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Ancient Leprosy Genome Reconstructed

06/14/2013
Rachael Moeller Gorman

For the first time, researchers have reconstructed an ancient microbial genome without using a reference genome. Find out how they did it...


Bones and teeth from skeletons of medieval lepers harbor enough Mycobacterium leprae DNA for researchers to sequence the genome of the ancient bacteria and compare it to those of modern strains. As it turns out, modern and medieval M. leprae are actually very similar.

Side view of the skull of a medieval leprosy case from Odense, Denmark. Source: Ben Krause-Kyora




“The bacteria are really well preserved,” said Kay Nieselt, head of the Integrative Transcriptomics group at the University of Tübingen, Germany and co-author of a new study published today in Science. “That was, for us, a spectacular finding.”

Since the advent of next-generation DNA sequencing technologies, short DNA fragments, such as those often found in partially degraded ancient samples, have become easier to sequence. In 2011, some of Nieselt’s co-authors sequenced Yersinia pestis, which caused many of the plagues that have decimated humans throughout history, including the Black Death in 14th century Europe.

This time, the team set out to learn about the M. leprae microbe, which causes leprosy. The disease, with its painful sores and social stigma, struck many of the world’s medieval populations but declined in Europe during the 16th century. It still, however, infects 225,000 people annually in the developing world and requires a multi-drug therapy for treatment.

Lepers’ remains are slightly easier to identify than those of plague victims, since the microbe leaves its mark on bone. The researchers worked with several cemeteries in medieval leper colonies in Sweden, Denmark, and the UK, gathering samples from bone and tooth lesions in exhumed skeletons.

Using a bead-capture approach, the team screened 22 skeletons for 3 key M. leprae genes and evaluated the DNA sequences for damage, comparing them to control human mitochondrial DNA (mtDNA). The team found typical age-related damage in the human mtDNA but surprisingly little damage to the M. leprae DNA. This, the authors posit, is perhaps due to the strong layer of mycolic acids that protect the leprosy microbe.

The five samples with the most preserved DNA were selected for further analysis. The researchers enriched four of these samples for M. leprae DNA using DNA array capture with a modern M. leprae array. This would have been impossible to do with traditional Sanger-based gene sequencing.

One sample from a tooth, however, was so complete that it didn’t need the enrichment step. Using second generation shotgun sequencing, the group created a de novo reconstruction of the ancient M. leprae genome that precisely aligned with the modern reference version. “That is unique, no one was able to do that before, a de novo reconstruction of an ancient microbial genome,” said Nieselt.

The team reconstructed the whole genomes for these 5 M. leprae samples; when compared to 11 modern M. leprae strains from patient biopsies, they found that not much has changed since medieval times, identifying just 755 single nucleotide polymorphisms and 57 small insertions or deletions in 16 genes.

So if the bacteria hasn’t become less virulent, why did the disease disappear from Europe in the 16th century? Perhaps the presence of other infectious diseases played a role, or maybe an overall improvement in health and sanitation helped.

The team now hopes to apply the technique to an array of ancient illnesses. “It would be, of course, interesting now to go for tuberculosis, which is one of these really devastating diseases, historically speaking,” said Nieselt. “This work opens up the door to go further back.”

Reference

1. Schuenemann, V.J., P. Singh, T.A. Mendum, B. Krause-Kyora, G. Jäger, K.I. Bos, A. Herbig, C. Economou, A. Benjak, P. Busso, et al. 2013. Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae. Science. Published online June 13, 2013.

Keywords:  ancient genomics