Mycobacterium lepromatosis genomic data

This project aims to reconstruct the epidemiological history and current diversity of M. lepromatosis, a recently discovered species responsible for leprosy. Since its discovery in 2008, over a hundred cases have been reported, primarily in North America. However, genomic data has only been obtained from three human-infecting strains and seven strains infecting red squirrels in the British Isles (Avanzi et al., Science, 2016). The scarcity of genomic information is largely due to the pathogen's unculturable and intracellular nature, which makes sequencing its DNA from biopsies (which is dominated by host DNA) extremely challenging. In this project, we conducted an extensive screening of a large collection of biopsies from humans and animals with suspected M. lepromatosis infections and successfully produced new genomes, increasing the genomic data for human-infecting strains severalfold. Additionally, using long-read sequencing data from a strain grown in mouse footpads, we generated a de novo assembled genome in a single contig of higher quality than the currently available reference genome for this species