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A 16th century Escherichia coli draft genome associated with an opportunistic bile infection

It is the first ancient genome of Escherichia coli and was also responsible for creating several gallstones.

Jun 16, 2022

Authors: George S. Long, Jennifer Klunk, Ana T. Duggan, Madeline Tapson, Valentina Giuffra, Lavinia Gazzè, Antonio Fornaciari, Sebastian Duchene, Gino Fornaciari, Olivier Clermont, Erick Denamur, G. Brian Golding & Hendrik Poinar



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 recon-struction of the first ancient E. coli genome from a 16th 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.


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Listing image: Provided by the Department of Paleopathology, University of Pisa



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