Table 1.

Paired comparisons of culture, Xpert and smear microscopy results for Pooled vs gastric aspirate (GA), Pooled vs induced sputum (IS) and Pooled vs nasopharyngeal aspirate (NPA)¹, and paired comparisons of culture, Xpert and smear microscopy results for Pooled vs the combined yield of GA, IS and NPA by per-protocol and pragmatic approaches

		Day 1 GA Culture (n=294)		Day 1 IS Culture (n=298)		Day 1 NPA Culture (n=242)		Day 1 Combined cultures, per-protocol (n=2342)		Day 1 Combined cultures, pragmatic (n=304)
Type of test	Outcome	M.tb+	M.tb−3	M.tb+	M.tb−	M.tb+	M.tb−	M.tb+	M.tb−	M.tb+	M.tb−
Pooled Culture	M.tb +	20	8	18	13	9	15	17	5	25	6
	M.tb −	8	258	2	265	0	218	7	205	10	263
	Difference (95% CI)	0.0 (−0.03, 0.03)		0.04 (0.01, 0.07)		0.06 (0.03, 0.10)		−0.01 (−0.04, 0.02)		−0.01 (−0.04, 0.02)
	McNemar’s p-value	1,000		0,0053		<0.0014		0,564		0,317
		Day 1 GA Xpert (n=281)		Day 1 IS Xpert (n=296)		Day 1 NPA Xpert (n=242)		Day 1 Combined Xpert, per-protocol (n=2232)		Day 1 Combined Xpert, Pragmatic (n=304)
		M.tb+	M.tb−	M.tb+	M.tb−	M.tb+	M.tb−	M.tb+	M.tb−	M.tb+	M.tb−
Pooled Xpert	M.tb+	12	8	14	9	8	11	13	3	19	4
	M.tb−	4	257	1	272	1	222	5	202	5	276
	Difference (95% CI)	0.01 (−0.01, 0.04)		0.03 (0.00, 0.05)		0.04 (0.01, 0.07)		0.00 (−0.04, 0.02)		0.00 (−0.03, 0.02)
	McNemar’s p-value	0,388		0,0114		0,0044		0,478		0,739
		Day 1 GA Culture/Xpert combined (n=294)		Day 1 IS Culture/Xpert Combined (n=298)		Day 1 NPA Culture/Xpert Combined (n=242)		Day 1 Combined culture/Xpert,per-protocol (n=2342)		Day 1 Combined culture/Xpert, pragmatic (n=304)
		M.tb+	M.tb−	M.tb+	M.tb−	M.tb+	M.tb−	M.tb+	M.tb−	M.tb+	M.tb−
Pooled Culture/Xpert combined	M.tb+	22	10	21	14	11	16	20	5	29	6
	M.tb−	7	255	2	261	0	215	6	203	9	260
	Difference (95% CI)	0.01 (−0.02, 0.04)		0.04 (0.01, 0.07)		0.07 (0.03, 0.10)		0.00 (−0.04, 0.03)		−0.01 (−0.04, 0.02)
	McNemar’s p-value	0,467		0,0034		<0.0014		0,763		0,439
		Day 1 GA Smear (n=294)		Day 1 IS Smear (n=298)		Day 1 NPA Smear (n=242)		NA		NA
		Positive	Negative	Positive	Negative	Positive	Negative
Pooled Smear	Positive	3	3	2	4	1	2
	Negative	1	287	1	291	0	239
	Difference (95% CI)	0.01 (−0.01, 0.02)		0.01 (−0.01, 0.03)		0.01 (−0.01, 0.02)
	McNemar’s p-value	0,317		0,180		0,157
		Day 1 GA Culture (n=294)		Day 1 IS Culture (n=298)		Day 1 NPA Culture (n=242)		Day 1 Combined cultures, per-protocol (n=2342)		Day 1 Combined cultures, Pragmatic (n=304)
		Contaminated	Not Contaminated	Contaminated	Not Contaminated	Contaminated	Not Contaminated	Contaminated	Not Contaminated	Contaminated	Not Contaminated
Pooled Culture	Contaminated	3	18	1	20	2	12	2	13	5	16
	Not Contaminated	16	257	9	268	5	223	23	196	27	256
	Difference (95% CI)	0.01 (−0.04, 0.05)		0.04 (0.00, 0.08)		0.03 (−0.01, 0.07)		−0.04 (−0.10, 0.01)		−0.04 (−0.08, 0.01)
	McNemar’s p-value	0,732		0,0414		0,090		0,096		0,093
		Day 1 GA Xpert (n=281)		Day 1 IS Xpert (n=296)		Day 1 NPA Xpert (n=242)		Day 1 Combined Xpert, per- Protocol (n=2232)		Day 1 Combined Xpert, Pragmatic (n=304)
		Error	Not Error	Error	Not Error	Error	Not Error	Error	Not Error	Error	Not Error
Pooled Xpert	Error	0	3	0	3	0	3	0	3	0	3
	Not error	0	278	2	291	0	239	2	218	2	299
	Difference (95% CI)	0.01 (0.00, 0.03)		0.00 (−0.01, 0.02)		0.01 (−0.01, 0.03)		0.00 (−0.02, 0.03)		0.00 (−0.01, 0.02)
	McNemar’s p-value	0,083		0,655		0,083		0,655		0,655

GA: gastric aspirate; IS: induced sputum; NPA: nasopharyngeal aspirate; M.tb: Mycobacterium tuberculosis; CI: confidence interval.

¹For an explanation for the different denominators used in these comparisons, see SDC4: Figure 1

²For the per-protocol analysis, 234/304 (77.0%) children had the same number and type of specimens collected on day 1 and for pooling. Of these, all 234 (100%) had culture on all specimens tested by culture, while 223 (95.3%) had Xpert on all specimens tested by Xpert.

³M. tb− includes all non-positive results (for culture: contaminated, NTM and negative; for Xpert: error/invalid or negative);

⁴Using the Benjamini-Hochberg method, P≤0.04 was defined as statistically significant (24).