| Title: | A quantitative and efficient approach to select MIRU–VNTR loci based on accumulation of the percentage differences of strains for discriminating divergent Mycobacterium tuberculosis sublineages |
| Authors: | Pan, Xin-Ling Browse this author |
| Zhang, Chun-Lei Browse this author |
| Nakajima, Chie Browse this author →KAKEN DB |
| Fu, Jin Browse this author |
| Shao, Chang-Xia Browse this author |
| Zhao, Li-Na Browse this author |
| Cui, Jia-Yi Browse this author |
| Jiao, Na Browse this author |
| Fan, Chang-Long Browse this author |
| Suzuki, Yasuhiko Browse this author →KAKEN DB |
| Hattori, Toshio Browse this author →KAKEN DB |
| Li, Di Browse this author |
| Ling, Hong Browse this author |
| Keywords: | Beijing genotype |
| Mycobacterium tuberculosis |
| mycobacterial interspersed repetitive units (MIRU)–variable number tandemrepeat (VNTR) |
| sublineage |
| Issue Date: | 26-Jul-2017 |
| Publisher: | Nature |
| Journal Title: | Emerging Microbes Infections |
| Volume: | 6 |
| Issue: | 7 |
| Start Page: | e68 |
| Publisher DOI: | 10.1038/emi.2017.58 |
| PMID: | 28745309 |
| 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. |
| Rights: | https://creativecommons.org/licenses/by/4.0/ |
| Type: | article |
| URI: | http://hdl.handle.net/2115/76484 |
| Appears in Collections: | 人獣共通感染症国際共同研究所 (International Institute for Zoonosis Control) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
国際連携研究教育局 : GI-CoRE (Global Institution for Collaborative Research and Education : GI-CoRE) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
|
