Abstract
Although several optimal mycobacterial interspersed repetitive units–variable number tandem repeat (MIRU–VNTR) loci have been suggested for genotyping homogenous Mycobacterium tuberculosis, including the Beijing genotype, a more efficient and convenient selection strategy for identifying optimal VNTR loci is needed. Here 281 M. tuberculosis isolates were analyzed. Beijing genotype and non-Beijing genotypes were identified, as well as Beijing sublineages, according to single nucleotide polymorphisms. A total of 22 MIRU–VNTR loci were used for genotyping. To efficiently select optimal MIRU–VNTR loci, we established accumulations of percentage differences (APDs) between the strains among the different genotypes. In addition, we constructed a minimum spanning tree for clustering analysis of the VNTR profiles. Our findings showed that eight MIRU–VNTR loci displayed disparities in h values of ≥0.2 between the Beijing genotype and non-Beijing genotype isolates. To efficiently discriminate Beijing and non-Beijing genotypes, an optimal VNTR set was established by adding loci with APDs ranging from 87.2% to 58.8%, resulting in the construction of a nine-locus set. We also found that QUB11a is a powerful locus for separating ST10s (including ST10, STF and STCH1) and ST22s (including ST22 and ST8) strains, whereas a combination of QUB11a, QUB4156, QUB18, Mtub21 and QUB26 could efficiently discriminate Beijing sublineages. Our findings suggested that two nine-locus sets were not only efficient for distinguishing the Beijing genotype from non-Beijing genotype strains, but were also suitable for sublineage genotyping with different discriminatory powers. These results indicate that APD represents a quantitative and efficient approach for selecting MIRU–VNTR loci to discriminate between divergent M. tuberculosis sublineages.Emerging Microbes & Infections (2017) 6, e68; doi:10.1038/emi.2017.58; published online 26 July 2017
Highlights
These results indicate that accumulations of percentage differences (APDs) represents a quantitative and efficient approach for selecting mycobacterial interspersed repetitive units (MIRU)–variable number tandem repeat (VNTR) loci to discriminate between divergent M. tuberculosis sublineages
Discriminatory power of the 22 VNTR loci for Beijing and nonBeijing isolates A total of 281 M. tuberculosis isolates were analyzed, with 252 strains belonging to the Beijing genotype strains and 29 strains identified as the Euro-American genotype
Genotyping loci for discriminating locally endemic sublineages According to the locus selection strategy described here and the loci exhibiting discriminatory power for local sublineages, we found that the nine-locus combination with the top APDs between Beijing and non-Beijing genotype strains classified all the strains into two clusters, with 100% of the Beijing strains belonging to one branch and 96.6% of the non-Beijing strains belonging to another branch (HGDI: 0.979; cluster rate: 30%) (Figure 4A), and that the ST22s and ST10s strains were effectively divided
Summary
The extensive spread of multidrug-resistant tuberculosis in Asia is predominantly driven by the rapid spread of the Mycobacterium tuberculosis Beijing genotype.[1,2,3,4] Beijing genotype strains have been proposed to have an increased capacity to acquire drug resistance, have an increased transmission ability, exhibit hypervirulence and result in a more rapid progression to disease after infection.[5,6,7,8,9,10] the association of infection with the Beijing strain with drug resistance and specific pathobiological or epidemiological characteristics has not been systematic.[11]. It remains unclear whether the distribution of sublineages in different geographic areas is causally related to the variations in tuberculosis (TB) transmission dynamics and/or the prevalence of drug-resistant TB
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