Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis

Abstract

Mycobacterium lepromatosis is an uncultured human pathogen associated with diffuse lepromatous leprosy and a reactional state known as Lucio's phenomenon. By using deep sequencing with and without DNA enrichment, we obtained the near-complete genome sequence of M. lepromatosis present in a skin biopsy from a Mexican patient, and compared it with that of Mycobacterium leprae, which has undergone extensive reductive evolution. The genomes display extensive synteny and are similar in size (∼3.27 Mb). Protein-coding genes share 93% nucleotide sequence identity, whereas pseudogenes are only 82% identical. The events that led to pseudogenization of 50% of the genome likely occurred before divergence from their most recent common ancestor (MRCA), and both M. lepromatosis and M. leprae have since accumulated new pseudogenes or acquired specific deletions. Functional comparisons suggest that M. lepromatosis has lost several enzymes required for amino acid synthesis whereas M. leprae has a defective heme pathway. M. lepromatosis has retained all functions required to infect the Schwann cells of the peripheral nervous system and therefore may also be neuropathogenic. A phylogeographic survey of 227 leprosy biopsies by differential PCR revealed that 221 contained M. leprae whereas only six, all from Mexico, harbored M. lepromatosis. Phylogenetic comparisons indicate that M. lepromatosis is closer than M. leprae to the MRCA, and a Bayesian dating analysis suggests that they diverged from their MRCA approximately 13.9 Mya. Thus, despite their ancient separation, the two leprosy bacilli are remarkably conserved and still cause similar pathologic conditions.

Keywords: Mycobacterium leprae; Mycobacterium lepromatosis; comparative genomics; genome sequencing; reductive evolution.

Fig. 1.

Genome synteny and salient features of M. leprae and M. lepromatosis. The 126 contigs of M. lepromatosis are distinguished with red and orange colors. Links between M. leprae and M. lepromatosis are BLAST hits, with two shades of gray to distinguish individual contigs. White stripes indicate no BLAST hits and account for 5–6% of each genome’s specific sequences. Light blue stripes indicate dispersed repeats in M. leprae. Black line indicates a confirmed structural variation between M. leprae and M. lepromatosis.

Fig. 2.

Nucleotide sequence identity between M. leprae and M. lepromatosis orthologs. Numbers above violins represent the number of ortholog pairs for that gene category. The most conserved are tRNA and rRNA genes, followed by the CDS. Pseudogenes are the least conserved. Identity of genes that are functional in one species but not in the other is between CDS and pseudogenes.

Fig. 3.

Synteny around the M. lepromatosis hemN locus and comparison with M. leprae and M. tuberculosis. Links between the genomes are BLAST hits; hemN and sirA are present in M. lepromatosis and M. tuberculosis (gray links) but have been deleted in M. leprae. The mbt cluster, present in M. tuberculosis, is deleted in M. leprae and M. lepromatosis. Scale is in kilobases. Note the genomic rearrangement between M. lepromatosis (first 10 kb of the contig) and M. leprae. Additionally, the sequence corresponding to the M. leprae genome between 780 and 795 kb is almost entirely deleted in M. lepromatosis.

Fig. 4.

Phylogeny of M. lepromatosis and M. leprae strains. Phylogenetic relationship of M. lepromatosis genome using a maximum parsimony tree, including M. tuberculosis, M. avium, and M. ulcerans as outgroups. SNP type is given at branch tips. Bootstrap support is indicated for each node. The long branch of S15 was split to reduce space.