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Researchers Genotype Tuberculosis Strain Using a Sequencing Approach


Using a next-generation sequencing-based approach, researchers were able to genotype a strain of Mycobacterium tuberculosis isolated from an individual buried in Leeds, England, during the 19th century.

Previously, archaeologists had determined whether or not a person had been suffering from tuberculosis at the time of burial based on damage the disease inflicts on the skeleton. But, as Terence Brown, a professor at the University of Manchester, points out, such damage is not unique to tuberculosis, and so researchers have turned to ancient DNA from those skeletons to obtain more definitive diagnoses. "Gradually, we've just tried to use better and better techniques to make those kinds of experiments more secure and more informative," he says.

As Brown and his colleagues reported in the Proceedings of the National Academy of Sciences in October, they examined the DNA found within a rib bone, which showed evidence of tuberculosis infection, from an individual buried in the UK in the 1800s. They targeted 260 regions from the M. tuberculosis genome for enrichment in this sample. From this, the researchers obtained 726,484 reads, of which 664,500 mapped to those targeted regions. Brown adds that those regions were chosen for enrichment as they can be used to differentiate various strains of M. tuberculosis.

He and his colleagues then compared their tuberculosis strain to known, modern strains — and found a match. This strain, isolated from Leeds, was very similar to one called H37 that was isolated in New York in 1905. "It was just kind of neat," Brown says. "There was obviously a lot of contact between Europe and North America at that time, and to find a similar strain in Leeds in England as was in New York at about the same time makes a bit of sense."

Of course working with such historic strains of DNA raises the issue of contamination from the lab and from environmental, nonpathogenic strains of Mycobacterium. "I must admit, we spent a year writing this paper, and a large part of that time was agonizing over whether the results were real or some contamination," Brown adds.

He notes that his lab took a number of precautions, such as wearing sterile clothing, to prevent cross-contamination in the lab as well as using larger stretches of DNA to prevent the analysis of harmless Mycobacterium. "Through looking at so much more of the DNA, we have a better opportunity to find pieces which might indicate that it is not Mycobacterium tuberculosis," he says.

Such an approach could be applied to study how widespread certain tuberculosis strains were, or determine how strains moved through a geographic area. Brown says that his lab has collected a number of skeletons from across Europe and from a number of time periods. "One could look at archeological samples covering [a] time span in a single location, [and] we could perhaps see how a strain disappears and is replaced by another," he says. There are now the samples and the techniques to do so.