Genetic variability, genotyping, and genomics of Mycobacterium leprae

Abstract

Leprosy, caused by Mycobacterium leprae and Mycobacterium lepromatosis, remains a significant global health issue despite a tremendous decline in its worldwide prevalence in the last four decades. Mycobacterium leprae strains possess very limited genetic variability, making it difficult to distinguish them using traditional genotyping tools. Successful genome sequencing of a considerable number of M. leprae strains in the recent past has allowed development of improved genotyping tools for the molecular epidemiology of leprosy. Comparative genomics has identified distinct M. leprae genotypes and revealed their characteristic genomic markers. This review summarizes the progress made in M. leprae genomics, with special emphasis on the development of genotyping schemes. Further, an updated genotyping scheme is introduced that also includes the newly reported genotypes 1B_Bangladesh, 1D_Malagasy, 3K-0/3K-1, 3Q and 4N/O. Additionally, genotype-specific markers (single nucleotide polymorphisms, Insertion/Deletion) have been incorporated into the typing scheme for the first time to enable differentiation of closely related strains. This will be particularly useful for geographic regions where M. leprae strains characterized by a small number of genotypes are predominant. The detailed compilation of genomic markers will also enable accurate identification of M. leprae genotypes, using targeted analysis of variable regions. Such markers are good candidates for developing artificial intelligence-based algorithms for classifying M. leprae genomic datasets.

Keywords: Mycobacterium leprae; comparative genomics; genetic diversity; genomic variability; genotyping; phylogeography.

Figure 1.

Families of repeats in M. leprae and M. lepromatosis, and the percentage of sequence similarity between them. There are four families of repetitive elements in both M. leprae and M. lepromatosis. The similarity between repeat groups (A, B, C, and D) in both species is very low (75–87%) and repeat copy number and length size (bases) also vary a lot. Mycobacterium leprae multicopy repeats REPLEP have very few differences in repeat size compared with the multicopy repeats REPLPM of M. lepromatosis .

Figure 2.

Mycobacterium leprae genomes representing various genotypes from different continents. The size of circles corresponds to the number of samples of a particular genotype and colors represent the different continents. α: Bangladesh; β: Malagasy.

Figure 3.

Updated informative markers for genotyping in Mycobacterium leprae. Starting from the third column, the header row indicates SNP-groups (SNP-Grp-01 to 16) whose SNPs are mentioned at the bottom of the column. The left-side column shows SNP types (1–4) and their 19 subtypes (1A-4P). The SNPs mentioned at the bottom represent the full list of SNPs for every SNP group. A red rectangle is shown in each row corresponding to all known 19 genotypes. For the genotype on the terminal sides of this scheme, i.e. 1A and 4P, the rectangle covers only one cell representing one SNP-Grp. Genotype 1A can be identified by a single SNP from all wild-type positions (shown in yellow color for SNP-Grp-1), as is the case for genotype 4P (all alternative nucleotides, shown in green color in SNP-Grp 16). The corresponding rectangle for the remaining genotypes includes two adjoining SNP-Grps: the first possessing alternative bases (dark green color) at the corresponding positions, while the second SNP-Grp exhibits wild-type bases (yellow color). A single marker per SNP group from the corresponding rectangle is considered to be sufficient for identifying the respective genotype. The SNPs shown in orange highlighted cells are newly identified genomic markers added in this figure. The total number of SNPs for every SNP-Grp is mentioned at the start of the SNP list at the bottom of each column. The subtypes that are newly incorporated in this genotyping scheme are underlined. The genomic positions are based on original reference genome M. leprae TN strain (GenBank ID AL450380.1 version 1, genome size 3268203).

Figure 4.

(A) The best five genomic markers specific to each SNP-genotype of M. leprae strains. These SNPs can be used for decision trees for automated and accurate identification of genotypes from the SNP list obtained from whole genome sequencing of M. leprae strains. This can help with accurate and reproducible identification of sub-genotypes of M. leprae. (B) SNPs uniquely present in strains belonging to these genotypes. *The genotypes 3L, 3Q, and 3M are represented by only a single strain for which genome information is available. That is why some or all of the SNPs uniquely present in these strains (Fig. 4b) might be strain-specific instead of genotype-specific. Likewise, the genotypes 1B and 4N/O are represented by two and six strains, respectively. However, SNPs specific to these two genotypes are not known.

Figure 5.

Genotype-specific SNPs in M. leprae. The number of genomes currently known for each subtype is indicated in parentheses. It should be noted that the markers indicated for the subtypes represented by only one strain (3L, 3Q, and 3M) could be strain-specific also. *represents the genotypes (1B and 4N/O) for which currently genotype-specific markers are not known.

Figure 6.

Updated SNP-genotyping scheme of M. leprae. Wild-type bases are in yellow while the green indicates the SNPs compared with the M. leprae TN reference strain. The blue color indicates the SNPs restricted to only one genotype. The SNP genomic positions are based on the reference genome M. leprae TN strain (GenBank ID AL450380.1 version 1, genome size 3268203).