Table 1.

Clustering method overview for each clustering method, the general features are outlined in the table. Median ages and 95% HPD ranges are based upon the BEAST-2 estimates of clade heights (see methods).

Method	Strains in clusters	Number of clusters	Percent of strains in clusters	Cluster sizes	Maximum SNP distances	Clustering rate	Mean timespan	Timespan 95% HPD
Spoligotyping	276	33	85.19	2–39	1–685	0.75	178.35	0.34–7747
MIRU-VNTR	207	38	63.89	2–30	0–611	0.5216	35.58	0–1830
Spoligo-MIRU	174	36	53.7	2–25	0–611	0.4259	36.38	0–1969
12 SNP cluster	242	47	74.69	2–34	0–23	0.6019	23.63	0–102.58
5 SNP cluster	147	40	45.37	2–27	0–10	0.3302	10.86	0–47.07
1 SNP cluster	74	29	22.84	2–6	0–2	0.1389	3.91	0–23.54
12 allele cgMLST	254	45	78.4	2–39	0–51	0.6451	24.06	0–112.25
5 allele cgMLST	173	42	53.4	2–28	0–22	0.4043	13.4	0–68.53
1 allele cgMLST	80	31	24.69	2–6	0–4	0.1512	4.73	0–24.65