Metagenomics' contribution to archival and paleopathological research: leprosy and the case of Father Petrus Donders at the Leprosarium 'Batavia', Suriname.

Petrus Donders (1809 - 1887) was a Roman Catholic priest from The Netherlands and a member of the Redemptorist Congregation. He won recognition for his ministry in the Dutch colony of Suriname, where he cared for people with leprosy who lived under government-sanctioned isolation in Batavia, a former plantation along the Coppename River. After more than 26 years of caring for the spiritual, physical, and emotional needs of those in the leper colony, he died in the leprosarium in 1887. Herein, we combined archival research with paleopathological, metagenomic and molecular examinations of Petrus Donders's skeletal remains to establish whether or not he suffered from leprosy. Neither his correspondence nor church archives, nor an examination of his skeletal remains revealed characteristics of Mycobacterium (M.) eprae infection. Metagenomic analysis revealed no DNA of M. leprae. However, we confirmed the total absence of teeth and discovered that he had a severe lumbosacral scoliosis.By contrast, we did detect preserved M. leprae DNA (83% coverage of genome, RLEP PCR positive) in the skeleton of a female adolescent which displayed characteristic signs of leprosy. She was excavated at the cemetery of the Batavia leprosarium as a positive control. Using stringent PCRs and Sanger sequencing of the PCR products, we determined that this M. leprae strain - the first archeological M. leprae strain solated in South America - belonged to the SNP type 4, which most likely evolved in West Africa. Thus, our findings are in line with the hypothesis that the African slave trade contributed to leprosy in Suriname. However, we also found evidence for the presence of M. leprae SNP type 1 or 2 in soil samples taken near armadillo holes at the Batavia leprosarium and at Groot Chatillon, another Surinamese leprosarium, ndicating multiple origins of M. leprae in Suriname.In conclusion, by taking a tripartite approach, we found no evidence that the priest Petrus Donders had contracted leprosy during his lifetime despite almost 27 years of ntense contact with lepers at the Batavia Leprosarium in Suriname. Our findings of M. eprae strains in the control skeleton as well as soil samples from the same area underscore the importance of including metagenomic analysis to allow for genomic reconstruction and genotyping of past pathogens, and provide unique information beyond classical paleopathological investigation.