We expect that most other researchers studying TB in the past will also adopt the method with their specimens. The same method could be used to study other diseases that leave a DNA trace in the bones.
Professor Terry Brown
A collaboration between scientists from the University of Manchester
and Durham University
is applying an established approach to the novel problem of rapidly and accurately identify strains of tuberculosis (TB) in ancient bones. Their findings have appeared today in the journal of the Proceedings of the National Academy of Sciences (PNAS)
The technique, which includes the use of hybridisation capture technology, enables the researchers to analyse millions of gene sequences very quickly. The team used it, as part of a wider effort to chart the strains of TB present in skeletons dating from 100 AD up to the 19th
Century, to locate TB genes in the remains of a 19th
Century woman in a Leeds crypt.
Among infectious diseases, TB is second only to HIV in terms of the number of deaths caused, and rates of TB have been on the increase across the globe. It is hoped that research into the history of the disease will help in the ongoing search for vaccines and treatments as it continues to evolve. Some strains can affect the bones, the spine in particular, leaving marks which remain long after death.
Durham’s Professor Charlotte Roberts used these marks to identify 500 skeletons of potential TB sufferers. Samples of these bones, sourced from across Europe and dating from Roman times up to the 1800s, were screened for the presence of tuberculosis DNA and 100 of those went on to be used in the study.
Professor Terry Brown from the Manchester Institute of Biotechnology
and his team performed the genetic analysis, with the data they obtained able to identify the particular strain of TB as one known to be present in North America in the 1800s. Indeed, it is very similar to one recorded in a patient in New York in 1905.
Although one of the flaws of the hybridisation capture technique is the possibility of mistakenly identifying DNA, the results were proved to be accurate by cross-checking with polymerase chain reactions. As Professor Brown explained, this has given the team hope that the method can be applied to other skeletons, in other studies, and even for investigation of other diseases…
What is the aim of the wider research of which this study is a part?
We hope to be able to compare the strains of tuberculosis that were present at different places at different times in the past. This may help us to, for example, trace the origin of TB in Britain. We think TB came to Britain from the Mediterranean region, possibly in Roman times, but to confirm this idea we would have to compare the particular strain present in early British skeletons with that present in bones from southern Europe. Similarly, we believe that there were changes in the frequencies of different strains of TB over time, and these changes were possibly influenced by factors such as immigration, changes in population density, and changes in the environment.
How does the new process you have developed work?
The process itself is not new – the techniques of hybridisation capture and next generation sequencing have been around for several years and have been used a lot in more conventional types of genetic study. However, we are the first to apply them to ancient TB.
Hybridisation capture is a way of enriching a DNA extract for fragments of DNA that cover particular genes you are interested in. It uses ‘baits’, which are synthetic pieces of DNA made in the lab, that have the same sequences as the genes you’re interested in. The corresponding fragments in the ancient DNA extract stick to these baits, so the rest of the extract can be washed away, and the ‘captured’ fragments then released and sequenced. Next generation sequencing is simply the modern version of DNA sequencing.
How is this an improvement on methods used in the past?
Previously we had to sequence each gene individually in separate experiments, which was laborious and took a lot of time, and also meant that you used up all of your ancient DNA extract just trying to sequence four genes or so. Next generation sequencing lets you sequence lots of genes in parallel in a single experiment.
What is the research telling us about the spread of TB and the development of different strains of the disease?
At present it is not telling us a lot because this is the first skeleton that we have studied in this way. Answering those questions is the longer term aim.
Do you see the use of this technique being extended in future? What are the next steps for your research?
We are now planning to apply the method to other skeletons that show signs of TB. We expect that most other researchers studying TB in the past will also adopt the method with their specimens. The same method could be used to study other diseases that leave a DNA trace in the bones – because the causative bacteria get into the bones before the person dies – such as leprosy, for example.