. Invisible, fragile, tiny cells that invade our bodies. Their DNA is protected only by a cell wall which can be easily degraded over the years. This cell wall is especially thin in the Gram-negative bacteria, which are the majority of human pathogens. Despite these challenges, in recent years, researchers have found various ways to isolate, identify and authenticate bacterial aDNA. They find bacteria preserved e.g. in skeletal lesions or mummified soft tissue, they optimize aDNA isolation techniques and they use various comparative methods to see if their sequence is truly one of an ancient pathogen. This way they can reveal the genomic sequence of the fragile ancient Gram-negative bacteria, such as Escherichia coli, hiding in the remains of our ancestors!

Renaissance infection opportunity 

In a recent paper published in Communications Biology, researchers described obtaining the genome of E. coli that caused an infection five centuries ago. Most strains of the bacterial celebrity, E. coli, do not infect humans easily. They can be present in our gut microbiome, being our symbiotic friend. Well… apart from the times when our immune system is too weak to sustain this relationship and E. coli causes an opportunistic infection. This is exactly what happened in 1586, to Giovani d’Avalos. This poor Neapolitan nobleman’s mummified gallbladder and gallstones were inspected to find the microbial reason for his death. 

Mummified liver and gallbladder of Giovani d’Avalos. Gallstones are indicated with the red square. Note the dark color of the stones which signifies the bacterial infection. 
Photo credit: Long et al. (2022), doi: 10.1038/s42003-022-03527-1

What can Giovani’s gallstone tell us? 

While many human diseases can lead to gallstone formation, the gallstones caused by bacterial infections are quite unique. Their bacterial genesis makes them brown instead of yellow. This type of colouration made Giovani’s remains interesting to the scientists as they researched the mummy. Indeed, the dissection of the gallstone and DNA isolation and sequencing revealed the historical E. coli genome sequence. As we know, the aDNA can be protected from degradation by the physical barriers that shield it from the environment, which means that the gallstones should be protecting the longer strands of bacterial DNA if bacteria were involved in their formation. And indeed, aDNA was found in the case of Giovani’s opportunistic pathogen that most likely was the reason for his death.

More bacterial history in the genes

Ironically, the genetic analysis revealed that the E. coli that killed Giovani was not particularly dangerous. It was a mild strain that does not infect people who have a properly working immune system. Additionally, it had no genes for antibiotic resistance (well, not that Giovani had the access to antibiotics in 1586 anyway). However, it had the advantage of acquiring some virulence genes (such as type IV secretion system (T6SS) from Klebsiella aerogenes, another bacterial human pathogen) during the infection. Finally, this E. coli strain was classified as belonging to a lineage of related strains that is still viable today and still causing gallstones 400 years later!

Why bother? 
Learning from the past is essential to predict the future. Giovani’s gallstones gave us an insight into how the modern E. coli evolves and adapts. This study specifically adds to our knowledge on antibiotic resistance as we can learn that this phenomenon is absent even in lethal infections that happened before the antibiotic era. The researchers hope their efforts will help others who explore such hidden pathogens and will provide information for the ones that try to model infections of the future.

Link to the original post: Long GS et al. (2022). A 16th century Escherichia coli draft genome associated with an opportunistic bile infection. Communications Biology, 5:599.

Featured image: Mummy of Giovani d’Avalos. Credit: The Division of Paleopathology, University of Pisa (Italy)