Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide

Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide

Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide

Results of the genome-wide analysis for the samples with sufficient coverage.

<p>Results of the genome-wide analysis for the samples with sufficient coverage.</p

Worldwide distribution of the ancient and modern <i>M</i>. <i>leprae</i> strains analyzed in this study.

<p>Skulls represent strains from osteological specimens dated to the Medieval Period. Human silhouettes represent modern strains, sized to scale according to the number of samples, ranging from 1 (e.g. India) to 36 (South America) Animal silhouettes represent strains from the red squirrel, the nine-banded armadillo, and naturally infected nonhuman primates (a chimpanzee from Sierra Leone, a sooty mangabey from West Africa, and a cynomolgus macaque from The Philippines). Skulls outlined in black are the new <i>M</i>. <i>leprae</i> genomes reconstructed in this study, while skulls outlined in blue represent previously sequenced ancient genomes. Grey skulls are leprosy samples from this study that did not yield sufficient sequence for whole-genome analysis. The main <i>M</i>. <i>leprae</i> lineages, represented by branches (see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006997#ppat.1006997.g002" target="_blank">Fig 2</a>) are color-coded.</p

Phylogenetic analysis of ancient and modern <i>M</i>. <i>leprae</i> strains.

<p>(<b>A</b>) Maximum parsimony tree reconstructed from 3124 informative SNP positions. The tree is drawn to scale, with branch lengths representing number of substitutions. <i>M</i>. <i>lepromatosis</i> was used as outgroup. The novel strains from this study are labelled in red, and the previously published ancient strains are labelled in blue. Animal symbols indicate strains isolated from red squirrels, armadillos and non-human primates. The main branches are color-coded, and the SNP subtypes are marked with dotted vertical bars. Bootstrap values (500 replicates) are shown next to each node. (<b>B</b>) Bayesian phylogenetic tree based on 2371 SNP positions calculated with BEAST 1.8.1. Median divergence times in years B.C.E. and C.E. are shown on the main nodes (the 95% Highest Posterior Density ranges are given in square brackets). Tip labels for each sample show the name, the country of origin and the isolation date, or the radiocarbon dates. The novel strains from this study are labelled in red, and the previously published ancient strains are labelled in blue. Posterior probabilities for each node are shown in grey. The main branches are color-coded. The hypermutator strains 85054, Amami, S15, Br14-3, Br2016-15, Zensho-4, Zensho-5 and Zensho-9 (as described in [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006997#ppat.1006997.ref014" target="_blank">14</a>]) were excluded from this analysis.</p

Time to the most recent common ancestor (tMRCAs) for the entire <i>M</i>. <i>leprae</i> tree and individual branches (HPD = Highest Posterior Density).

<p>Time to the most recent common ancestor (tMRCAs) for the entire <i>M</i>. <i>leprae</i> tree and individual branches (HPD = Highest Posterior Density).</p