Table 2.

Isolate subspecies determined by PCR and WGS

	Pulmonary isolates (n=548)	Extrapulmonary isolates (n=392)	Total isolates (n=940)
Mycobacterium tuberculosis	535 (97·6%)	378 (96·4%)	913 (97·1%)*
Mycobacterium orygis	1 (0·2%)	6 (1·5%)	7 (0·7%)†
Mycobacterium bovis	0	0	0
Mycobacterium bovis BCG	1 (0·2%)	4 (1·0%)	5 (0·5%)†
Non-tuberculous mycobacteria	11 (2·0%)	4 (1·0%)	15 (1·6%)

WGS=whole-genome sequencing.

^*Including two M tuberculosis isolates negative for RD12 on PCR but confirmed by WGS (both extrapulmonary); eight inconclusive isolates on PCR identified as M tuberculosis by WGS (six pulmonary, two extrapulmonary); and one pulmonary isolate identified as M bovis BCG by PCR and M tuberculosis by WGS.

^†All detected by PCR and confirmed by WGS.