Data_Sheet_1_The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation.PDF

The 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping has been used as an international standard method for Mycobacterium tuberculosis (Mtb) genotyping. However, different optimized VNTR loci sets for improving the discrimination of specific Mtb genotypes have been proposed. In this regard, we investigated the efficacy of accumulation of the percentage differences (APDs) compared with the least absolute shrinkage and selection operator (LASSO) regression strategy to identify a customized genotype-specific VNTR loci set which provides a resolution comparable to 24-loci MIRU-VNTR in divergent Mtb populations. We utilized Spoligotyping and 24-loci MIRU-VNTR typing for genotyping 306 Mtb isolates. The APD and LASSO regression approaches were used to identify a customized VNTR set in our studied isolates. Besides, the Hunter-Gaston discriminatory index (HGDI), sensitivity, and specificity of each selected loci set were calculated based on both strategies. The selected loci based on LASSO regression compared with APD-based loci showed a better discriminatory power for identifying all studied genotypes except for T genotype, which APD-based loci showed promising discriminative power. Our findings suggested the LASSO regression rather than the APD approach is more effective in the determination of possible discriminative VNTR loci set to precise discrimination of our studied Mtb population and may be beneficial to be used in finding reduced number loci sets in other Mtb genotypes or sublineages. Moreover, we proposed customized genotype-specific MIRU-VNTR loci sets based on the LASSO regression and APD approaches for precise Mtb strains identification. As the proposed VNTR sets offered a comparable discriminatory power to the standard 24 MIRU-VNTR loci set could be promising alternatives to the standard genotyping for using in resource-limited settings.

24位点分枝杆菌散在重复单位-可变数目串联重复序列（MIRU-VNTR）基因分型技术已被用作结核分枝杆菌（Mtb）基因分型的国际标准方法。然而，已有研究提出多种优化的VNTR位点组合，用于提升特定Mtb基因型的鉴别能力。为此，本研究对比了百分比差异累积法（APDs）与最小绝对收缩和选择算子（LASSO）回归两种策略的效能，旨在筛选出可在异质性Mtb群体中实现与24位点MIRU-VNTR相当分型分辨率的定制化基因型特异性VNTR位点组合。本研究对306株Mtb分离株采用间隔区寡核苷酸分型（Spoligotyping）与24位点MIRU-VNTR分型进行基因分型。本研究采用APD与LASSO回归两种方法，从受试分离株中筛选定制化VNTR位点组合。此外，基于两种策略分别计算了各筛选得到的位点组合的亨特-加斯顿鉴别指数（HGDI）、灵敏度与特异度。相较于基于APD筛选得到的位点组合，经LASSO回归筛选的位点组合对除T基因型外的所有受试基因型均展现出更优的鉴别能力；而基于APD筛选的位点组合对T基因型亦具备可观的鉴别效能。本研究结果表明，相较于APD法，LASSO回归在筛选可精准区分受试Mtb群体的鉴别性VNTR位点组合方面更为有效，该方法或可用于其他Mtb基因型或亚谱系的精简位点组合筛选。此外，本研究基于LASSO回归与APD两种方法，提出了用于精准鉴定Mtb菌株的定制化基因型特异性MIRU-VNTR位点组合。由于所提出的VNTR位点组合可实现与标准24位点MIRU-VNTR相当的鉴别能力，因此有望在资源有限的环境中作为标准基因分型方法的替代方案。