TABLE 2.
Comparing pairwise single nucleotide polymorphisms and probable recent transmission by reference genome, using CDC1551 as gold standard
| Reference genome species | Reference genome name | Median pairwise SNP compared to reference (IQR)a | Median pairwise SNP between isolates (IQR)b | Sensitivity for recent transmission (95% CI)c | Specificity for recent transmission (95% CI) |
|---|---|---|---|---|---|
| Mycobacterium tuberculosis | |||||
| Lineage 4 | H37Rv | 781 (780–781) | 3 (2–6) | 100 (98.7–100) | 100 (99.6–100) |
| Lineage 4 | CDC1551 | 619 (618–619) | 3 (2–6) | ||
| Lineage 2 | CCDC5079 | 1,247 (1,246–1,247) | 3 (2–6) | 100 (98.7–100) | 100 (99.6–100) |
| Mycobacterium africanum | GN041182 | 1,908 (1,907–1,908) | 3 (2–6) | 100 (98.7–100) | 100 (99.6–100) |
| Mycobacterium bovis | AF2122/97 | 2,000 (1,999–2,000) | 3 (2–6) | 100 (98.7–100) | 100 (99.6–100) |
| Mycobacterium canettii | CIPT 140010059 | 16,637 (16,636–16,637) | 3 (2–6) | 100 (98.7–100) | 100 (99.6–100) |
| Mycobacterium kansasii | ATCC 12478 | 34,081 (34,081–34,081) | 0 (0–0) | 100 (98.7–100) | 0.1 (0.0–0.06) |
a
49 pairwise comparisons with reference genome. IQR, interquartile range.
b
1,176 pairwise comparisons.
c
95% CI, 95% confidence interval.