Swiss Tropical and Public Health Institute, Basel, Switzerland.
University of Basel, Basel, Switzerland.
PLoS One. 2022 Mar 1;17(3):e0264472. doi: 10.1371/journal.pone.0264472. eCollection 2022.
Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats (MIRU-VNTR) typing has been widely used for molecular epidemiological studies of tuberculosis (TB). However, genotyping tools for Mycobacterium tuberculosis (Mtb) may be limiting in some settings due to high cost and workload. In this study developed a customized stepwise MIRU-VNTR typing that prioritizes high discriminatory loci and validated this method using penitentiary system cohort in the country of Georgia.
We used a previously generated MIRU-VNTR dataset from recurrent TB cases (32 cases) in Georgia and a new dataset of TB cases from the penitentiary system (102 cases) recruited from 2014 to 2015. A Hunter-Gaston Discriminatory Index (HGDI) was calculated utilizing a 24 standard loci panel, to select high discriminatory power loci, subsequently defined as the customized Georgia-specific set of loci for initial typing. The remaining loci were scored and hierarchically grouped for second and third step typing of the cohort. We then compared the processing time and costs of the customized stepwise method to the standard 24-loci method.
For the customized Georgia-specific set that was used for initial typing, 10 loci were selected with a minimum value of 0.32 to the highest HGDI score locus. Customized 10 loci (step 1) typing of 102 Mtb patient isolates revealed 35.7% clustered cases. This proportion was reduced to 19.5% after hierarchical application of 2nd and 3rd step typing with the corresponding groups of loci. Our customized stepwise MIRU-VNTR genotyping approach reduced the quantity of samples to be typed and therefore overall processing time and costs by 42.6% each.
Our study shows that our customized stepwise MIRU-VNTR typing approach is a valid alternative of standard MIRI-VNTR typing panels for molecular epidemiological investigation in Georgia that saves time, workload and costs. Similar approaches could be developed for other settings.
分枝杆菌散在重复单位-可变数目串联重复（MIRU-VNTR）分型已广泛用于结核病（TB）的分子流行病学研究。然而，由于成本高和工作量大，分枝杆菌结核（Mtb）的基因分型工具在某些情况下可能受到限制。在本研究中，我们开发了一种定制的分步 MIRU-VNTR 分型方法，该方法优先考虑高区分度的基因座，并使用该国的监狱系统队列验证了这种方法。
我们使用了格鲁吉亚复发性结核病（32 例）的先前生成的 MIRU-VNTR 数据集和 2014 年至 2015 年从监狱系统招募的新的结核病病例数据集（102 例）。利用 24 个标准基因座面板计算了 Hunter-Gaston 区分指数（HGDI），以选择具有高区分能力的基因座，随后将其定义为初始分型的定制格鲁吉亚特定基因座集。对其余基因座进行评分，并对队列的第二和第三步分型进行层次分组。然后，我们比较了定制分步方法与标准 24 基因座方法的处理时间和成本。
对于用于初始分型的定制的格鲁吉亚特定基因座集，选择了 10 个基因座，最低值为 0.32 到最高 HGDI 评分基因座。对 102 株 Mtb 患者分离株进行的定制的 10 基因座（第 1 步）分型显示 35.7%的聚类病例。在应用第二和第三步分型以及相应的基因座组后，这一比例降低至 19.5%。我们的定制分步 MIRU-VNTR 基因分型方法减少了要分型的样本数量，从而使总体处理时间和成本分别降低了 42.6%。
我们的研究表明，我们的定制分步 MIRU-VNTR 分型方法是格鲁吉亚分子流行病学研究中标准 MIRI-VNTR 分型面板的有效替代方法，可节省时间、工作量和成本。类似的方法可以在其他环境中开发。
