Whole-genome sequencing of Mycobacterium leprae genomes from the Pacific Islands

As one of the oldest known human diseases, leprosy remains a public health concern around the world with over 200,000 new cases in 2018. The global pattern of genomic variation in M. leprae is not well understood. Particularly in the Pacific Islands, the origins of leprosy are disputed. Historically, it has been argued that leprosy arrived on the islands during 19th century colonialism, but oral traditions and paleopathological evidence suggest an older introduction. To address this, as well as investigate patterns of pathogen exchange across the Pacific Islands, we extracted and sequenced DNA from 15 formalin fixed paraffin embedded biopsy blocks dating from 1998 to 2015. Using whole genome enrichment and Next Generation Sequencing, we produced nine M. leprae genomes ranging from 4 to 63x depth of coverage. Phylogenetic analyses indicate that these strains belong to basal lineages within the M. leprae phylogeny, specifically falling in branches 0 and 5. Here are the NGS data for all of the samples sequenced as part of this project.