Table 2.
Different molecular typing systems for Mycobacterium leprae strains.
| Typing system | Principle and applications | Merits | Limitations | Ref. |
|---|---|---|---|---|
| Variable number of tandem repeats | ||||
| TTC repeats | Ten to 37 repeats of trinucleotides (TTC); also known as (GAA) 20 | Very high allelic number variation at a single locus Easy and cost effective |
Poor geographical associability Inherent instability at some loci due to slipped stranded mispairing Low resolution Hypervariability making them unreliable for some loci Not all the strains can be clustered Stuttering phenomenon at some loci has been observed when the stability was studied |
[72,73,103–107] |
| rpoT (sigA) | Based upon biased geographical distribution of three and four copies of hexanucleotide GACATC repeat | Geographical relationship, but very limited discriminations Easy and cost effective |
[108–111] | |
| Study of many loci or multiple-locus VNTR analysis | 16 polymorphic STRs are studied together Genotyping based on various polymorphic loci |
12 (of 13) STRs were found to be stable over the 5 years of passage in armadillo tissues | [74,75,112] | |
| 15 VNTRs (including six mini- and nine microsatellites) multi-locus coverage for increased discriminatory capacity | Multiplex-PCR approach and hence saves the amount of reagents and the DNA template FLA-based detection Easy and cost effective Automation of work-flow possible |
[77,78,80,113,114] | ||
| SNP and single base insertion/deletion | ||||
| SNP typing | Based on informative SNPs/InDel, four principle types are further differentiated into 16 subtypes Phylogeographical analysis of M. leprae strains around the globe, correlation with known routes of ancient human migrations |
Stable, strong geographical association In nonendemic countries, strains in immigrant population can be related to their origin and source of autochthonous transmission can be traced |
Too little diversity for monitoring short-range transmission Differentiation of closely related strains difficult |
[22,66,72,115] |
FLA: Fragment length analysis; InDel: Insertion-deletion; SNP: Single nucleotide polymorphism; STR: Short tandem repeat; VNTR: Variable number of tandem repeats.