Investigation of a Medieval Pilgrim Burial Excavated from the Leprosarium of St Mary Magdalen Winchester, UK

Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host

Leprosy, one of the oldest recorded diseases in human history, remains prevalent in Asia, Africa, and South America, with over 200,000 cases every year.1,2 Although ancient DNA (aDNA) approaches on the major causative agent, Mycobacterium leprae, have elucidated the disease's evolutionary history,3,4,5 the role of animal hosts and interspecies transmission in the past remains unexplored. Research has uncovered relationships between medieval strains isolated from archaeological human remains and modern animal hosts such as the red squirrel in England.6,7 However, the time frame, distribution, and direction of transmissions remains unknown. Here, we studied 25 human and 12 squirrel samples from two archaeological sites in Winchester, a medieval English city well known for its leprosarium and connections to the fur trade. We reconstructed four medieval M. leprae genomes, including one from a red squirrel, at a 2.2-fold average coverage. Our analysis revealed a phylogenetic placement of all strains on branch 3 as well as a close relationship between the squirrel strain and one newly reconstructed medieval human strain. In particular, the medieval squirrel strain is more closely related to some medieval human strains from Winchester than to modern red squirrel strains from England, indicating a yet-undetected circulation of M. leprae in non-human hosts in the Middle Ages. Our study represents the first One Health approach for M. leprae in archaeology, which is centered around a medieval animal host strain, and highlights the future capability of such approaches to understand the disease's zoonotic past and current potential.

Bioarchaeological investigation of individuals with suspected multibacillary leprosy from the mediaeval leprosarium of St Mary Magdalen, Winchester, Hampshire, UK

Introduction. We have examined four burials from the St Mary Magdalen mediaeval leprosarium cemetery in Winchester, Hampshire, UK. One (Sk.8) was a male child, two (Sk.45 and Sk.52) were adolescent females and the fourth (Sk.512) was an adult male. The cemetery was in use between the 10th and 12th centuries. All showed skeletal lesions of leprosy. Additionally, one of the two females (Sk.45) had lesions suggestive of multi-cystic tuberculosis and the second (Sk.52) of leprogenic odontodysplasia (LO), a rare malformation of the roots of the permanent maxillary incisors.Gap statement. Relatively little is known of the manifestations of lepromatous leprosy (LL) in younger individuals from the archaeological record.Aims and Methodology. To address this, we have used ancient DNA testing and osteological examination of the individuals, supplemented with X-ray and microcomputed tomography (micro-CT) scan as necessary to assess the disease status.Results and Conclusions. The presence of Mycobacterium leprae DNA was confirmed in both females, and genotyping showed SNP type 3I-1 strains but with a clear genotypic variation. We could not confirm Mycobacterium tuberculosis complex DNA in the female individual SK.45. High levels of M. leprae DNA were found within the pulp cavities of four maxillary teeth from the male child (Sk.8) with LO, consistent with the theory that the replication of M. leprae in alveolar bone may interfere with root formation at key stages of development. We report our biomolecular findings in these individuals and review the evidence this site has contributed to our knowledge of mediaeval leprosy.

Presenting the Compendium Isotoporum Medii Aevi, a Multi-Isotope Database for Medieval Europe

Here we present the Compendium Isotoporum Medii Aevi (CIMA), an open-access database gathering more than 50,000 isotopic measurements for bioarchaeological samples located within Europe and its margins, and dating between 500 and 1500 CE. This multi-isotope (δ¹³C, δ¹⁵N, δ³⁴S, δ¹⁸O, and ⁸⁷Sr/⁸⁶Sr) archive of measurements on human, animal, and plant archaeological remains also includes a variety of supporting information that offer, for instance, a taxonomic characterization of the samples, their location, and chronology, in addition to data on social, religious, and political contexts. Such a dataset can be used to identify data gaps for future research and to address multiple research questions, including those related with studies on medieval human lifeways (i.e. human subsistence, spatial mobility), characterization of paleo-environmental and -climatic conditions, and on plant and animal agricultural management practices. Brief examples of such applications are given here and we also discuss how the integration of large volumes of isotopic data with other types of archaeological and historical data can improve our knowledge of medieval Europe.

Measurement(s)	Isotopes
Technology Type(s)	Mass Spectrometry
Factor Type(s)	Carbon isotopes • nitrogen isotopes • sulfur isotopes • oxygen isotopes • strontium isotopes
Sample Characteristic - Organism	Humans • Animals • Plants
Sample Characteristic - Location	Europe and Periphery

Creating communities of care: Sex estimation and mobility histories of adolescents buried in the cemetery of St. Mary Magdalen leprosarium (Winchester, England)

Objectives

This study examines the biological sex and geographical origins of adolescents buried at the St Mary Magdalen leprosarium (Winchester, UK). The data are combined with archaeological and palaeopathological evidence to broaden the understanding of mobility and its relationship to leprosy and leprosaria in Medieval England.

Materials and Methods

Nineteen individuals (~10–25 at death) with skeletal lesions diagnostic of leprosy were analyzed using standard osteological methods. Amelogenin peptides were extracted from five individuals whose biological sex could not be assessed from macroscopic methods. Enamel samples were analyzed to produce ⁸⁷Sr/⁸⁶Sr and δ¹⁸O values to explore mobility histories.

Results

Amelogenin peptides revealed three males and two females. Tooth enamel samples provided an ⁸⁷Sr/⁸⁶Sr ratio range from 0.7084 to 0.7103 (mean 0.7090, ±0.0012, 2σ). δ¹⁸O_P values show a wide range of 15.6‰–19.3‰ (mean 17.8 ± 1.6‰ 2σ), with corresponding δ¹⁸O_DW values ranging from −9.7‰ to −4.1‰ (mean −6.3 ± 2.4‰ 2σ).

Discussion

Amelogenin peptide data reveal the presence of adolescent females with bone changes of leprosy, making them the youngest confirmed females with leprosy in the archaeological record. Results also show at least 12 adolescents were local, and seven were from further afield, including outside Britain. Since St. Mary Magdalen was a leprosarium, it is possible that these people traveled there specifically for care. Archaeological and palaeopathological data support the notion that care was provided at this facility and that leprosy stigma, as we understand it today, may not have existed in this time and place.

One Health Approaches to Trace Mycobacterium leprae's Zoonotic Potential Through Time

Hansen's disease (leprosy), mainly caused by infection with Mycobacterium leprae, has accompanied humanity for thousands of years. Although currently rare in Europe, there are over 200,000 new infections annually in South East Asia, Africa, and South America. Over the years many disciplines - palaeopathology, ancient DNA and other ancient biomolecules, and history - have contributed to a better understanding of leprosy's past, in particular its history in medieval Europe. We discuss their contributions and potential, especially in relation to the role of inter-species transmission, an unexplored phenomenon in the disease's history. Here, we explore the potential of interdisciplinary approaches that understand disease as a biosocial phenomenon, which is a product of both infection with M. leprae and social behaviours that facilitate transmission and spread. Genetic evidence of M. leprae isolated from archaeological remains combined with systematic zooarchaeological and historical analysis would not only identify when and in what direction transmission occurred, but also key social behaviours and motivations that brought species together. In our opinion, this combination is crucial to understand the disease's zoonotic past and current potential.

Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

BACKGROUND

Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period.

RESULTS

Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria.

CONCLUSIONS

Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.

Leprosy in medieval Denmark: Exploring life histories through a multi-tissue and multi-isotopic approach

OBJECTIVES

By focusing on two Danish leprosaria (Naestved and Odense; 13th-16th c. CE) and using diet and origin as proxies, we follow a multi-isotopic approach to reconstruct life histories of patients and investigate how leprosy affected both institutionalized individuals and the medieval Danish community as a whole.

MATERIALS AND METHODS

We combine archaeology, historical sources, biological anthropology, isotopic analyses (δ¹³ C, δ¹⁵ N, δ³⁴ S, ⁸⁷ Sr/⁸⁶ Sr) and radiocarbon dating, and further analyze bones with different turnover rates (ribs and long bones).

RESULTS

The δ¹³ C, δ¹⁵ N and δ³⁴ S results indicate a C₃ terrestrial diet with small contributions of marine protein for leprosy patients and individuals from other medieval Danish sites. A similar diet is seen through time, between males and females, and patients with and without changes on facial bones. The isotopic comparison between ribs and long bones reveals no significant dietary change. The δ³⁴ S and ⁸⁷ Sr/⁸⁶ Sr results suggest that patients were local to the regions of the leprosaria. Moreover, the radiocarbon dates show a mere 50% agreement with the arm position dating method used in Denmark.

CONCLUSIONS

A local origin for the leprosy patients is in line with historical evidence, unlike the small dietary contribution of marine protein. Although only 10% of the analyzed individuals have rib/long bone offsets that undoubtedly show a dietary shift, the data appear to reveal a pattern for 25 individuals (out of 50), with elevated δ¹³ C and/or δ¹⁵ N values in the ribs compared to the long bones, which points toward a communal type of diet and reveals organizational aspects of the institution.

Archival, paleopathological and aDNA-based techniques in leprosy research and the case of Father Petrus Donders at the Leprosarium 'Batavia', Suriname

OBJECTIVE

We assessed whether Petrus Donders (died 1887), a Dutch priest who for 27 years cared for people with leprosy in the leprosarium Batavia, Suriname, had evidence of Mycobacterium (M.) leprae infection. A positive finding of M. leprae ancient (a)DNA would contribute to the origin of leprosy in Suriname.

MATERIALS

Skeletal remains of Father Petrus Donders; two additional skeletons excavated from the Batavia cemetery were used as controls.

METHODS

Archival research, paleopathological evaluation and aDNA-based testing of skeletal remains.

RESULTS

Neither archives nor inspection of Donders skeletal remains revealed evidence of leprosy, and aDNA-based testing for M. leprae was negative. We detected M. leprae aDNA by RLEP PCR in one control skeleton, which also displayed pathological lesions compatible with leprosy. The M. leprae aDNA was genotyped by Sanger sequencing as SNP type 4; the skeleton displayed mitochondrial haplogroup L3.

CONCLUSION

We found no evidence that Donders contracted leprosy despite years of intense leprosy contact, but we successfully isolated an archaeological M. leprae aDNA sample from a control skeleton from South America.

SIGNIFICANCE

We successfully genotyped recovered aDNA to a M. leprae strain that likely originated in West Africa. The detected human mitochondrial haplogroup L3 is also associated with this geographical region. This suggests that slave trade contributed to leprosy in Suriname.

LIMITATIONS

A limited number of skeletons was examined.

SUGGESTIONS FOR FURTHER RESEARCH

Broader review of skeletal collections is advised to expand on diversity of the M. leprae aDNA database.

Revisiting the tuberculosis and leprosy cross-immunity hypothesis: Expanding the dialogue between immunology and paleopathology

OBJECTIVE

Our primary objective is to re-visit the tuberculosis and leprosy cross-immunity. hypothesis through the careful integration of immunology and paleopathology.

METHODS

Using an integrated theoretical analysis that evaluates clinical literature on human innate immunological responses, paleomicrobiology, bioarchaeology, and paleopathology, we develop a multifactorial model.

RESULTS

Past populations do not represent homogeneous immunological landscapes, and therefore it is likely that leprosy in Medieval Europe did not uniformly decline due to cross-immunity.

CONCLUSIONS

We recommend that bioarchaeological reconstructions of past disease experience take into consideration models that include variation in immune function based on past environments and social contexts. This provides a unique opportunity to conduct comprehensive analyses on complex immunological processes.

SIGNIFICANCE

Extrapolating results from experimental immunology to larger populations elucidates complexities of disease cross-immunity and highlights the importance of synthesizing archaeological, social, paleopathological and biological data as a means of understanding disease in the past.

LIMITATIONS

All extrapolations from data produced from in vitro studies to past populations, using living donors, pose significant limitations where, among other factors, the full reconstruction of past environmental and social contexts can frequently be sparse or incomplete.

SUGGESTIONS FOR FUTURE RESEARCH

To reduce the limitations of integrating experimental immunology with bioarchaeological reconstructions (i.e. how to use skeletal samples to reconstruct inflammatory phenotypes), we propose that osteoimmunology, or the study of the interplay between immune cells and bone cells, should be considered a vital discipline and perhaps the foundation for the expansion of paleoimmunology.

Harnessing ancient genomes to study the history of human adaptation

The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone.

Life not death: Epidemiology from skeletons

Analytically sophisticated paleoepidemiology is a relatively new development in the characterization of past life experiences. It is based on sound paleopathological observations, accurate age-at-death estimates, an explicit engagement with the nature of mortality samples, and analytical procedures that owe much to epidemiology. Of foremost importance is an emphasis on people, not skeletons. Transforming information gleaned from the dead, a biased sample of individuals who were once alive at each age, into a form that is informative about past life experiences has been a major challenge for bioarchaeologists, but recent work shows it can be done. The further development of paleoepidemiology includes essential contributions from paleopathology, archaeology or history (as appropriate), and epidemiology.