TABLE 1.

Comparison of the three genotyping methods with respect to predicting Mycobacterium tuberculosis transmission by clustering

	Total generated clusters	Total patients in clusters	Cluster patients with epidemiological link	Sensitivity^#	Specificity^¶	PPV⁺	NPV^§	Accuracy^ƒ
d5WGS	87	351	134	99.3 (95.9–100)	79.1 (76.4–81.5)	38.2 (33.1–43.5)	99.9 (99.2–100)	81.2 (78.9–83.4)
MIRU–VNTR	131	471	131	97.0 (94.2–99.9)	67.2 (64.3–70.0)	27.8 (23.8–31.9)	99.4 (98.9–100)	70.6 (68.0–73.2)
IS6110 DNA fingerprint	110	417	131	97.0 (94.2–99.9)	72.4 (69.7–75.1)	31.4 (27.0–35.9)	99.5 (99.0–100)	75.2 (72.8–77.7)

Data are presented as n or % (95% CI). Total patients n=1171; of those, 135 patients had a confirmed epidemiological link. PPV: positive predictive value; NPV: negative predictive value; d5WGS: five-single nucleotide polymorphism genetic distance between any two strains as a cut-off for whole-genome sequencing; MIRU–VNTR: mycobacterial interspersed repetitive units–variable number of tandem repeats. ^#: percentage of cluster patients with a confirmed link among all patients with a confirmed transmission link; ^¶: percentage of unclustered patients among all patients without confirmed transmission; ⁺: percentage of clustered patients with a confirmed transmission among all clustered patients; ^§: percentage of patients assigned as unclustered among those without a confirmed transmission; ^ƒ: (true positives + true negatives)/(true positives + false positives + true negatives + false negatives).