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A New Reference Genome for Shigella: SMRT Sequencing of a Historic Sample

Thursday, December 4, 2014

In a special issue of The Lancet dedicated to World War I, an article by scientists from the Wellcome Trust Sanger Institute used Single Molecule, Real-Time (SMRT®) Sequencing to decode the genome of the first isolate ever collected of Shigella flexneri.

The bacterium, a descendant of E. coli and first identified as a separate strain in 1902, was responsible for severe dysentery among World War I troops due to poor hygienic conditions in the trenches. Today, S. flexneri is one of the leading causes of diarrheal death among children in developing countries and other areas of poor sanitation.

Hoping to learn more about the evolution of S. flexneri in the last hundred years, the Sanger team used the PacBio® RS II to construct the reference genome of an isolate collected from a British soldier in 1915. They then compared that genome sequence to other isolates collected in the time since, finding that the pathogen’s acquisition of new genetic material has almost exclusively centered on heightened virulence and increased antimicrobial resistance.

In a video describing the work, lead author Kate Baker explained the need to use PacBio long-read sequencing for this project. “Normally when we sequence a bacterial genome, we shred it into sections and we try and put it back together like a jigsaw. With Shigella, though, throughout their genome they have hundreds of repeated elements so when we try to put the jigsaw back together it’s not obvious how we reconstruct the genome,” she said. “Understanding these repeat elements in Shigella is actually a really important part of their evolution because it’s what allows them to exchange DNA with other bacteria.”

With SMRT Sequencing, Baker and her team got a comprehensive look at the Shigella genome. As Baker and her collaborators compared the genomes representing different evolutionary points, they found that modern isolates had more pathogenicity islands and new virulence factors, like Shigella enterotoxin. They also determined that the 1915 isolate was already resistant to penicillin and erythromycin. More results from their work can be found in the paper: “The extant World War 1 dysentery bacillus NCTC1: a genomic analysis.”

Interestingly, the 1915 S. flexneri isolate included in this project was the very first contribution to Public Health England’s National Collection of Type Cultures, the longest-running collection of human pathogen samples in the world. Dubbed NCTC1, the sample was taken from a soldier who died in France. As part of their work, the Sanger scientists traced the sample’s history and for the first time identified the soldier it came from as Private Ernest Cable, who died on March 13, 1915.

This work is part of an ongoing collaboration with the Wellcome Trust Sanger Institute and Public Health England to complete the genome sequences of 3,000 bacterial strains from samples at NCTC.

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