Evaluation of the GeneXpert MTB/RIF assay performance in sputum samples with various characteristics from presumed pulmonary tuberculosis patients in Shiselweni region, Eswatini

Figures & data

Figure 1. Shows a map of Eswatini showing the location of Shiselweni in green [11].

Table 1. Sputum GeneXpert MTB/RIF and MGIT culture Positive by exposure variables.

	GeneXpert			MGIT culture
Variable	GeneXpert negative n (%)	GeneXpert positive n (%)	P-value (X^2/F exact test)	MGIT culture negative n (%)	MGIT culture positive n (%)	P-value (X^2/F exact test)
Gender
Male	279 (69.06%)	125 (30.94%)	.088 (2.9021)**	277 (68.56%)	127 (31.44%)	.039 (4.2554)**
Female	395 (74.11%)	138 (25.89%)		398 (74.67%)	135 (25.33%)
Age groups
(0–15)years	15 (65.22%)	8 (34.78%)	.608 (3.6002)**	15 (65.22%)	8 (34.78%)	.787 (2.4297)**
(16–30)years	194 (72.12%)	75 (27.88%)		193 (71.75%)	76 (28.25%)
(31–45)years	332 (73.13%)	122 (26.87%)		332 (73.13%)	122 (26.87%)
(46–60)years	85 (72.65%)	32 (27.35%)		87 (74.36%)	30 (25.64%)
(61–75)years	15 (57.69%)	11 (41.31%)		17 (65.38%)	9 (34.62%)
(76–90)years	13 (68.42%)	6 (31.58%)		12 (63.16%)	7 (36.84%)
Repeat (test runs)
1^st Test (1^st run)	792 (72.86%)	295 (27.14%)	.122 (7.5723)***	782 (71.94%)	305 (28.06%)	.863 (0.6924)***
2^nd run (Repeat )	20 (90.91%)	2 (9.09%)		17 (77.27 %)	5 (22.73%)
3^rd rerun (2nd repeat)	1 (100.00%)	0 (0.00%)		1 (100%)	0 (0.00%)
Sputum volume
1ml	29 (74.36%)	10 (25.64%)	.036 (13.4663)**	29 (74.36%)	10 (25.64%)	.071 (11.6220)**
2ml	210 (72.16%)	81 (27.84%)		207 (71.13%)	84 (28.87%)
3ml	251 (75.68%)	81 (24.32%)		247 (74.17%)	86 (25.96%)
4ml	107 (67.30%)	52 (32.70%)		105 (66.04%)	54 (33.96%)
5ml	149 (79.68%)	38 (20.32%)		146 (78.07%)	41 (21.93%)
6ml	42 (60.87%)	27 (39.13%)		42 (60.87%)	27 (39.13%)
7ml	24 (75.00%)	8 (25.00%)		24 (75.00%)	8 (25.00%)
Sputum quality
Bloody	31 (68.89%)	14 (31.11%)	.796 (0.4551)**	32 (71.11%)	13 (28.89%)	.766 (0.5326)**
Mucopurulent	537 (73.46%)	194 (26.54%)		532 (72.78%)	199 (27.22%)
Salivary	245 (73.35%)	89 (26.65%)		236 (70.66%)	98 (29.34%)

Table 2. GeneXpert MTB/RIF and MGIT positive samples adjusted for multivariable covariates.

				MGIT culture
GeneXpert results	GeneXpert	Odds ratio	P-value (95% CI)	Odds ratio	P-value (95% CI)
Sputum volume	1 ml	1		1
	2 ml	0.95451	.908 (0.43400–2.09926)	0.98559	.971 (0.44814–2.16760)
	3 ml	0.93606	.870 (0.42491–2.06213)	0.94135	.881 (0.42718–2.07437)
	4 ml	1.33319	.492 (0.58659–3.03001)	1.32222	.505 (0.58133–3.00733)
	5 ml	0.77321	.552 (0.33129–1.80465)	0.69059	.395 (0.29406–1.62185)
	6 ml	1.36668	.502 (0.54959–3.39858)	1.26982	.609 (0.50833–3.17201)
	7 ml	0.921212	.893 (0.27969–3.03422)	0.70856	.586 (0.20536–2.44478)
Gender	Male	1		1
	Female	0.79065	.128 (0.58413–1.07018)	0.74529	.057 (0.55045–1.00910)
Test run	1	1		1
	2	0.20645	.132 (0.02645–1.60901)	0.48753	.354 (0.106754–2.22645)
	3	1	Ommitted
	(0–15) years	1		1
	(16–30) years	0.71839	.476 (0.28904–1.78545)	0.75766	.549 (0.30564–1.87816)
	(31–45) years	0.72176	.476 (0.29419–1.77077)	0.75539	.539 (0.30868–1.84859)
	(46–60) years	0.73239	.528 (0.27843–1.92648)	0.70344	.476 (0.26719–1.85176)
	(61–75) years	1.49393	.511 (0.45078–4.95102)	1.31664	.655 (0.39407–4.39906)
	(76–90) years	1.02227	.974 (0.27270–3.83212)	0.59599	.380 (0.18769–1.89253)

Table 3. Sensitivity and specificity of GeneXpert MTB/RIF assay compared to MGIT culture.

	GeneXpert				MGIT culture
	Sensitivity (CI%)	Specificity (CI%)	PPV	NPV	Sensitivity (CI%)	Specificity (CI%)	PPV	NPV
Gender
Male	87.7% (81.0–92.7)	96.5% (94.1–98.0)	86.1%	96.9%	93.7% (88.0–97.2)	97.8% (95.3–99.2)	91.5%	98.4%
Female	95.2% (89.8–98.2)	97.1% (94.4–98.8)	89.2%	98.8%	89.6% (83.2–94.2)	95.7% (93.2–97.5)	84.0%	97.4%
Age
(0–15) years	100% (63.1–100)	100% (78.2–100)	100%	100%	100% (63.1–100)	100% (78.2–100)	100%	100%
(16–30) years	92.0% (83.4–97.0)	96.4% (92.7–98.5)	86.4%	98%	90.8% (81.9–96.2)	96.9% (93.4–98.9)	88.0%	97.7%
(31–45) years	89.3% (82.5–94.2)	96.1% (93.4–97.9)	85.1%	97.3%	89.3% (82.5–94.2)	96.1% (93.4–97.9)	85.1%	97.3%
(46–60) years	93.8% (79.2–99.2)	100% (95.8–100)	100%	98.5%	100% (88.4–100)	97.7% (91.9–99.7)	91.6%	100%
(61–75) years	81.8% (48.2- 97.7)	100% (78.2–100)	100%	95.7%	100% (66.4–100)	88.2% (63.6–98.5)	68.0%	100%
(76–90) years	100% ( 54.1–100)	92.3% ( 64.0–99.8)	76.5%	100%	85.7% (42.1–99.6)	100% (73.5–100)	100%	96.6%
Volume
1 ml	100% (69.2–100)	100% (88.1–100)	100%	100%	100% ( 69.2–100)	100% (88.1–100)	100%	100%
2 ml	91.4% (83.0–96.5)	95.2% (91.4–97.7)	82.7%	97.8%	88.1% (79.2–94.1)	96.6% (93.2–98.6)	86.7%	97.0%
3 ml	91.4% (83.0–96.5)	95.2% (91.8–97.5)	82.7%	97.8%	86.0% (76.9–92.6)	97.2% (94.2–98.9)	88.4%	96.5%
4 ml	92.3% (81.5–97.9)	94.4% (88.2–97.9)	80.5%	98.0%	88.9% (77.4–95.8)	96.2% (90.5–99.0)	85.4%	97.2%
5 ml	89.5% (75.2–97.1)	95.3% (90.6–98.1)	82.6%	97.3%	82.9% (67.9–92.8)	97.3% (93.1–99.2)	88.3%	95.8%
6 ml	92.6% (75.7–99.1)	95.2% (83.8–99.4)	82.9%	98.1%	92.6% (75.7–99.1)	95.2% (83.8–99.4)	82.9%	98.1%
7 ml	87.5% (47.3–99.7)	95.8% (78.9–99.9)	84.0%	96.8%	87.5% (47.3–99.7)	95.8% ( 78.9–99.9)	84.0%	96.8%
Quality
Bloody	92.9% (66.1–99.8)	100% (88.8–100)	100%	98.2%	100% (75.3–100)	96.9% (83.8–99.9)	88.9%	100%
Mucopurulent	90.7% ( 85.7–94.4)	95.7% (93.6–97.3)	84.1%	97.6%	88.4% (83.2%–92.5%)	96.6% (94.7–98.0)	86.7%	97.1%
Salivary	93.3% (85.9–97.5)	93.9% (90.1–96.5)	79.2%	98.2%	84.7% (76.0–91.2)	97.5% (94.5–99.1)	89.3%	96.2%
Test run
1st	91.5% (87.7–94.4)	95.6% (93.9–96.9)	83.8%	97.8%	88.5% (84.4–91.9)	96.8% (95.3–97.9)	87.5%	96.8%
2nd (Repeat )	100% (15.8–100)	85% (62.1–96.8)	62.5%	100%	40% (5.27–85.3)	100% (80.5–100)	100%	87.0%
3rd (2nd repeat)

Central statistics and population’s office. 2019. Ministry of Home Affairs, Eswatini. [cited 2020 Sept 8].

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