A genomic study of Mycobacterium leprae in medieval Northern Europe

Leprosy is an infectious disease mainly caused by the obligate intracellular pathogen Mycobacterium leprae (M. leprae). In Northern Europe, the disease reached its highest prevalence in the Middle-Ages, between the 11th and 15th centuries. It disappeared around the 16th century before the introduction of modern medicine. Besides archaeological and medical studies, the direct recovery and analysis of medieval M. leprae genomes can greatly improve our understanding of the history and epidemiology of the disease. This thesis aims to analyse numerous medieval M. leprae genomes from Northern Europe at high genomic coverage using next-generation sequencing. Teeth from 140 human skeletal remains were collected from three cemeteries in Denmark and Germany (1000-1560 AD) in order to 1) screen the remains for M. leprae DNA with PCR, 2) use high-throughput sequencing to recover high-quality M. leprae genomes, 3) place the recovered genomes within the M. leprae phylogeny, and 4) investigate in- silico the possible effects of the genomic variations.Lepra ist eine chronische Infektionskrankheit, welche durch das obligat intrazelluläre Bakterium Mycobacterium leprae (M. leprae) ausgelöst wird. In Nordeuropa erreichte die Prävalenz der Krankheit im Mittelalter zwischen dem 11. und 15. Jahrhundert ihren Höhepunkt. Im 16. Jahrhundert verschwand die Krankheit weit vor der Einführung moderner Medizin. Neben archäologischen sowie medizinischen Studien kann die Isolierung und Analyse des mittelalterlichen M. leprae Genoms zum Verständnis der Geschichte sowie der Epidemiologie der Krankheit beitragen. Die vorliegende Arbeit hat die Analyse zahlreicher, gut abgedeckter mittelalterlicher M. leprae Genome aus Nordeuropa unter Verwendung von Hochdurchsatzsequenzierung zum Ziel. Im Laufe des Projektes wurden Zähne von insgesamt 140 Individuen von drei unterschiedlichen mittelalterlichen Friedhöfen in Dänemark sowie Deutschland gesammelt (1000 – 1560 AD). Das Projekt umfasste folgende Arbeitsschritte: 1) Test auf M. leprae positive Proben mittels PCR, 2) Rekonstruktion möglichst gut abgedeckter M. leprae Genome unter Verwendung der Hochdurchsatzsequenzierung, 3) Einbindung der alten M. leprae Genome in einen phylogenetischen Baum, und 4) In silico-Modellierung der möglichen Effekte genomischer Variationen

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

Effect of X-ray irradiation on ancient DNA in sub-fossil bones - Guidelines for safe X-ray imaging

International audienceSub-fossilised remains may still contain highly degraded ancient DNA (aDNA) useful for palaeogenetic investigations. Whether X-ray computed [micro-] tomography ([mu]CT) imaging of these fossils may further damage aDNA remains debated. Although the effect of X-ray on DNA in living organisms is well documented, its impact on aDNA molecules is unexplored. Here we investigate the effects of synchrotron X-ray irradiation on aDNA from Pleistocene bones. A clear correlation appears between decreasing aDNA quantities and accumulating X-ray dose-levels above 2000 Gray (Gy). We further find that strong X-ray irradiation reduces the amount of nucleotide misincorporations at the aDNA molecule ends. No representative effect can be detected for doses below 200 Gy. Dosimetry shows that conventional mu CT usually does not reach the risky dose level, while classical synchrotron imaging can degrade aDNA significantly. Optimised synchrotron protocols and simple rules introduced here are sufficient to ensure that fossils can be scanned without impairing future aDNA studie

Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

Leprosy, a chronic infectious disease caused by Mycobacterium leprae (M. leprae), was very common in Europe till the 16th century. Here, we perform an ancient DNA study on medieval skeletons from Denmark that show lesions specific for lepromatous leprosy (LL). First, we test the remains for M. leprae DNA to confirm the infection status of the individuals and to assess the bacterial diversity. We assemble 10 complete M. leprae genomes that all differ from each other. Second, we evaluate whether the human leukocyte antigen allele DRB1*15:01, a strong LL susceptibility factor in modern populations, also predisposed medieval Europeans to the disease. The comparison of genotype data from 69 M. leprae DNA-positive LL cases with those from contemporary and medieval controls reveals a statistically significant association in both instances. In addition, we observe that DRB1*15:01 co-occurs with DQB1*06:02 on a haplotype that is a strong risk factor for inflammatory diseases today

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

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