Diagnostic Utility of GeneXpert MTB/RIF Assay in EPTB Detection in Formalin Fixed Paraffin Embedded Tissue Biopsies in South Western Uganda

Figures & data

Table 1 Demographic Characteristics of Analysed Specimens

Variable	Description	Frequency (n)	Percentage (%)
Sex	Female	40	45%
	Male	49	55%
Age	Mean (Range)	34.3 (1–88)
Topographic site	Lymph node	57	64%
	Prostate	4	4.5%
	Testis	3	3.4%
	Skin	3	3.4%
	Gastric	2	2.2%
	Bone	2	2.2%
	Gingiva	2	2.2%
	Ileum	2	2.2%
	Omental	2	2.2%
	Others	12	13.5%

Note: Age was a continuous variable which was presented as mean (range).

Figure 1 Flow chart of specimen.

Table 2 Test Results for H&E, ZN and GeneXpert

TEST	CATEGORY	POSITIVE f (%)	NEGATIVE f (%)
H&E	Classical granuloma	45/89 (50.6%)
	Non-classical granuloma		16/89 (17.9%)
	No granuloma		28/89 (31.5%)
ZN		15/89 (16.9%)	74/89 (83.1%)
GeneXpert	Trace	21/27 (77.8%)
	Very low	5/27 (18.5%)
	Low	1/27 (3.7%)
	RR indeterminate	21/27 (77.8%)
	RR not detected	6/27 (22.2%)

Abbreviations: RR, Rifampicin Resistance; H&E, Haematoxylin and Eosin; ZN, Ziehl-Neelsen; f, Frequency; %, Percentage.

Table 3 Test Results for ZN, H&E and GeneXpert by Sex, Age and Tissue Types

VARIABLE	DESCRIPTION	ZN		H&E		GENEXPERT
		Pos. f (%)	Neg. f (%)	Pos. f (%)	Neg. f (%)	Pos. f (%)	Neg. f (%)
Sex	Female	6 (40)	34 (45.9)	23 (51.1)	17 (38.6)	15 (55.6)	25 (40.3)
	Male	9 (60)	40 (54.1)	22 (48.9)	27 (61.4)	12 (44.4)	37 (59.7)
Age group	0–30 years	7 (46.7)	37 (50)	20 (44.4)	24 (54.5)	16 (59.3)	28 (45.1)
	31–61 years	5 (33.3)	28 (37.8)	16 (35.6)	16 (36.4)	8 (29.6)	24 (38.7)
	62–92 years	3 (20.0)	9 (12.2)	9 (20.0)	4 (9.1)	3 (11.1)	10 (16.1)
Tissue	Lymph nodes	13 (86.7)	44 (59.5)	33 (73.3)	24 (54.5)	22 (81.5)	35 (56.5)
	Non-lymph nodes	2 (13.3)	30 (40.5)	12 (26.7)	20 (45.5)	5 (18.5)	27 (43.5)

Abbreviations: ZN, Ziehl-Neelsen; H&E, Haematoxylin and Eosin; Pos, Positive; Neg, Negative; f, Frequency; %, Percentage.

Table 4 Overall Contingence Table for All Tissues

GeneXpert (Diagnostic Test)	Composite Reference Standard (H&E&ZN)
	Positive	Negative	Total
Positive	23	4	27
Negative	24	38	62
Total	47	42	89

Abbreviations: H&E, Haematoxylin and Eosin; ZN, Ziehl-Neelsen.

Table 5 Contingence Table for Lymph Node and Non Lymph Node Tissues

GeneXpert (Diagnostic Test)		Composite Reference Standard (ZN &H&E)
		Positive	Negative	Total
Lymph node	Positive	18	4	22
	Negative	16	19	35
	Total	34	23	57
Non-Lymph node	Positive	5	0	5
	Negative	8	19	27
	Total	13	19	32

Abbreviations: H&E, Haematoxylin and Eosin; ZN, Ziehl-Neelsen.

Table 6 Diagnostic Utility of GeneXpert Against ZN and H&E as Composite Reference Standard

Diagnostic utility	GeneXpert
Sensitivity % (95% CI)	48.94 (38.55–59.32)
Specificity % (95% CI)	90.48 (84.38–96.57)
Positive predictive value % (95% CI)	85.19 (77.80–92.57)
Negative predictive value % (95% CI)	61.29 (51.17–71.41)

Abbreviations: CI, Confidence Interval; %, Percentage.

Table 7 Diagnostic Utility of GeneXpert by Tissue Type Against ZN and H&E as Composite Reference Standard

Diagnostic utility	GeneXpert
	Lymph nodes Tissues	Non-Lymph nodes Tissues
Sensitivity % (95% CI)	52.9 (40.0–65.9)	38.5 (21.6–55.3)
Specificity % (95% CI)	82.6 (72.8–92.5)	100 (100–100)
PPV % (95% CI)	81.8 (71.8–91.8)	100 (100–100)
NPV % (95% CI)	54.3 (41.4–67.2)	70.4 (54.6–86.2

Abbreviations: CI, Confidence Interval; PPV, Positive predictive value; NPV, Negative predictive value; %, Percentage.

Figure 2 Area under ROC curve for all Tissues.

Abbreviation: ROC, Receiver operating characteristic curve.

Figure 3 Area under ROC curve for Lymph node Tissues.

Abbreviation: ROC, Receiver operating characteristic curve.

Figure 4 Area under ROC curve for non-lymph node Tissues.

Abbreviation: ROC, Receiver operating characteristic curve.