Table 2. Genetic distances of pairs of isolates clustered by WGS only and not by MIRU-VNTR in five distinct international WGS data analysis pipelines and the associated 24-loci MIRU-VNTR patterns.
| Sample 1 | Sample 2 | Genetic distance in SNPs/alleles by pipeline | 24-loci MIRU-VNTR ordera | |||||
|---|---|---|---|---|---|---|---|---|
| RIVM SNP | Oxford University SNP | Research Center Borstel (MTBseq) SNP | SSI SNP | cgMLST (allele) | MIRU-VNTR pattern sample 1 | MIRU-VNTR pattern sample 2 | ||
| ERX2465161 | ERX2465207 | 12 | 14 | 12 | 8 | 8 | 2-5-3-5-3-3-2-3-3-4-1-3-6-3-5-2-5-2-2-1-3-4-2-3 | 2-5-3-5-3-3-2-3-3-4-1-3-6-3-6-2-5-2-2-1-3-4-2-3 |
| ERX2465178b | ERX2465568b | 14 | 12 | 8 | 5 | 5 | 2-1-4-7-4-3-4-2-4-2-2-4-2-3-5-2-5-3-2-1-3-4-2-3 | 2-1-4-7-4-4-4-2-4-2-2-4-2-3-5-2-5-3-2-1-3-4-2-3 |
| ERX2465292 | ERX2465259 | 17 | 19 | 16 | 15 | 12 | 2-5-1-3-3-3-2-5-3-2-6-2-5-2-5-1-6-2-2-1-3-4-2-3 | 2-7-1-3-3-3-2-4-3-2-6-2-5-2-5-1-6-2-2-1-3-4-2-3 |
| ERX2465308 | ERX2465278 | 16 | 15 | 11 | 9 | 12 | 2-5-2-5-4-5-3-2-4-2-4-4-2-4-7-2-5-3-2-1-3-4-2-3 | 2-5-2-6-4-5-3-2-4-2-3-4-2-4-7-2-5-3-2-1-3-4-2-3 |
| ERX2465418c,d | ERX2465573 | 133 | 0 | 2 | 41 | 0 | 2-5-2-6-4-5-3-2-4-2-3-4-2-4-8-2-5-3-2-1-3-4-2-3 | 2-4-3-5-4-5-2-2-4-2-3-4-2-4-8-2-5-3-2-1-3-4-2-3 |
| ERX2465418c,d | ERX2465330 | 132 | 0 | 3 | 41 | 1 | 2-5-2-6-4-5-3-2-4-2-3-4-2-4-8-2-5-3-2-1-3-4-2-3 | 2-4-3-5-4-5-2-2-4-2-3-4-2-4-8-2-5-3-2-1-3-4-2-3 |
| ERX2465418c,d | ERX2465391d | 123 | 0 | 255 | 189 | 185 | 2-5-2-6-4-5-3-2-4-2-3-4-2-4-8-2-5-3-2-1-3-4-2-3 | 2-5-3-5-4-5-3-2- -2-2-3-4-2-3-8-2-5-3-2-1-3-4-2-3 |
| ERX2465512 | ERX2465223 | 7 | 7 | 6 | 4 | 4 | 2-5-4-3-1-3-2-4-3-2-3-2-3-2-2-2-5-2-2-1-3-4-2-3 | 2-5-4-3-1-4-2-4-3-2-3-2-3-2-2-2-5-2-2-1-3-4-2-3 |
| ERX2465622b | ERX2465178b | 6 | 6 | 4 | 3 | 4 | 2-1-4-7-4-4-4-2-4-2-2-4-2-3-5-2-5-4-2-1-3-4-2-3 | 2-1-4-7-4-3-4-2-4-2-2-4-2-3-5-2-5-3-2-1-3-4-2-3 |
| ERX2465622b | ERX2465568b | 10 | 8 | 6 | 4 | 5 | 2-1-4-7-4-4-4-2-4-2-2-4-2-3-5-2-5-4-2-1-3-4-2-3 | 2-1-4-7-4-4-4-2-4-2-2-4-2-3-5-2-5-3-2-1-3-4-2-3 |
| ERX2465631e | ERX2465366 | 1 | 0 | 0 | 0 | 0 | 2-6-2-7-3-4-2-3-3-4-7-3-2-2-7-2-5-2-2-1-3-4-2-2 | 2-6-2-7-3-4-2-3-3-4-7-3-2-6-7-2-5-2-2-1-3-4-2-2 |
| ERX2465631e | ERX2465636 | 2 | 1 | 1 | 2 | 0 | 2-6-2-7-3-4-2-3-3-4-7-3-2-2-7-2-5-2-2-1-3-4-2-2 | 2-6-2-7-3-4-2-3-3-4-7-3-2-6-7-2-5-2-2-1-3-4-2-2 |
MIRU-VNTR: mycobacterial interspersed repeat unit-variable number of tandem repeat; MTB: Mycobacterium tuberculosis; RIVM: National Institute for Public Health and the Environment; SNPs: single nucleotide polymorphisms; SSI: Statens Serum Institut; WGS: whole genome sequencing.
a The 24-loci MIRU-VNTR order was 580-2996-802-960-1644-3192-424-577-2165-2401-3690-4156-2163b-1955-4052-154-2531-4348-2059-2687-3007-2347-2461-3171.
b This isolate clustered by WGS only with two isolates belonging to two different MIRU-VNTR clusters.
c This isolate clustered by WGS only with three isolates belonging to two different MIRU-VNTR clusters.
d This isolate likely contains subpopulations due to the presence of low frequency variants.
e This isolate clustered by WGS only with two isolates belonging to the same MIRU-VNTR cluster.
Variation in the 24-loci MIRU-VNTR patterns between the pairs of isolates are bold and underlined.