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Readout of Xpert MTB/RIF assay for a TB positive, rifampicin‐susceptible specimen. Courtesy: Karin Weyer, The WHO STOP TB Department.
Figuras y tablas -
Figure 1

Readout of Xpert MTB/RIF assay for a TB positive, rifampicin‐susceptible specimen. Courtesy: Karin Weyer, The WHO STOP TB Department.

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Flow diagram of studies in the review.
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Figure 2

Flow diagram of studies in the review.

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Risk of bias and applicability concerns graph: review authors' judgements about each domain presented as percentages across the 27 included study centres (18 studies). The reference standard domain pertains to TB as the target condition. See text for the reference standard pertaining to rifampicin resistance.
Figuras y tablas -
Figure 3

Risk of bias and applicability concerns graph: review authors' judgements about each domain presented as percentages across the 27 included study centres (18 studies). The reference standard domain pertains to TB as the target condition. See text for the reference standard pertaining to rifampicin resistance.

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Risk of bias and applicability concerns summary: review authors' judgements about each domain for each included study centre.
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Figure 4

Risk of bias and applicability concerns summary: review authors' judgements about each domain for each included study centre.

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Forest plots of Xpert sensitivity and specificity for TB detection, Xpert used as an initial test replacing smear microscopy. The individual studies are ordered by decreasing sensitivity. TP = True Positive; FP = False Positive; FN = False Negative; TN = True Negative. Between brackets are the 95% CI of sensitivity and specificity. The figure shows the estimated sensitivity and specificity of the study (blue square) and its 95% CI (black horizontal line). Xpert specificity could not be estimated in one study.
Figuras y tablas -
Figure 5

Forest plots of Xpert sensitivity and specificity for TB detection, Xpert used as an initial test replacing smear microscopy. The individual studies are ordered by decreasing sensitivity. TP = True Positive; FP = False Positive; FN = False Negative; TN = True Negative. Between brackets are the 95% CI of sensitivity and specificity. The figure shows the estimated sensitivity and specificity of the study (blue square) and its 95% CI (black horizontal line). Xpert specificity could not be estimated in one study.

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Summary plots of Xpert sensitivity and specificity for TB detection, Xpert used as an initial test replacing smear microscopy. Each individual study is represented by an empty square. The size of the square is proportional to the sample size of the study such that larger studies are represented by larger squares. The filled circle is the pooled median estimate for sensitivity and specificity. The solid curves represent the 95% credible region around the summary estimate; the dashed curves represent the 95% prediction region.
Figuras y tablas -
Figure 6

Summary plots of Xpert sensitivity and specificity for TB detection, Xpert used as an initial test replacing smear microscopy. Each individual study is represented by an empty square. The size of the square is proportional to the sample size of the study such that larger studies are represented by larger squares. The filled circle is the pooled median estimate for sensitivity and specificity. The solid curves represent the 95% credible region around the summary estimate; the dashed curves represent the 95% prediction region.

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Forest plots of Xpert for TB detection, Xpert used as an add‐on test following a negative smear microscopy result. TP = True Positive; FP = False Positive; FN = False Negative; TN = True Negative. Between brackets the 95% CI of sensitivity and specificity. The figure shows the estimated sensitivity and specificity of the study (blue square) and its 95% CI (black horizontal line).
Figuras y tablas -
Figure 7

Forest plots of Xpert for TB detection, Xpert used as an add‐on test following a negative smear microscopy result. TP = True Positive; FP = False Positive; FN = False Negative; TN = True Negative. Between brackets the 95% CI of sensitivity and specificity. The figure shows the estimated sensitivity and specificity of the study (blue square) and its 95% CI (black horizontal line).

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Summary plots of Xpert sensitivity and specificity for TB detection, Xpert used as an add‐on test following a negative smear microscopy result. Each individual study is represented by an empty square. The size of the square is proportional to the sample size of the study such that larger studies are represented by larger squares. The filled circle is the pooled median estimate for sensitivity and specificity. The solid curve represents the 95% credible region around the summary estimate; the dashed curves represent the 95% prediction region.
Figuras y tablas -
Figure 8

Summary plots of Xpert sensitivity and specificity for TB detection, Xpert used as an add‐on test following a negative smear microscopy result. Each individual study is represented by an empty square. The size of the square is proportional to the sample size of the study such that larger studies are represented by larger squares. The filled circle is the pooled median estimate for sensitivity and specificity. The solid curve represents the 95% credible region around the summary estimate; the dashed curves represent the 95% prediction region.

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Forest plot of Xpert sensitivity for TB detection in smear‐positive subgroup. The squares represent the sensitivity and specificity of one study, the black line its CI. TP = true positive; FP = false positive; FN = false negative; TN = true negative. Xpert specificity could not be estimated in these studies.
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Figure 9

Forest plot of Xpert sensitivity for TB detection in smear‐positive subgroup. The squares represent the sensitivity and specificity of one study, the black line its CI. TP = true positive; FP = false positive; FN = false negative; TN = true negative. Xpert specificity could not be estimated in these studies.

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Forest plots of Xpert sensitivity and specificity for TB detection in HIV‐positive and HIV‐negative subgroups. The squares represent the sensitivity and specificity of one study and the black line represent its CI. TP = true positive; FP = false positive; FN = false negative; TN = true negative.
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Figure 10

Forest plots of Xpert sensitivity and specificity for TB detection in HIV‐positive and HIV‐negative subgroups. The squares represent the sensitivity and specificity of one study and the black line represent its CI. TP = true positive; FP = false positive; FN = false negative; TN = true negative.

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Summary plots of Xpert sensitivity and specificity for TB detection in HIV‐positive (red colour) and HIV‐negative subgroups (black colour). Each individual study is represented by an empty square. The size of the square is proportional to the sample size of the study such that larger studies are represented by larger squares. The filled circles are the median estimates for sensitivity and specificity. The solid curves represent the 95% credible region around the summary estimates; the dashed curves represent the 95% prediction region.
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Figure 11

Summary plots of Xpert sensitivity and specificity for TB detection in HIV‐positive (red colour) and HIV‐negative subgroups (black colour). Each individual study is represented by an empty square. The size of the square is proportional to the sample size of the study such that larger studies are represented by larger squares. The filled circles are the median estimates for sensitivity and specificity. The solid curves represent the 95% credible region around the summary estimates; the dashed curves represent the 95% prediction region.

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Forest plots of Xpert sensitivity and specificity for detection of rifampicin resistance, Xpert used as an initial test replacing conventional drug susceptibility testing as the initial test. The individual studies are ordered by decreasing sensitivity and decreasing number of true positives. The squares represent the sensitivity and specificity of one study, the black line its CI. TP = true positive; FP = false positive; FN = false negative; TN = true negative.
Figuras y tablas -
Figure 12

Forest plots of Xpert sensitivity and specificity for detection of rifampicin resistance, Xpert used as an initial test replacing conventional drug susceptibility testing as the initial test. The individual studies are ordered by decreasing sensitivity and decreasing number of true positives. The squares represent the sensitivity and specificity of one study, the black line its CI. TP = true positive; FP = false positive; FN = false negative; TN = true negative.

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Summary plots of Xpert sensitivity and specificity for detection of rifampicin resistance, Xpert used as an initial test replacing conventional drug susceptibility testing as the initial test. Each individual study is represented by an empty square. The size of the square is proportional to the sample size of the study such that larger studies are represented by larger squares. The filled circle is the pooled median estimate for sensitivity and specificity. The solid curves represent the 95% credible region around the summary estimate; the dashed curves represent the 95% prediction region.
Figuras y tablas -
Figure 13

Summary plots of Xpert sensitivity and specificity for detection of rifampicin resistance, Xpert used as an initial test replacing conventional drug susceptibility testing as the initial test. Each individual study is represented by an empty square. The size of the square is proportional to the sample size of the study such that larger studies are represented by larger squares. The filled circle is the pooled median estimate for sensitivity and specificity. The solid curves represent the 95% credible region around the summary estimate; the dashed curves represent the 95% prediction region.

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Bayesian bivariate hierarchical model, likelihood
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Figure 14

Bayesian bivariate hierarchical model, likelihood

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Bayesian bivariate hierarchical model, prior distributions
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Figure 15

Bayesian bivariate hierarchical model, prior distributions

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TB detection, all studies.
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Test 1

TB detection, all studies.

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Add on.
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Test 2

Add on.

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Smear positive.
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Test 3

Smear positive.

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Smear negative.
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Test 4

Smear negative.

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HIV positive.
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Test 5

HIV positive.

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HIV negative.
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Test 6

HIV negative.

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TB detection, condition of specimen.
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Test 7

TB detection, condition of specimen.

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TB detection, specimen preparation.
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Test 8

TB detection, specimen preparation.

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TB prevalence.
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Test 9

TB prevalence.

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Income status.
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Test 10

Income status.

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Rifampicin resistance.
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Test 11

Rifampicin resistance.

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RIF resistance prevalence.
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Test 12

RIF resistance prevalence.

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Summary of findings Summary of results: all patients and subgroups

Review question: What is the diagnostic accuracy of Xpert MTB/RIF assay for detection of pulmonary TB and detection of rifampicin resistance?

Patients/population: Adults suspected of having pulmonary TB or MDR‐TB (for TB detection); confirmed TB cases (for rifampicin resistance detection)

Purpose: TB detection: Xpert MTB/RIF assay used as an initial test replacing microscopy and used as an add‐on test following a negative smear microscopy result. Rifampicin resistance detection: Xpert MTB/RIF assay as an initial test replacing conventional phenotypic drug susceptibility testing

Setting: Basic laboratories and primary health facilities (peripheral health services level)

Index test: Xpert MTB/RIF assay

Importance: Compared with culture and conventional drug susceptibility testing, Xpert MTB/RIF assay could have considerable advantages for scaling up programmatic management of TB by offering rapid diagnosis nearer to the point of care, standardized testing, potential for high throughput, and fewer requirements for laboratory biosafety

Reference standards: TB: solid or liquid culture; rifampicin resistance: phenotypic drug susceptibility testing

Studies: Cross‐sectional

Diagnostic accuracy for TB detection

Type of analysis

Effect

(95% credible interval)

No. of participants (studies)

What do these results mean given 5% prevalence of TB among individuals suspected of having pulmonary TB?

 

What do these results mean given 15% prevalence of TB among individuals suspected of having pulmonary TB?

What do these results mean given 30% prevalence of TB among individuals suspected of having pulmonary TB?

 

TB detection, Xpert used as an initial test replacing microscopy

Pooled median sensitivity 88% (83, 92) and pooled median specificity 98% (97, 98)

 

7517  

(15)

With a prevalence of 5%, 50/1000 individuals will have pulmonary TB. Of these, 44 (TP) will be identified; 6 (FN) will be missed. Of the 950 individuals without TB, 931 (TN) will not be treated; 19 (FP) may be unnecessarily treated

With a prevalence of 15%, 150/1000 individuals will have pulmonary TB. Of these, 132 (TP) will be identified; 18 (FN) will be missed. Of the 850 individuals without TB, 833 (TN) will not be treated; 17 (FP) may be unnecessarily treated

With a prevalence of 30%, 300/1000 individuals will have pulmonary TB. Of these, 264 (TP) will be identified; 36 (FN) will be missed. Of the 700 individuals without TB, 686 (TN) will not be treated; 14 (FP) may be unnecessarily treated

TB detection, Xpert used as an add‐on test following a negative smear microscopy result

Pooled median sensitivity 67% (58, 74) and pooled median specificity 98% (97, 98)

 

5719 

(14)

With a prevalence of 5%, 50/1000 individuals will have pulmonary TB. Of these, 34 (TP) will be identified; 16 (FN) will be missed. Of the 950 individuals without TB, 931 (TN) will not be treated; 19 (FP) may be unnecessarily treated

With a prevalence of 15%, 150/1000 individuals will have pulmonary TB. Of these, 101 (TP) will be identified; 49 (FN) will be missed. Of the 850 individuals without TB, 833 (TN) will not be treated; 17 (FP) may be unnecessarily treated

With a prevalence of 30%, 300/1000 individuals will have pulmonary TB. Of these, 201 (TP) will be identified; 99 (FN) will be missed. Of the 700 individuals without TB, 686 (TN) will not be treated; 14 (FP) may be unnecessarily treated

Smear‐positive, culture‐positive subgroup, within‐ study comparison

Pooled median sensitivity 98% (97, 99); specificity of Xpert could not be estimated in these studies

1735 

(15)

With a prevalence of 5%, 50/1000 individuals will have pulmonary TB. Of these, 49 (TP) will be identified; 1 (FN) will be missed

With a prevalence of 15%, 150/1000 individuals will have pulmonary TB. Of these, 147 (TP) will be identified; 3 (FN) will be missed

With a prevalence of 30%, 300/1000 individuals will have pulmonary TB. Of these, 294 (TP) will be identified; 6 (FN) will be missed

Smear‐negative, culture‐positive subgroup

Pooled median sensitivity 68% (59, 75) and pooled median specificity 98% (97, 99)

5771

(15)

With a prevalence of 5%, 50/1000 individuals will have pulmonary TB. Of these, 34 (TP) will be identified; 16 (FN) will be missed. Of the 950 individuals without TB, 931 (TN) will not be treated; 19 (FP) may be unnecessarily treated

With a prevalence of 15%, 150/1000 individuals will have pulmonary TB. Of these, 102 (TP) will be identified; 48 (FN) will be missed. Of the 850 individuals without TB, 833 (TN) will not be treated; 17 (FP) may be unnecessarily treated

With a prevalence of 30%, 300/1000 individuals will have pulmonary TB. Of these, 204 (TP) will be identified; 96 (FN) will be missed. Of the 700 individuals without TB, 686 (TN) will not be treated; 14 (FP) may be unnecessarily treated

HIV‐positive subgroup

Pooled median sensitivity 80% (67, 88) and pooled median specificity 97% (93, 99)

1163 

(4)

With a prevalence of 5%, 50/1000 individuals will have pulmonary TB. Of these, 40 (TP) will be identified; 10 (FN) will be missed. Of the 950 individuals without TB, 922  (TN) will not be treated; 28 (FP) may be unnecessarily treated

With a prevalence of 15%, 150/1000 individuals will have pulmonary TB. Of these, 120 (TP) will be identified; 30 (FN) will be missed. Of the 850 individuals without TB, 825 (TN) will not be treated; 25 (FP) may be unnecessarily treated

With a prevalence of 30%, 300/1000 individuals will have pulmonary TB. Of these, 240 (TP) will be identified; 60 (FN) will be missed. Of the 700 individuals without TB, 679 (TN) will not be treated; 21 (FP) may be unnecessarily treated

HIV‐negative subgroup

Pooled median sensitivity 89% (81, 94) and pooled median specificity 99% (96, 99)

1981  

(4)

With a prevalence of 5%, 50/1000 individuals will have pulmonary TB. Of these, 45 (TP) will be identified; 5 (FN) will be missed. Of the 950 individuals without TB, 941  (TN) will not be treated; 9 (FP) may be unnecessarily treated

With a prevalence of 15%, 150/1000 individuals will have pulmonary TB. Of these, 134 (TP) will be identified; 16 (FN) will be missed. Of the 850 individuals without TB, 842 (TN) will not be treated; 8 (FP) may be unnecessarily treated

With a prevalence of 30%, 300/1000 individuals will have pulmonary TB. Of these, 267 (TP) will be identified; 33 (FN) will be missed. Of the 700 patients individuals without TB, 693 (TN) will not be treated; 7 (FP) may be unnecessarily treated

Diagnostic accuracy for detection of rifampicin resistance

Type of analysis

Effect

(95% credible interval)

No. of participants (studies)

What do these results mean given 2% prevalence of rifampicin resistance among individuals with TB?

What do these results mean given 15% prevalence of rifampicin resistance among individuals with TB?

What do these results mean given 30% prevalence of rifampicin resistance among individuals with TB?

Rifampicin resistance detection,

Xpert used as an initial test replacing conventional drug susceptibility testing

Pooled median sensitivity 94% (87, 97) and pooled median specificity 98% (97, 99)

2340  

(11)

With a prevalence of 2%, 20/1000 will have rifampicin resistance. Of these, 19 (TP) will be identified; 1 (FN) will be missed. Of the 980 patients with TB sensitive to rifampicin, 960 (TN) will not be treated; 20 (FP) may be unnecessarily treated

With a prevalence of 15%, 150/1000 will have rifampicin resistance. Of these, 141 (TP) will be identified; 9 (FN) will be missed. Of the 850 patients with TB sensitive to rifampicin, 833 (TN) will not be treated; 17 (FP) may be unnecessarily treated

With a prevalence of 30%, 300/1000 will have rifampicin resistance Of these, 282 (TP) will be identified; 18 (FN) will be missed. Of the 700 patients with TB sensitive to rifampicin, 686 (TN) will not be treated; 14 (FP) may be unnecessarily treated

TP, true positive; FN, false negative; TN, true negative; FP, false positive
Figuras y tablas -
Summary of findings Summary of results: all patients and subgroups
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Table 1. Xpert MTB/RIF assay for detection of TB and rifampicin resistance

Type of analysis

(Number of studies)

Pooled sensitivity

Median (95% credible interval)

Pooled specificity

Median (95% credible interval)

Predicted sensitivity

Median (95% credible interval)

Predicted specificity

Median (95% credible interval)

Xpert used as an initial test for TB detection replacing microscopy (15)*

 

88%

(83, 92)

98%

(97, 99)

88%

(66, 97)

98%

(92, 100)

Xpert used as an add‐on test for TB detection following a negative smear microscopy result (14)

67%

(58, 74)

98%

(97, 99)

66%

(40, 86)

98%

(93, 100)

Xpert used as an initial test for rifampicin resistance detection replacing conventional drug susceptibility testing as the initial test (11)

94%

(87, 97)

98%

(97, 99)

94%

(75, 99)

98%

(91, 100)

*Three studies that preferentially enrolled smear‐positive or smear‐negative patients were excluded

Figuras y tablas -
Table 1. Xpert MTB/RIF assay for detection of TB and rifampicin resistance
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Table 2. Impact of covariates on heterogeneity of Xpert sensitivity and specificity for TB detection

Covariate

Sensitivity

Median (95% credible interval)

Specificity

Median (95% credible interval)

Smear status

 

 

Smear +

98% (97, 99)

***

Smear ‐

68% (59, 75)

98% (97, 99)

Difference (Smear+ minus Smear‐)

31% (23, 39)

**

P (Smear+ > Smear‐)

1.00

**

HIV status

 

 

HIV+

80% (67, 88)

97% (93, 99)

HIV‐

89% (81, 94)

99% (96, 99)

Difference (HIV+ minus HIV‐)

‐9% (‐22, 3)

‐1% (‐5, 2)

P (HIV+ > HIV‐)

0.06

0.21

Condition of specimen

 

 

Fresh

88% (80, 93)

99% (98, 100)

Frozen

85% (77, 91)

97% (95, 99)

Difference (Fresh minus Frozen)

3% (‐7, 13)

2% (0.1, 4)

P (Fresh > Frozen)

0.73

0.98

Specimen preparation

 

 

Unprocessed

92% (87, 96)

99% (97, 99)

Processed

85% (79, 90)

98% (96, 99)

Difference (Unprocessed minus Processed)

7% (0.2, 14)

0.8% (‐1, 3)

P (Unprocessed > Processed)

0.98

0.84

TB prevalence

 

 

High (> 30%)

89% (84, 93)

98% (96, 99)

Low (≤ 30%)

86% (77, 92)

99% (97, 99)

Difference (High minus Low)

3% (‐5, 12)

‐0.4% (‐2, 1)

P (High > Low)

0.80

0.29

Country income level

 

 

High‐income

92% (86, 96)

98% (95, 99)

Low‐ and middle‐income

85% (79, 90)

99% (97, 99)

Difference (High‐income minus Low‐ and middle‐income)

6% (‐1, 14)

‐1% (‐3, 1)

P (High‐income > Low‐ and middle‐income)

0.96

0.23

P = probability
Figuras y tablas -
Table 2. Impact of covariates on heterogeneity of Xpert sensitivity and specificity for TB detection
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Table 3. Impact of covariates on heterogeneity of Xpert sensitivity and specificity for rifampicin resistance detection

Covariate

Sensitivity

Median (95% credible interval)

Specificity

Median (95% credible interval)

Parameter value (delta cycle threshold cutoff)

 

 

Parameter value 5

94% (86, 97)

98% (96, 99)

Parameter value 3.5

96% (81, 100)

100% (98, 100)

Difference (Parameter value 5 minus Parameter value 3)

‐3% (‐10, 11)

‐2% (‐4, ‐0.3)

P (Parameter value 5 > Parameter value 3)

0.26

0.01

Rifampicin resistance prevalence

 

 

High (> 15%)

94% (85, 98)

98% (95, 99)

Low (≤ 15%)

93% (80, 99)

98% (96, 99)

Difference (High minus Low)

0.4% (‐8, 13)

‐0.4% (‐4, 2)

P (High > Low)

0.54

0.34

P = probability
Figuras y tablas -
Table 3. Impact of covariates on heterogeneity of Xpert sensitivity and specificity for rifampicin resistance detection
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Table 4. Selected patient‐important outcomes as reported in the included studies

Study and year of publication

Time to TB detection

Time to detection of rifampicin resistance

Time to treatment initiation

 

Boehme 2011a; Boehme 2011b; Boehme 2011c; Boehme 2011d; Boehme 2011e; Boehme 2011f

Median (IQR)  

Xpert: 0 days (0, 1)

Smear: 1 day (0, 1)

Solid culture: 30 days (23, 43)

Liquid culture: 16 days (13‐21)

Median (IQR) 

Xpert: 1 day (0, 1)

Line probe assay (direct testing): 20 days (10, 16)

Phenotypic DST: 106 days (30, 124)

Median (IQR)

Smear‐, culture+ TB

Before Xpert introduced: 56 days (39, 81)

After Xpert introduced: 5 days (2, 8)

Helb 2010

Xpert (1 sample): 1 hour 55 minutes

Xpert (8 samples processed together): 2 hours

 

 

Lawn 2011

Median* (IQR)

Xpert: 4 days (3, 6)

Smear: 3 days (2, 5)

Liquid culture (smear+): 12 days (10,14)

Liquid culture (smear‐): 20 days (17, 27)

Xpert: mean 2 days

MTBDRplus assay (with positive culture isolate): mean 21 days

Phenotypic DST (liquid culture): mean 40 days

 

 

Marlowe 2011

Xpert: hands‐on time was 5 minutes; run time was less than 2 hours

 

 

Miller 2011

Xpert: hands‐on time was 15 minutes: run time was 113 minutes

 

 

Moure 2011

Xpert: total time of 2 hours

 

 

Rachow 2011

Xpert: within two hours

 

 

Zeka 2011**

Xpert (routine practice): 3‐24 hours

Liquid culture: 19 days mean (range 3‐42 days)

 

 

*Delays between sputum collection and results being available to the clinic

**Times provided for both pulmonary and extrapulmonary specimens jointly; DST, drug susceptibility testing; IQR, interquartile range

Figuras y tablas -
Table 4. Selected patient‐important outcomes as reported in the included studies
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Table Tests. Data tables by test

Test

No. of studies

No. of participants

1 TB detection, all studies Show forest plot

27

7816

2 Add on Show forest plot

23

5719

3 Smear positive Show forest plot

24

1735

4 Smear negative Show forest plot

25

5878

5 HIV positive Show forest plot

11

1557

6 HIV negative Show forest plot

13

1981

7 TB detection, condition of specimen Show forest plot

24

7453

8 TB detection, specimen preparation Show forest plot

27

7816

9 TB prevalence Show forest plot

27

7816

10 Income status Show forest plot

27

7816

11 Rifampicin resistance Show forest plot

20

2340

12 RIF resistance prevalence Show forest plot

20

2340
Figuras y tablas -
Table Tests. Data tables by test
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