ArticlePloS one2017
Evaluation of spoligotyping, SNPs and customised MIRU-VNTR combination for genotyping Mycobacterium tuberculosis clinical isolates in Madagascar.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Development, Evaluation, and Implementation of a House-Made Targeted Next-Generation Sequencing Spoligotyping in a French Laboratory.International journal of molecular sciences · 2022Article
- Consistency of Mycobacterium tuberculosis Complex Spoligotyping between the Membrane-Based Method andMicrobiology spectrum · 2022Article
- Developing customized stepwise MIRU-VNTR typing for tuberculosis surveillance in Georgia.PloS one · 2022Article
- The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing forFrontiers in microbiology · 2022Article
- A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TBFrontiers in cellular and infection microbiology · 2021Article
- Enhancing the differentiation of specific genotypes in Mycobacterium tuberculosis population.Scientific reports · 2019Article
- Introducing the Best Six Loci in Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat (MIRU-VNTR) Typing forReports of biochemistry & molecular biology · 2019Article
- Exploring the "Latin American Mediterranean" family and the RDBMC microbiology · 2019Article
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6 authors.
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Abstract
backgroundCombining different molecular typing methods for Mycobacterium tuberculosis complex (MTBC) can be a powerful tool for molecular epidemiology-based investigation of TB. However, the current standard method that provides high discriminatory power for such a combination, mycobacterial interspersed repetitive units-variable numbers of tandem repeats typing (MIRU-VNTR), is laborious, time-consuming and often too costly for many resource-limited laboratories. We aimed to evaluate a reduced set of loci for MIRU-VNTR typing in combination with spoligotyping and SNP-typing for routine molecular epidemiology of TB.
methodSpoligotyping and SNP-typing, in combination with the 15 loci MIRU-VNTR typing, were first used to type clinical MTBC isolates (n = 158) from Madagascar. A step by step reduction of MIRU-VNTR loci number was then performed according to the Hunter and Gaston Discriminatory Index (HGDI) and to the Principal component analysis (PCA) correlation with the spoligotype profiles to evaluate the discrimination power inside the generated spoligotype clusters. The 15 MIRU-VNTR was used as reference and SNP-typing was used to determine the main MTBC lineages.
resultsOf the 158 clinical isolates studied, the SNP-typing classified 23 into Lineage 1 (14.6%), 31 into Lineage 2 (19.6%), 23 into Lineage 3 (14.6%) and 81 into Lineage 4 strains (51.3%). 37 different spoligotypes profiles were obtained, 15 of which were unique and 20 in clusters. 15-loci MIRU-VNTR typing revealed 144 different genotypes: 132 isolates had a unique MIRU-VNTR profile and 27 isolates were grouped into 12 clusters. After a stepwise reduction of the MIRU-VNTR loci number within each main spoligotype families, three different sets composed of 5 customised MIRU-VNTR loci had a similar discrimination level to the reference 15 loci MIRU-VNTR in lineage 1, lineage 2 and lineage 3. For lineage 4, a set of 4 and 3 MIRU-VNTR loci were proposed to subtype the Harleem and LAM spoligotype families, respectively. For the T spoligotype family, a set of 5 MIRU-VNTR loci was proposed.
conclusionAccording to the lineages and the spoligotype families, the number of MIRU-VNTR loci can be reduced to get an optimal classification of MTBC. These customized sets of MIRU-VNTR loci reduce workload and save resources while maintaining optimal discriminatory power.
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