Abstract
Today, significant attention is directed towards the global lineages and sublineages of Mycobacterium tuberculosis (Mtb). NEW-1 (SIT 127) and CAS1-Delhi (SIT 26) strains are recognized as growing and circulating Mtb genotypes, especially in Asian countries. It is crucial to develop or enhance Mtb genotyping methods for a more accurate and simple differentiation of these families. We used 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing for genotyping 217 Mtb isolates. To select the optimal MIRU-VNTR loci, we calculated the Hunter-Gaston discriminatory index (HGDI), allelic diversity, and accumulation of percentage differences (APDs) between the strains among different groups of genotypes (NEW-1 and non-NEW-1; CAS1-Delhi and non-CAS). Finally, the minimum spanning tree was constructed for clustering analysis. In the NEW-1 population, loci with APD > 60% were found to have a high discriminatory power. VNTR loci with APD > 50% showed high discrimination power for the CAS population. Our findings suggest that APDs, which are valuable for the selection of VNTR loci sets, may improve the discriminatory power of MIRU-VNTR typing for identification of Mtb genotypes in specific regions.
Highlights
Today, significant attention is directed towards the global lineages of Mycobacterium tuberculosis (Mtb)
The Minimum Spanning Tree (MST) plot, which was constructed based on highly discriminative VNTR loci and loci with an Hunter-Gaston discriminatory index (HGDI) difference ≥0.2, showed low potential to classify the genotypes into distinct branches (Fig. 1A,B)
In a study which conducted in Madagascar, VNTR loci 960 (MIRU10), 4156 (Qub4156), 1644 (MIRU16), 802 (MIRU40), 577 (ETRC), 3690 (Mtub39), 4052 (Qub26), 2163b (Qub11b), 3192(MIRU31) and 424 (Mtub04) have been reported as a set of ten optimized VNTR loci for discrimination of CAS sub-lineage based on HGDI value
Summary
Significant attention is directed towards the global lineages of Mycobacterium tuberculosis (Mtb). NEW-1 (SIT 127) and CAS1-Delhi (SIT 26) strains have been identified as growing and circulating Mtb genotypes, especially in Asian countries including Iran, Afghanistan, and Pakistan[2,3,4,5,6,7]. In these regions, the prevalence of NEW-1 is strongly associated with multidrug resistance (MDR)[7,8]. The ongoing increase in the circulation of NEW-1 (SIT 127) and CAS1-Delhi strains in West of Asia seems more alarming for the NEW-1 clone population, which is prone to MDR9 These reports demonstrate the need for developing or enhancing Mtb genotyping methods. We conducted this study to explore a VNTR loci set for discriminating NEW-1 and CAS1-Delhi (the main sub-lineages of lineages 4 and 3, respectively) from other genotypes by different approaches
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