Table 2.

Cycle threshold values of the 40 samples that were Xpert resistant very low, pyrosequencing, and Mycobacterial Growth Indicator Tube drug susceptibility testing results

Sample	Xpert – Ct of probes					PSQ RIF mutations	DST RIF
	A	B	C	D	E
Biopsy	29.7	29.4	29.8	30.3	0	531 TTG	R
LN BX	28.6	28.7	28.6	29.3	0	531 TTG	R
Sputum	29	29.9	28.9	30	0	531 TTG	R
LN	29.9	28.8	30.1	30	0	531 TTG	R
Sputum	29.7	30	29.9	30.5	0	531 TTG	R
BX	29.5	34.9	29.4	30.1	31.4	WT	S
Bal	29.8	30.1	30	30.6	0	531 TTG	R
BX	30.5	31	31	31.3	0	531 TTG	R
Abscess	32	32.7	30.3	33.8	34.9	WT	S
Aspirate	28.3	30.3	28	28.9	32.6	WT	S
LN BX	33.4	32.2	32.7	33.4	0	531 TTG	R
Tissue	32.4	33	31.8	32.4	0	531 TTG	R
LN BX	32.1	31.8	0	32.4	34	522 TTG	S
Pus	29.1	0	30.8	31.3	32.4	516 GGC	R
Aspirate	37.8	37.4	36.3	40.9	0	531 TTG	R
Left elbow pus	29	29.1	29.4	29.7	0	531 TTG	R
Tissue	32.8	31.5	31.3	34.4	0	531 TTG	R
Sputum	30.2	30	30.2	30.9	0	531 TTG	R
Sputum	28	33	28	29.3	30	516 GTC	R
Tissue	32.2	31.8	31.6	33.3	0	531 TGG	R
CSF	0	31.2	0	0	31.1	WT	S
Biopsy	38.3	38	37.7	0	0	WT	S
Pus	28.1	0	29.1	30.3	29.6	516 GTC	R
Pus	29.2	30.2	28.4	30.3	0	531 TTG	R
LN	30.9	31.1	31.2	31.8	0	531 TTG	R
LN biopsy	29.3	30.1	29.9	30.6	0	531 TTG	R
Urine	28.3	30.3	28	28.9	0	531 TTG	R
Ct-guided BX	29	29.9	28.9	30	0	531 TTG	R
LN BX	33.6	32	32	35.4	0	531 TTG	R
Pericardial fluid	35.8	36.7	35.5	36.8	38.5	WT	S
Pleural tap	28.7	28.2	28.5	29.2	0	531 TTG	R
Tissue	24.4	25.3	24.9	25.6	0	531 TTG	R
Tissue	32.8	31.5	30.6	35	35.2	WT	S
Abscess	30.2	30.2	30.6	0	32.2	526 AAC	S
Biopsy	34.6	30.2	29.5	31.7	32.7	WT	S
Mesenteric LN	33.2	32	31.3	35.4	35.3	WT	S
Biopsy	28.9	0	29.3	31.3	32.2	516 TAC	S
Biopsy	33.2	31.7	31.6	35.1	35.9	WT	S
Tissue	28.4	30.6	31	31.8	0	531 TTG	R
Biopsy	29.6	31.4	29.8	32.3	0	531 TTG	R

LN: Lymph node, BX: Biopsy, WT: Wild type, S: Susceptible, R: Resistant, DST: Drug susceptibility testing, PSQ: Pyrosequencing, CSF: Cerebral spinal fluid, Ct: Cycle threshold, RIF: Rifampicin