Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol) pptx

Xpert MTB/RIF test for detection of pulmonary tuberculosis
and r ifampicin resistance (Protocol)
Sohn H, Pai M, Dendukuri N , Kloda LA, Boehme CC, Steingart KR
This is a reprint of a Cochrane protocol, prepared and maintained by The Cochrane Collaboration and published in The Cochrane
Library 2012, Issue 1
cochranelibrar y.com
Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
T A B L E O F C O N T E N T S
1HEADER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1ABSTRACT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2BACKGROUND . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3OBJECTIVES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4METHODS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7ACKNOWLEDGEMENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10APPENDICES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
21HISTORY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
21CONTRIBUTIONS OF AUTHORS . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
21DECLARATIONS OF INTEREST . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
iXpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
[Diagnostic Test Accuracy Protocol]
Xpert MTB/RIF test for detection of pulmonary tuberculosis
and rifampicin resistance
Hojoon Sohn
2
, Madhukar Pai
3
, Nandini Dendukuri
4

, Lorie A Kloda
5
, Catharina C Boehme
6
, Karen R Steingart
1
1
Department of Health Services, University of Washington, School of Public Health, Seattle, Washington, USA.
2
Department of
Epidemiology & Biostatistics, McGill University, Montreal, Canada.
3
Dept of Epidemiology and Biostatistics, McGill University,
Montreal, Canada.
4
Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada.
5
Life
Sciences Library, McGill University, Montreal, Canada.
6
FIND, Geneva, Switzerland
Contact address: Karen R Steingart, Department of Health Ser vices, University of Washington, S chool of Public Health, Seattle,
Washington, 98195-7230, USA.

Editorial group: Cochrane Infectious Diseases Group.
Publication status and date: New, published in Issue 1, 2012.
Citation: Sohn H, Pai M, Dendukuri N, Kloda LA, Boehme CC, Steingart KR. Xpert MTB/RIF test for detection of pul-
monary tuberculosis and rifampicin resistance. Cochrane Database of Systematic Reviews 2012, Issue 1. Art. No.: CD009593. DOI:
10.1002/14651858.CD009593.
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.

A B S T R A C T
This is the protocol for a review and there is no abstract. The objectives are as follows:
Primary objectives
Review question A: To obtain summary estimates of the diagnostic accuracy of Xpert MTB/RIF for the diagnosis of pulmonary TB,
using solid or liquid culture as a reference standard.
Purpose of index test:
A.1 Xpert MTB/RIF as a replacement test for smear microscopy.
A.2. Xpert MTB/RIF as an add-on test after smear microscopy.
Review question B: To obtain summary estimates of the diagnostic accuracy of Xpert MTB/RIF for detection of rifampicin resistance,
using solid or liquid culture as a reference standard (
WHO 2008).
Purpose of index test:
B.1 Xpert MTB/RIF as a replacement test for WHO-approved tests for detection of rifampicin resistance.
1. To summarize evidence on time to treatment initiation.
2. To summarize evidence on time to diagnosis.
Although these secondary outcomes will not be systematically reviewed, we will extract data when present in the included accuracy
studies.
We will investigate whether HIV-infection status; sputum smear statu s; country income status; setting; or storage condition s of specimen
can explain the expected heter ogeneity in estimates of test sensitivity and specificity.
1Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
B A C K G R O U N D
Tuberculosis (TB) is one of the world’s most important infectious
causes of morbidity and mortal ity among adults. An estimated
one-third of the world’s population is infected with TB. In 2010,
there were 8.8 million new, and 12.0 million prevalent cases of
TB; 1.1 million deaths occurred among HIV-uninfected people
and an additional 0.35 million deaths among HIV-infected peo-
ple (
WHO 2011a). Of the total new TB cases, an estimated 12%

to 14% occurred among people living with HIV. Approximately
one million TB cases occur in chil dren younger than 15 years old
annually (
Marais 2010a). In 2010, the three countries with the
highest number of new TB cases were India, China, and South
Africa (
WHO 2011a). In 2010, there were an estimated 650,000
cases of multidrug-resistant TB (MDR-TB), defined as resistance
to at least isoniazid and rifampicin, the two most powerful first-
line anti-TB drugs (
WHO 2011a). TB is a treatable and curable
disease; according to the World Health Organization (WHO), up
to six million lives were saved with th e expansion of Directly Ob-
served Treatment Short-Course (DOTS; the basic package that
underpins the Stop TB Strategy) (
WHO 2010a). Early and ac-
curate diagnosis and effective treatment is the cornerstone of TB
care and control (
Dye 2010). A basic tenet of early and accurate
diagnosis is the identification of smear-negative disease (associated
with HIV infection) and MDR-TB (
WHO 2010b).
In 2011, poor diagnosis remains an obstacle to TB care and con-
trol, partly because TB diagnosis continues to rely on century-
old tests. In most TB endemic countries, TB diagnosis is based
on direct Ziehl-Neelsen sputum microscopy or chest radiography,
tests with known shortcomings, especially in people with HIV in-
fection (
Harries 2004; Perkins 2007; Steingart 2006). Mycobac-
terial cultures are time consuming and have biosafety and train-

ing requirements, and culture capacity is limited in underserved
and remote areas. Nucleic acid-amplification (NAA) tests, includ-
ing polymerase chain reaction (PCR) tests, can rapidly detect My-
cobacterium tuberculosis (M. tuberculosis), but studies of conven-
tional NAA tests have shown relatively low sensitivity in sputum
smear-negative patients (
Flores 2005; Greco 2006; Ling 2008) and
these assays can only be performed in laboratories with specialized
equipment and expertise. The disappointing performance of these
tools is compounded by the lack of access to health services with
diagnostic laboratories (WHO 2010a). A substantial proportion
(~35%) of the estimated TB cases worldwide remain undiagnosed,
including a staggering proportion (~85%) of patients with MDR-
TB (
WHO 2011a). In addition, because of delays in diagnosis,
TB patients have often been symptomatic for months, leading to
increased illness and mortality, secondary drug resistance, and on-
going transmission. Simple and rapid diagnostic tests at the point
of treatment in high-TB burden countries are urgently needed.
Target condition being diagnosed
TB is an airborne disease caused by the bacterium, M. tuberculosis,
and is spread primarily by droplet nuclei expelled by a person who
has infectious active TB. Although TB most commonly affects the
lungs, any organ or tissue may be involved. Signs and symptoms of
pulmonary TB include cough for at least two weeks, fever, chills,
night sweats, weight loss, haemoptysis (coughing up blood), and
fatigue; symptoms of extrapulmonary TB depend on the site of
disease. From 1970 to 1986, wide-scale international multicen-
tre randomized controlled trials conducted by the British Medical
Research Council and its collaborators established the pivotal role

of rifampicin in TB treatment leading to modern short-course TB
therapy (
Fox 1999). TB, even when resistant to rifampicin, can be
cured; however,to be effective, TB treatment regimens must con-
tain multiple drugs to which the organisms are susceptible. Inter-
national guidelines for the treatment of TB are issued by a WHO
Expert Group and are regularly updated. The current WHO treat-
ment guidelines are based on evidence assessed according to the
GRADE (Grading of Recommendations Assessment, Develop-
ment and Evaluation) approach for developing health care recom-
mendations (
Guyatt 2008; WHO 2009).
Index test(s)
The Xpert MTB/RIF© test is an automated PCR test utilizing the
GeneXpert© platform. Xpert MTB/RIF can detect TB as well as
rifampicin resistance in less than two hours with minimal hands-
on technical time. Xpert MTB/RIF is considered to be ground-
breaking because the test comes close to meeting the niche for a
TB point-of-care test. Unlike conventional NAA tests, this test
is unique because all steps involved in the PCR are completely
automated and self-contained, allowing the technology to be taken
out of the laboratory, into the clinic setting, where it can be used
nearer to the patient (
Small 2011).
Although, Xpert MTB/RIF provides testing for both M. tubercu-
losis and rifampicin resistance, it is really only one test. The test
uses five molecular beacons. Molecular beacons are nucleic acid
probes that recognize and report the presence or absence of the
normal, susceptible, ’wild type’ sequence of the RNA polymerase
(rpoB) gene of M. tuberculosis. When a beacon fluoresces or ’lights

up’, this indicates the presence of the gene sequence which is char-
acteristic of rifampicin-susceptible M. tuberculosis. The number of
positive beacons allows the test to distinguish among the following
results: ’No TB dete cted’ (none of the five beacons is positive);
’TB detected, rifampicin resistance de tected’ (from two to four
beacons are positive); ’TB detected, no rifampicin resistance de-
tected’ (five beacons are positive); and an ’invalid result’ (one bea-
con is positive). Xpert MTB/RIF occupies one physical unit and
uses the same sputum sample to provide results for both detection
of M. tuberculosis and rifampicin resistance. One cannot switch
rifampicin resistance testing off and only do TB testing, although
it is possible for the laboratory to omit results for rifampicin resis-
tance testing when reporting to the healthcare provider.
2Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
The physical unit for Xpert MTB/RIF has two main components:
1) a plastic cartridge containing liquid sample pr ocessing buffers
and PCR buffers and reagents; and 2) a device that controls the
fluidics inside the cartridge and performs real-time PCR analysis
(Helb 2009). The Xpert MTB/RIF assay amplifies a sequence of
the rpoB gene specific to members of M. tuberculosis complex. In
greater than 95% of M. tuberculosis clinical isolates, resistance to
rifampicin has been associated with single amino acid alterations
in a limited region (81 base pairs (bp) also called rifampicin-re-
sistance determining region of the rpoB gene (Telenti 1993). Ri-
fampicin-susceptible isolates show no mutations in this region.
With Xpert MTB/RIF, the limit of detection for M. tuberculosis
DNA was found to be 4.5 genomes per PCR reaction (95% confi-
dence interval (CI) 3.3 to 9.7) and for M. tuberculosis cells in clin-
ical sputum samples, 131 colony-forming units (cfu)/mL (95%

CI 106.2 to 176.4)
Helb 2009). In investigations using clinical or
experimental samples, all 23 81-bp mutants were correctly iden-
tified as rifampicin-resistant (
Helb 2009).
Alternative test(s)
The most widely used te st for TB diagnosis in low- and middle-
income countries is Ziehl-Neelsen smear microscopy. Sensitivity is
low (from 50 to 60% on average) and variable (from 20 to 80%),
and microscopy does not detect smear-negative TB which may
account for 24% to 61% of all pulmonary cases in HIV-infected
individuals (
Steingart 2006; Getahun 2007).
Chest radiography f or TB diagnosis is limited by high inter- and
intra-observer differences in reporting of radiographs, and absence
of typical findings in people living with HIV who have advanced
immunosuppression (
Harries 2004).
Improved diagnostic tests such as mycobacterial culture and NAA
tests are available in high-income countries, but are often too ex-
pensive and complex for routine use by TB control programmes
in resource-limited TB-endemic settings. Lack of access to diag-
nostic services in resource-limited settings presents an additional
barrier to using these tests.
Rationale
Existing diagnostic tools for TB are not accurate, or cannot be
done rapidly at the point-of-care; therefore, th ere is an urgent need
for a diagnostic tool that is accurate, simple to operate, and can be
placed nearer to the patient in facilities such as h ealth posts and mi-
croscopy centres. While rapid, simple point-of-care tests exist for

infections like HIV and malaria, there is currently no such option
for TB. Such a tool would have significant impact on TB control
through interruption of transmission and potentially earlier, more
efficient diagnosis of TB, including the detection of smear-nega-
tive disease and MDR-TB. In December 2010, WHO announced
its endorsement of the Xpert MTB/RIF test (
WHO 2011). The
WHO decision to endorse this test was based on a large multicen-
tre study (
Boehme 2010) and other preliminary data, reviewed by
an Expert Group (
WHO 2010b). These studies showed that Xpert
MTB/RIF has a comparable level of diagnostic performance to
mycobacterial culture, even in resource-limited settings. A subse-
quent implementation study (
Boehme 2011) demonstrated high
sensitivity of Xpert MTB/RIF in smear-negative patients (a con-
cern in HIV co-infected individuals, and in children) (
Mugusi
2006
; Perkins 2006; Perkins 2007), while conventional NAA tests
have low sensitivity in smear-negative patients (
Greco 2006; Ling
2008
). The WHO now recommends that Xpert MTB/RIF should
be used as the initial diagnostic test in individuals suspected of
MDR-TB or HIV-associated TB (
WHO 2010b). Furthermore,
Xpert may be used as an add-on test to microscopy in settings
where MDR-TB or HIV, or both, are of lesser concern, especially

in smear-negative patients. While several studies of Xpert MTB/
RIF have shown excellent performance, this assay has not been
fully validated in all settings. Since the WHO’s endorsement, sev-
eral new studies h ave been published on Xpert MTB/RIF, and
several other s are expected to be published shortly. At the time of
this writing, a systematic review on the diagnostic accuracy of this
new test has not been published.
O B J E C T I V E S
Primary objectives
Review question A: To obtain summary estimates of the diagnostic
accuracy of Xpert MTB/RIF for the diagnosis of pulmonary TB,
using solid or liquid culture as a reference standard.
Purpose of index test:
A.1 Xpert MTB/RIF as a replacement test for smear microscopy.
A.2. Xpert MTB/RIF as an add-on test after smear microscopy.
Review question B: To obtain summary estimates of the diagnostic
accuracy of Xpert MTB/RIF for detection of rifampicin resistance,
using solid or liquid culture as a reference standard (
WHO 2008).
Purpose of index test:
B.1 Xpert MTB/RIF as a replacement test for WHO-approved
tests for detection of rifampicin resistance.
Secondary objectives
1. To summarize evidence on time to treatment initiation.
2. To summarize evidence on time to diagnosis.
Although th ese secondary outcomes will not be systematically re-
viewed, we will extract data when present in the included accuracy
studies.
3Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.

Investigation of sources of heterogeneity
We will investigate whether HIV-infection status; sputum smear
status; country income status; setting; or storage conditions of
specimen can explain the expected heterogeneity in estimates of
test sensitivity and specificity.
M E T H O D S
Criteria for considering studies for this review
Types of studies
We will include primary studies that compared the results of the
index test with the reference standard. Diagnostic accuracy studies
are typically cross sectional in design. However,we will also include
randomized controlled trials and cohort studies.
Only studies that report data from which we can extract true posi-
tives (TP), true negatives (TN), false positives (FP), and false neg-
atives (FN) will be included.
We will exclude case-control studies. We will exclude studies that
are reported in abstracts.
Participants
Included participants for review question A.1 will be adults (15
years and older) suspected of having pulmonary TB or MDR-TB,
from all settings and all countries.
Included participants for review question A.2 will be adults sus-
pected of having pulmonary TB or MDR-TB that are determined
to be microscopy smear negative. In this diagnostic strategy, smear
microscopy may be performed pr ior to, or concurrently with,
Xpert MTB/RIF test.
Included participantsfor review question B will be adults suspected
of having pulmonary TB or MDR-TB, from all settings and all
countries.
Patients suspected of having MDR-TB may include patients with

a histor y of TB, patients on TB treatment for pulmonary TB
without sputum conversion, and symptomatic contacts of patients
with known MDR-TB.
Three categories of participants will be classified:
1. Definite TB - culture positive.
2. Probable TB (clinically considered as TB, culture negative).
3. Non-TB (clinically not considered as non-TB, culture
negative).
Index tests
We will include studies that evaluated the Xpert MTB/RIF assay.
Comparator tests
For review question A, we will include studies that evaluated smear
microscopy as a comparator.
Target conditions
Review question A: Active pulmonary TB.
Review question B: Rifampicin resistance.
Reference standards
Review question A: The reference standard for the diagnosis of
active pulmonary TB is solid or liquid mycobacterial culture.
Review question B: The reference standard for detection of ri-
fampicin resistance is 1) solid culture, or 2) a commercial liquid
culture system (BACTEC 460, MGIT 960, and MGIT Manual
System, Becton Dickinson, USA; BacT/ALERT MP, Biomerieux,
France; VersaTREK, Trek Diagnostic Systems, USA) (
Canetti
1963
; Laszlo 1997; WHO 2008).
Search methods for identification of studies
We will attempt to identify all relevant studies regardless of lan-
guage or publication status (published, unpublished, in press, and

ongoing).
Electronic searches
To identify all relevant studies, we will search the follow-
ing databases using the search terms and strategy described
in
Appendix 1: Cochrane Infectious Diseases Group Special-
ized Register; MEDLINE; EMBASE; ISI Web of Knowledge;
MEDION; LILACS; BIOSIS; and SCOPUS. We will also search
the metaRegister of Controlled Trials (mRCT) and the search por-
tal of the WHO International Clinical Trials Registry Platform (
www.who.int/trialsearch), to identify ongoing trials.
Searching o ther resources
We will review reference lists of included articles and any relevant
review articles identified through the above methods. We will con-
tact the test manufacturer (Ceph eid Inc.) to identify unpublished
studies. We will also handsearch WHO reports on Xpert MTB/
RIF. We will contact researchers at the Foundation for Innovative
New Diagnostics (FIND), members of th e Stop TB Partnership’s
New Diagnostics Working Group, and other experts in the field of
TB diagnostics for information on ongoing or unpublished stud-
ies.
4Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
Data collection and analysis
Selection of studies
Two independent reviewers (HS and KRS) will first look at titles
and abstracts identified by electronic literature searching to iden-
tify potentially eligible studies. Any citation identified by either
reviewer during this screen (screen 1) will be selected for full-text
review. Two independent reviewers (HS and KRS) will then re-

view full-text papers (screen 2) for study eligibility using the pre-
defined inclusion and exclusion criteria. In screen 2, any discrep-
ancies will be resolved by discussion between the reviewers, or if
they are unable to resolve, by decision of a third reviewer (MP).
A list of excluded studies and their reasons for exclusion will be
maintained.
Data extraction and management
Two independent reviewers (HS and KRS) will extract a set of data
from each study using a piloted data extraction form. Based on
the pilot, the extraction form will be finalized. Two independent
reviewers (HS and KRS) will then extract data on the following
characteristics:
• Details of study: first author; publication year; case country
of residence; World Bank country income status; setting
(outpatient, inpatient, laboratory); study design; manner of
participant selection; number participants enrolled; number
participants for whom results available; industry sponsorship.
• Characteristics of par ticipants: HIV status; smear status;
history of TB.
• Target conditions: review question A: pulmonary TB;
review question B: rifampicin resistance.
• Reference standards: review question A: culture type (solid
or liquid); percentage of contaminated cultures; review question
B: the name and manufacturer of the reference standard.
• Details of index test: software version of test.
• Details of comparator: type of microscopy: light or
fluorescence; type of smear: direct or concentrated; number of
smears used to determine smear positivity.
• Details of sputum specimen: type (such as expectorated
sputum, induced sputum, bronchoalveolar lavage); condition

(fresh or frozen); definition of a positive smear.
• Details of outcomes: the number of true positives (TP),
true negatives (TN), false positives (FP), and false negatives
(FN); number of missing or unavailable test results.
Time to treatment initiation is defined as the time from specimen
collection until patient starts treatment.
Time to diagnosis is defined as the time from specimen collection
until there is an available TB result in lab or clinic, if the test was
performed in a clinic.
Country income status will be classified as low/middle-income or
high-income, according to the World Bank List of Economies.
Country income status will serve as a surrogate indicator for TB
incidence.
Review question A: Additional data about (a) proportion of inde-
terminate results, and (b) discordant results between Xpert MTB/
RIF and the reference standard (Xpert positive/culture negative
results) will be recorded.
Indeterminates
Review question A: other possible test results are invalid, error,
or no result. These results will be combined and considered as
’indeterminate’.
The pr oportion of indeterminate results will be the number of
tests classified as ’invalid’, error’, or ’no result’ divided by the total
number of tests performed.
Review question B: RIF indeterminate means that the M. tuber-
culosis concentration was very low and resistance could not be de-
termined. Proportion of indeterminate results will be the number
of tests classified as ’ indeterminate’ divided by the total number
of tests performed.
Culture contamination will be defined as 1) growth of non-TB

bacteria or fungi or 2) cross-contamination as determined after a
standard laboratory evaluation. Per centage of contaminated cul-
tures will be the (number of contaminated cultures/total number
of cultures performed) x 100.
We will contact authors of primary studies for missing data or
clarifications. All data will be entered into a database manager. A
draft data extraction form is included in
Appendix 2
Assessment of methodological quality
Two reviewers will independently assess study quality with the
modified version of Quality Assessment of Diagnostic Accuracy
Studies (QUADAS) (
Reitsma 2009). Items 1 to 11 from the
QUADAS list will be scored as yes, no, or unclear. Disagreements
will be resolved by discussion between the reviewers or by a third
reviewer (MP). Results will be described in the text and presented
graphically. Appendix 3 describes the criteria that need to be met
for each study to be rated as yes, no, or unclear for each of the
QUADAS items.
Statistical analysis and data synthesis
The first step in data analysis will be a descriptive analysis of th e
results of the primary studies. For both review question A and
review question B, the results will be based on categorical (binary)
test results. For both review questions, the index test results are
automatically generated and the user is provided with a printable
test result. Example s are:
1. MTB detected; RIF resistance not detected.
2. MTB detected; RIF resistance detected.
3. MTB detected; RIF resistance indeterminate.
4. MTB not detected; RIF not detected.

5Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
Descriptive analysis will be perf ormed using Stata 2009 and key
study characteristics will be displayed in tables. For each study,
sensitivity and specificity of the test along with the 95% CI will
be calculated using exact methods, and forest plots generated us-
ing Review Manager 5 (RevMan). The primary analysis will be
performed for participants with definite TB (culture positive) and
non-TB (culture negative). Secondary analyses will estimate ac-
curacy using definite TB and probable-TB patients combined for
sensitivity calculations, and non-TB and probable TB patients
combined for specificity calculations.
For review question B, we will sort the studies in RevMan by “year
of study” to look for a trend with time, since software and cartridge
changes have been made to improve the specificity for rifampicin
detection.
Where sufficient data are available, meta-analyses will be carried
out to estimate sensitivity and specificity of the index test (primary
objective). The exact method used, either bivariate or HSROC,
will depend on data pr ovided by the included studies. For review
question A, detection of M. tuberculosis, since the test uses a com-
mon threshold for a positive result, we will use the bivariate ran-
dom effects regression model (
Macaskill 2010; Reitsma 2005).
The model will be estimated using a Bayesian approach with non-
subjective prior distributions and implemented using WinBUGS
(Version 1.4.1) (
Spiegel halter 2004).
For review question B, detection of rifampicin resistance, if most
studies report one or two and the same threshold (the same am-

plification cycle used for detection of rifampicin resistance), meta-
analysis can also be done by using the bivariate method. However,
where the studies report several different thresholds, it may be
more appropriate to use the Hierarchical Summary Receiver Op-
erating Characteristic (HSROC) model (
Rutter 2001; Macaskill
2010
).
We will also compare the sensitivity and specificity of Xpert MTB/
RIF with that of smear microcopy. For smear microscopy, the re-
sults will be based on categorical results, either positive or negative.
If most studies report one and th e same threshold (for example,
smear positive is greater than or equal to one acid-fast bacillus), we
will pool results using the bivariate method, but if studies report
several different thresholds, it may be more appropriate to use the
HSROC model (
Macaskill 2010; Rutter 2001).
Our approach to Xpert MTB/RIF used as an add-on test to smear
microscopy will be as follows: in patients found to be smear neg-
ative/culture positive for pulmonary TB, we will consider sensi-
tivity and specificity e stimates to be a proxy for Xpert MTB/RIF
used as an add-on test to microscopy, even if the primary study
objective was not explicit for this outcome and both tests were run
concurrently.
Approach to indeterminate index test results
For both review questions A and B, we will exclude indeterminate
index test results from the main analysis.
For both review questions A and B, we will determine pooled
estimates and the predicted interval for indeterminate index test
results.

For both review questions A and B, where data are available, we
will perform sensitivity analyses to determine the potential impact
of indeterminate index test results considered to be false/true pos-
itives or false/true negatives. In the discussion section, we will dis-
cuss the consequences of an indeterminate index test result con-
sidered to be a true negative result (may l ead to missed/delayed
diagnosis, with potential for increased morbidity, mortality, and
TB transmission), or considered to be true positive result (may
lead to unnecessary treatment with adverse effects and increased
anxiety).
Subgroup analyses
For both review questions A and B, we will first stratify studies
by country income status (low- and middle-income versus high-
income). We expect the majority of studies to report TP, TN, FP,
and FN stratified by smear status and/or HIV status. For these
subgroups, we will compare summary estimates of accuracy in
HIV infected and uninfected subgroups, and smear positive and
smear negative subgroups. If there are sufficient studies, we will
also determine summary accuracy estimates for smear-negative,
HIV-infected versus smear-positive, HIV-infected subgroups.
Investigations of heterogeneity
Heterogeneity between diagnostic accuracy studies is to be ex-
pected (
Harbord 2007). Initially, heterogeneity will be addressed
by pre-specifying subgroups. We will assess heterogeneity by vi-
sual inspection of forest plots. We will further investigate potential
sources of heterogeneity by adding covariates in the models. All
covariates will be study level, dichotomous.
Review question A
Condition of specimen (categorical covariate): 1. fresh; 2. frozen.

TB prevalence (categorical covariate): 1. low; 2. high.
Setting in which Xpert was used (categorical covariate): 1. clinical
(outpatient or inpatient); 2. laboratory.
Review question B
Software version (amplification cycle thresholds of the test, di-
chotomous): 1. Versions 1 and 2 (cycle threshold 3.5); 2. Versions
3 (cycle threshold 5.0) and 4.
MDR-TB prevalence (categorical covariate): 1. low; 2. high.
Sensitivity analyses
If sufficient studies are available, we will perform sensitivity anal-
ysis for QUADAS items to explore whether the results we found
are robust with respect to methodological quality of the studies.
6Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
Assessment of reporting bias
Data included in this review will not allow for formal assessment
of publication bias using methods such as funnel plots or regres-
sion tests because such techniques have not been found to be help-
ful for diagnostic test accuracy studies (Tatsioni 2005 Macaskill
2010
). However, being a new test for which there is going to be
considerable attention and scrutiny, we believe reporting bias will
be minimal.
Other
We will summarize, if feasible, evidence on outcomes important
to Xpert users, including time to diagnosis and time to treatment
initiation. We will also summarize hands-on time for specimen
processing and work-flow, instrument ease-of-use, and user satis-
faction. This information will be excluded from the formal proto-
col. We will address these outcomes in a section of the discussion

and present summary data in additional tables. In addition, if data
are available, we will prepare a qualitative de scription in the dis-
cussion section of Xpert positive/culture negative (false positive)
patients followed longitudinally, and report the number and per-
cent of these patients who become culture positive during follow
up.
A C K N O W L E D G E M E N T S
We are grateful to Vittoria Lutje, Liverpool School of Tropical
Medicine, for help with the search strategy. The e ditorial base for
the Cochrane Infectious Disease Group is funded by the Depar t-
ment for International Development (DFID), UK, for the benefit
of low- and middle-income countries.
R E F E R E N C E S
Additional references
Armand 2011
Armand S, Vanhuls P, Delcroix G , Courcol R, Lemaitre
N. Comparison of the Xpert MTB/RIF test with an
IS6110-TaqMan real-time PCR assay for direct detection of
Mycobacterium tuberculosis in respiratory and nonrespiratory
specimens. Journal of Clinical Microbiology 2011;49(5):
1772–6.
Balshem 2010
Balshem H, Helfand M, Schunemann HJ, Oxman AD,
Kunz R, Brozek J, et al.GRADE guidelines: 3. Rating the
quality of evidence. Journal of Clinical Epidem iology 2010;
64(4):401–6.
Banada 2010
Banada PP, Sivasubramani SK, Blakemore R, Boehme C,
Perkins MD, Fennelly K, et al.Containment of bioaerosol
infection risk by the Xpert M TB/RIF assay and its

applicability to point-of-care settings. Journal of Clinical
Microbiology 2010;48(10):3551–7.
Blakemore 2010
Blakemore R, Story E, Helb D, Kop J, Banada P, Owens
MR, et al.Evaluation of the analytical performance of the
Xpert MTB/RIF assay. Journal of Clinic al Microbiology
2010;48(7):2495–501.
Boehme 2010
Boehme CC, Nabeta P, Hillemann D, Nicol MP, Shenai S,
Krapp F, et al.Rapid molecular detection of tuberculosis and
rifampin resistance. New England Journal of Medicine 2010;
363:1005–15.
Boehme 2011
Boehme CC, Nicol MP, Nabeta P, Michael JS, Gotuzzo
E, Tahirli R, et al.Feasibility, diagnostic accuracy, and
effectiveness of decentralised use of the Xpert MTB/RIF
test for diagnosis of tuberculosis and multidrug resistance: a
multicentre implementation study. Lancet 2011;377(9776):
1495–505.
Canetti 1963
Canetti G, Froman S, Grosset J, Hauduroy P, Langerova M,
Mahler HT, et al.Mycobacteria: Laboratory methods for
testing drug sensitivity and resistance. Bulletin of the World
Health Organization 1963;29:565–78.
Ciftci 2011
Ciftci IH, Aslan MH , Asik G. Evaluation of Xper t MTB/
RIF results for the detection of Mycobacterium tuberculosis
in clinical samples. Mikrobiyoloji Bulteni 2011;45(1):43–7.
Dye 2010
Dye C, Williams BG. The population dynamics and control

of tuberculosis. Science 2010;328(5980):856–61.
Fendall 1972
Fendall NR. Auxiliaries a nd primary medical care. Bulletin
of the New York Academy of Medicine 1972;48(10):
1291–300.
Flores 2005
Flores LL, Pai M, Colford JM Jr, Riley LW. In-house nucleic
acid amplification tests for the detection of Mycobacterium
tuberculosis in s putum specimens: meta-analysis and meta-
regression. BMC Microbiology 2005;5:55.
Foundation
Foundation for Innovative Diagnostics. Automated
molecular detection in 90 minutes for tuberculosis
and rifampicin resistance. Available from http://
www.finddia gnostics.org/export/sites/default/media/press/pdf/
XpertTB_factsheet.pdf (accessed 7 March 2011).
Fox 1999
Fox W, Ellard G A, Mitchison D A. Studies on the
treatment of tuberculosis undertaken by the British Medical
7Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
Research Council tuberculosis units, 1946-1986, with
relevant subsequent publications. International Journal of
Tuberculosis and Lung Disease 1999;3(10 Suppl 2):S231–79.
Gatsonis 2006
Gatsonis C, Paliwal P. Meta-analysis of diagnostic and
screening test accuracy evaluations: methodologic primer.
American Journal of Roentgenology 2006;187(2):271–81.
Getahun 2007
Getahun H, Harrington M, O’Brien R, Nunn P. [Diagnosis

of smear–negative pulmonary tuberculosis in people with
HIV infection or AIDS in resource–constrained settings:
informing urgent policy c hanges ]. Lancet 2007;369(9578):
2042–9.
Greco 2006
Greco S, Girardi E, Navarra A, Saltini C. Current evidence
on diagnostic accuracy of commercially based nuc leic
acid amplification tests for the diagnosis of pulmonary
tuberculosis . Thorax 2006;61(9):783–90.
Guyatt 2008
Guyatt GH, Oxman AD, Kunz R, Falck-Ytter Y, Vist GE,
Liberati A, et al.Going from evidence to recommendations.
BMJ 2008;336(7652):1049–51.
Harbord 2007
Harbord RM, Deeks JJ, Egger M , Whiting P, Sterne JA.
A unification of models for meta-analysis of diagnostic
accuracy studies. Biostatistics 2007;8(2):239–51.
Harries 2004
Harries A. [16. How does the diagnosis of tuberculosis in
persons infected with HIV differ from diagnosis in persons
not infected with HIV?]. In: Frieden T editor(s). Toman’s
Tuberculosis. Case detection, treatment and monitoring -
questions and answers. 2nd Edition. Geneva: World Health
Organization, 2004:80–3.
Helb 2009
Helb D, Jones M , Story E, Boehme C, Wallace E, Ho K,
et al.Rapid detection of Mycobacterium tuberculosis and
rifampin resistance by use of on-demand, near-patient
technology. Journal of Clinical Microbiology 2009;48(1):
229–37.

Hesseling 2011
Hesseling AC, Graham SM, Cuevas LE. Rapid molecular
detection of tuberculosis. New England Journal of Medicine
2011;364(2):183–5.
Hillemann 2011
Hillemann D, Ruesch-Gerdes S, Boehme C, Richter E.
Rapid molecular detection of extrapulmonary tuberculosis
by automated GeneXpert(R) MTB/RIF system. Journal of
Clinical Microbiology 2011;49(4):1202–5.
Laszlo 1997
Laszlo A, Rahman M, Raviglione M, Bustreo F. Quality
assurance programme for drug susceptibility testing
of Mycobacterium tuberculosis in the WHO/ IUATLD
Supranational Laboratory Network: first round of
proficiency testing. International Journal of Tuberculosis and
Lung Disease 1997;1(3):231–8.
Leeflang 2008
Leeflang MM, Deeks JJ, Gatsonis C, Boss uyt PM.
Systematic reviews of diagnostic test accuracy. Annals of
Internal Medicine 2008;149(12):889–97.
Lijmer 2002
Lijmer JG, Bossuyt PM, Heisterkamp SH . Exp loring
sources of heterogeneity in systematic reviews of diagnostic
tests. Statistics in Medic ine 2002;21(11):1525–37.
Ling 2008
Ling DI, Flores LL, Riley LW, Pai M. Commercial
nucleic-acid amplification tests for diagnosis of pulmonary
tuberculosis in respiratory specimens: meta-analysis and
meta-regression. PLoS One 2008;3(2):e1536.
Macaskill 2010

Macaskill P, Gatsonis C, Deeks JJ, Harbord RM, Y
Takwoingi. [Chapter 10: Analysing and Presenting Results.
In: Deeks JJ, Bossuyt P M, C Gatsonis (editors). Cochrane
Handbook for Systematic Reviews of Diagnostic Test
Accuracy Version 1.0. The Cochrane Collaboration 2010].
Available from />Malbruny 2011
Malbruny B, Le Marrec G, Courageux K, Leclercq R,
Cattoir V. Rapid and efficient detection of Mycobacterium
tuberculosis in respiratory and non-respiratory samples.
International Journal of Tuberculosis and Lung Disease 2011;
15(4):553–5.
Marais 2010
Marais BJ, Gupta A, Starke JR, El Sony A. Tuberculosis in
women and children. Lancet 2010;375(9731):2057–9.
Marais 2010a
Marais BJ, Schaaf HS. Childhood tuberculosis: an emerging
and previously neglected problem. Infect Disease Clinics of
North America 2010;24(3):727–49.
Marlowe 2011
Marlowe EM, Novak Weekley SM, Cumpio J, Sharp
SE, Momeny MA, Babst A, et al.Evaluation of the
Cepheid Xpert MTB/RIF assay for the direct detection
of Mycobacterium tuberculosis complex from respiratory
specimens. Journal of Clinical Microbiology 2011;49(4):
1621–3.
Moher 2009
Moher D, Liberati A, Tetzlaff J, Altman DG. Preferred
reporting items for systematic reviews and meta-analyses:
the PRISMA statement. PLoS Medicine 2009;6(7):
e1000097.

Moure 201 1
Moure R, Munoz L, Torres M, Santin M, Martin R, Alcaide
F. Rapid detection of Mycobacterium tuberculosis complex
and rifampin resistance in smear-negative clinical samples
by use of an integrated real-time PCR method. Journal of
Clinical Microbiology 2011;49(3):1137–9.
Mugusi 2006
Mugusi F, Villamor E, Urassa W, Saathoff E, Bosch RJ,
Fawzi WW. H IV co-infection, CD4 cell counts and clinical
correlates of bacillary density in pulmonary tuberculosis.
8Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
International Journal of Tuberculosis and Lung Disease 2006;
10(6):663–9.
Pai 2004
Pai M, McCulloch M, Enanoria W, Colford JM Jr.
Systematic reviews of diagnostic test evaluations: what’s
behind the scenes?. ACP Journal Club 2004;141(1):A11–3.
Pai 2010
Pai M, Minion J, Steingart K, Ramsay A. New and improved
tuberculosis diagnostics: evidence, policy, prac tice, and
impact. Current Opinion in Pulmonary Medicine 2010;16
(3):271–84.
Pai 2010a
Pai M, Minion J, Steingart K, Ramsay A. New and improved
tuberculosis diagnostics: evidence, policy, prac tice, and
impact. Current Opinion in Pulmonary Medicine 2010;16
(3):271–84.
Perkins 2002
Perkins MD, Kritski AL. Diagnostic testing in the control

of tuberculosis. Bulletin of the World Health Organization
2002;80(6):512–3.
Perkins 2006
Perkins MD, Small PM. Admitting defeat. International
Journal of Tuberculosis and Lung Disease 2006;10(1):1.
Perkins 2007
Perkins MD, Cunningham J. Facing the crisis: improving
the diagnosis of tuberculosis in the HIV era. Journal of
Infectious Disease 2007;196(Suppl 1):S15–27.
Raja 2005
Raja S, Ching J, Xi L, Hughes SJ, Chang R, Wong W,
et al.Technology for automated, rapid, and quantitative
PCR or reverse transcription-PCR clinical testing. Clinical
Chemistry 2005;51(5):882–90.
Ramsay 2010
Ramsay A, Steingart KR, Pai M. Assessing the impact of new
diagnostics on tuberculosis control. International Journal of
Tuberculosis and Lung Disease 2010;14(12):1506–7.
Reitsma 2005
Reitsma JB, Glas AS, Rutjes AW, Scholten RJ, Bossuyt
PM, Zwinderman AH. Bivariate analysis of sensitivity and
specificity produces informative summary measures in
diagnostic reviews. Journal of Clinical Epidemiology 2005;
58(10):982–90.
Reitsma 2009
Reitsma JB, Rutjes AWS, Whiting P, Vlassov VV, Leeflang
MMG, Deeks JJ. Chapter 9: Assessing methodological
quality. In: Deeks JJ, Bossuyt PM, Gatsonis C (editors).
Cochrane Handbook for Systematic Reviews of Diagnostic
Test Accuracy Version 1.0. The Cochrane Collaboration

2010. Available from: />Review Manager 5
The Nordic Cochrane Centre, The Cochrane Collaboration.
Review Manager (RevMan). 5.0. Copenhagen: The Nordic
Cochrane Centre, The Cochrane Collaboration, 2008.
Rutter 2001
Rutter CM, Ga tsonis CA. A hierarchical regression approach
to meta-analysis of diagnostic test accuracy evaluations.
Statisti cs in Medicine 2001;20(19):2865–84.
Schünemann 200 8
Schünemann HJ, Oxman AD, Brozek J, Glasziou P,
Jaeschke R, Vist GE, et al.Grading quality of evidence
and strength of recommendations for diagnostic tests and
strategies. BMJ 2008;336(7653):1106–10.
Schünemann 201 1
Schünemann HJ, Oxman AD, Gunn EV, Higgins JPT,
Deeks JL, Glasziou P, et al.[Chapter 11. Presenting results
and “Summary of findings” tables. In: Higgins JPT, Green
S (editors). Cochrane Handbook for Systematic Reviews of
Interventions Version 5.0.2. The Cochrane Collaboration
2011]. Available from www.cochrane-handbook.org.
Small 2011
Small PM, PaiM. Tuberculosis diagnosis time for a game
change. New England Journal of Medi cine 2011;363(11):
1070–1.
Spiegelhalter 2004
Spiegelhalter D, Thomas A, Best N, Lunn D. WinBUGS
user manual, Version 1.4.1. Available from -
bsu.cam.ac.uk/bugs.
Stata 2009
StataCorp. Stata Statistical Software: Release 11. College

Station, TX: StataCorp L P, 2009.
Steingart 2006
Steingart KR, Ng V, Henry M, Hopewell PC, Ramsay
A, Cunningham J, et al.Sputum processing methods to
improve the sensitivity of smear microscopy for tuberculosis:
a systematic review. Lancet Infectious Disease 2006;6(10):
664–74.
Steingart 2007
Steingart KR, Henry M, Laal S, Hopewell P C, Ramsay
A, Menzies D, et al.A systematic review of commercial
serological antibody detection tests for the diagnosis of
extrapulmonary tuberculosis. Thorax 2007;62(10):911–8.
Tatsioni 2005
Tatsioni A, Zarin DA, Aronson N, Samson DJ, Flamm
CR, Schmid C, et al.Challenges in systematic reviews of
diagnostic technologies. Annals of Internal Medicine 2005;
142(12 Pt 2):1048–55.
Telenti 1993
Telenti A, Imboden P, Marchesi F, Lowrie D, Cole S,
Colston M J, et al.Detection of rifampicin-resistance
mutations in Mycobacterium tuberculosis. Lancet 1993;341
(8846):647–50.
Traore 2000
Traore H, Fissette K, Bastian I, Devleeschouwer M, Portaels
F. Detection of rifampicin resistance in Mycobacterium
tuberculosis isolates from diverse countries by a commercial
line probe assay as an initial indicator of multidrug
resistance. International Journal of Tuberculosis and Lung
Disease 2000;4(5):481–4.
9Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)

Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
Van Rie 2010
Van Rie A, Page-Shipp L, Scott L, Sanne I, Stevens W. Xpert
((R)) MTB/RIF for point-of-care diagnosis of TB in high-
HIV burden, resource-limited countries: hype or hope?.
Expert Review of Molecular Diagnostics 2010;10(7):937–46.
Whiting 2003
Whiting P, Rutjes AW, Reitsma JB, Bossuyt PM, Kleijnen
J. The development of QUADAS: a tool for the quality
assessment of studies of diagnostic accuracy included in
systematic reviews. BMC Medical Research Methodology
2003;3:25.
WHO 2008
World Health Organization. Policy guidance on drug-
susceptibility testing (DS T) of second-line antituberculosis
drugs. Available at />2008/whohtmtb_2008_392/en/index.html Geneva:
WHO, 2008.
WHO 2009
World Health Organization. Treatment of tuberculosis:
guidelines - 4th edition. Available at http://
whqlibdoc.who.int/publications/2010/9789241547833_
eng.pdf Geneva: World Health Organization, 2009
(accessed 8 June 2011).
WHO 2010
[World Bank List of Economies]. Available: http:
//siteresources.worldbank.org/DATASTATISTICS/
Resources/CLASS.XLS. 2010 (accessed 7 June 2011).
WHO 2010a
World Health Organization. Global tuberculosis control:
WHO report 2010. Geneva: World Health Organization,

2010; Vol. WHO/HTM/TB/2010.7.
WHO 2010b
World Health Organization. Roadmap for rolling out
Xpert M TB/RIF for rapid diagnosis of TB and MDR-TB.
Available at />xpert_mtb-rif.pdf 2010 (acces sed 6 March 2011).
WHO 2010c
World Health Organization. Multidrug and extensively
drug-resistant TB (M/XDR-TB): 2010 global report on
surveillance and response 2010;WHO/HTM/TB/2010.3.
WHO 2010d
World Health Organization. WHO endorses new rapid
tuberculosis test Available at />features_archive/new_rapid_test/en/index.html 2010 (accessed
7 March 2011).
WHO 2011
World Health Orga nization. Rapid implementation of the
Xpert MTB/RIF diagnostic test. Technical and Operational
“How-to” Practical Considerations. Available at http://
whqlibdoc.who.int/publications/2011/9789241501569_
eng.pdf 2011.
WHO 2011a
World Health Organization. Global tuberculosis control:
WHO report. WHO; Geneva 2011:WHO/HTM/TB/
2011.16.
∗
Indicates the major publication for the study
A P P E N D I C E S
Appendix 1. Detailed search strategies
1. Xpert*.tw .
2. GeneXpert*.tw.
3. Cepheid.tw.

4. near* patient ti, ab
5. or 1-4
6. Tuberculosis/
7. exp Tuberculosis, Pulmonary/
8. exp Tuberculosis, Multidrug-Resistant/
9. Mycobacterium tuberculosis/
10. TB.tw.
11. tuberculosis.tw.
12. or/6-11
13. 5 and 12
14. limit 13 to yr=“2007 -Current”
10Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
This is the preliminary search strategy for MEDLINE. It will adapted for other electronic databases. All search strategies will be reported
in full in the final version of the review.
Appendix 2. Data extraction form
ID
ID substudy (for site-specific data: a, b, c, etc)
First Author
Corresponding author & email
Was author contacted? 1 - Yes
2 - No
If yes, dates(s)
Title
Year (of publication)
Year (study start date)
Language 1 - English
2 - Other
If other, specify:
Was the study conducted without industry sponsorship? 1 - Yes

2 - No
9 - Unk/NR
If industry sponsorship was present, select one item from the list Select one: answers ordered from least to most industry involve-
ment:
Donation of Xpert
®
for use in study
Xpert
®
at a special preferred price
Receipt of educational support, grants, or speaking fees
Financial relationship - author is employee/consultant/stock-
holder
Involvement in design, analysis, or manuscript production
Study addresses question A (detection of MTB) and/or B (detec-
tion of RIF resistance)?
1 - A
2 - B
3 - A and B
What was the purpose of this study? * if smear results are stratified,
indicate #3
1 - Only accuracy of Xpert as replacement test for microscopy?
2 - Only accuracy of Xpert as add-on test to microscopy
(include studies that evaluate incremental value of Xpert to the
index test)?
3 - Both purposes, 1 and 2
11Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
(Continued)
4 - Unclear/could not tell

For review question A, what reference standard was used? 1 - Solid Culture
(specify 1a)
2 - Liquid Culture
(specify 2a)
3 - Both Solid & Liquid Culture (specify 1a & 2a)
9 - Unk/NR
1a - Solid Culture
LJ
7H10
7H11
Other
2a - Liquid Culture
MGIT960
Bactec460
Other
For review question B, what reference standard was used? 1 - Solid Culture
(specify 1a)
2 - Liquid Culture
(specify 2a)
3 - Both Solid & Liquid Culture (specify 1a & 2 a)
9 - Unk/NR
1a - Solid Culture
LJ
7H10
7H11
Other
2a - Liquid Culture
MGIT960
Bactec460
Other

Review question A: smear status 1 - Positive only
2 - Negative only
3 - Both smear negative & smear positive
9 - Unk/NR
Clinical setting; describe as written in the paper 1 - Outpatient
2- Inpatient
3 - Both out- and in-patient
4 - Other, specify
5 - Laboratory
9 - Unk/NR
Also describe as in paper:
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Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
(Continued)
Country where study was conducted
Case country World Bank Classification 1 - Middle/Low
2 - High
3 - Both middle/ low and high
Study design 1 - Randomized Trial
2 - Cross-sectional
3 - Cohort
4 - Other, specify
9 - Unk/NR
If other, specify:
Participant selection 1 - Consecutive
2 - Random
3 - Convenience
7 - Other
9 - NR/Unclear
Direction of study data collection 1 - Prospective

2 - Retrospective
9 - Unk/NR
Comments about study design
Number after screening by exclusion & inclusion criteria 9 - Unk/NR
Number included in analysis (# screened - # withdrawals) 9 - Unk/NR
Did study include treated patients? 1 - Yes
2 - No
9 - Unk/NR
If yes, percentage treated patients included %
Unit of analysis 1 - Patient
2 - Specimen
9 - NR/Unclear
Describe as in paper, if unclear:
Prior testing by microscopy for triage
Review question A
1 - Yes
2 - No
9 - Unk/NR
Has the study included patients with previous TB history? 1 - Yes
2 - No
13Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
(Continued)
9 - Unk/NR
If so, what is the percentage? %
Specify numerator/denominator
HIV status of participants 0 - HIV -
1 - HIV +
2 - Both HIV+/-
9 - Unk/NR

If HIV-positive participants included, what is the per centage? %
Specify numerator/denominator
Type of specimen (may include expectorated, induced, bronchial
alveolar lavage (BAL), tracheal aspirates, gastric aspirates)
1 - All expectorated
2 - All induced
3 - All BAL
4 - Multiple types
5 - Other
9 - Unk/NR
If 4 or 5, describe types and record numbers:
Were Xpert sample and culture obtained from same specimen? 1 - Yes
2 - No
9 - Unk/NR
Number of cultures used to exclude TB 1 - One
2 - Two
3 - Three
4 - Four
5 - Other, specify
9 - Unk/NR
Specify, if > 4:
NOTES:
Pre-treatment processing procedure for Xpert 1 - None
2 - NALC-NaOH
3 - NaOH (Petroff)
4 - Other
9 - Unk/NR
Was microscopy used 1 - Yes
2 - No
9 - Unk/NR

Type of microscopy used 1 - Ziehl-Neelsen
2 - FM
9 - Unk/NR
14Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
(Continued)
Smear type 1 - Direct
2 - Concentrated (processed)
9 - Unk/NR
Minimum number of sputum specimens used to determine smear
positivity
1 - One
2 - Two
3 - Three
4 - >3
9 - Unk/NR
How was a positive smear defined? (if guideline referenced, look
up guideline)
≥˙˙˙˙bacilli per˙˙˙˙ high power fields
9 - Unk/NR
* complete both fields
For Xpert specimen, what was the condition of the specimen when
tested?
1 - Fresh
2 - Frozen
9 - Unk/NR
If fresh, specify: 1 - Tested after storage at room temperature or refrigerated w/in
48 hours of collection
2 - Tested after storage at room temperature or refrigerated >48
hours of collection

9 - Unk/NR
If frozen, specify: 1 - Tested after frozen < 1 year of storage
2 - Tested frozen ≥ 1 year of storage
9 - Unk/NR
Version of software for test interpretation 1 - Version 1
2 - Version 2
3 - Version 3
4 - Version 4
9 - Unk/NR
Enter percentage contaminated cultures, if provided:
# of contaminated culture
Total # cultures performed
˙˙˙˙˙˙˙˙˙˙˙˙˙
9 - Unk/NR
Were indeterminate results reported? Review question A 1 - Yes
2 - No
9 - Unk/NR
Were indeterminate results reported? Review question B 1 - Yes
2 - No
9 - Unk/NR
15Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
(Continued)
Were patient important outcomes evaluated 1 - Yes
2 - No
9 - Unk/NR
Time to diagnosis Xpert:
Culture:
9 - Unk/NR
Time to treatment initiation Xpert:

Culture:
9 - Unk/NR
Other patient outcomes Specify:
TAB LES
Question A: MTB Detection, Overall
* Only extract if not reporting by smear status
Definite TB
Yes No Total
Index Test Result Positive
Negative
Total
Indeterminate
Question A: MTB Detection, Smear
Positive
Definite TB
Yes No Total
Index Test Result Positive
Negative
Total
Indeterminate
16Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
Question A: MTB Detection, Smear
Negative
Confirmed TB
Yes No Total
Index Test Result Positive
Negative
Total
Indeterminate

Question A: MTB Detection, Culture
Negative
Probable TB*
Yes No Total
Index Test Result Positive
Negative
Total
Indeterminate
* Clinical TB (describe criteria used by authors)
Question A: MTB Detection,
HIV Positive
Definite TB
Yes No Total
Index Test Result Positive
Negative
Total
Indeterminate
17Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
Question A: MTB Detection,
HIV Negative
Definite TB
Yes No Total
Index Test Result Positive
Negative
Total
Indeterminate
Question B: RIF Resistance Confirmed rifampicin resistance
Yes No Total
Index Test Result Yes (resistant)

No (susceptible)
Total
Indeterminate
Discrepant analysis
Comments:
Criteria Number
Xpert+/culture - baseline
Deemed TB after further e valuation
Percent f ound to be TB on discrepant anal-
ysis
* Follow-up test included, circle all that apply
** Repeat culture, DNA sequencing, GenoType® MTBDRplus test, other, describe
18Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
Question A: MTB Detection
Direct comparison with
microscopy
Definite TB
Yes No Total
Microscopy Result Positive
Negative
Total
Appendix 3. Assess ment of methodological quality
Quality Item How to Score
Was the spectrum of patients representative of the patients who
will receive the test in practice?
Answer separately for review question A and B.
Review question A: Yes if persons suspected of having pulmonary
TB were consecutively or randomly enrolled in an outpatient set-
ting

No if patient sample is unrepresentative of spectrum of patients
with pulmonary TB
Unclear if patient characteristics or setting are inadequately de-
scribed
Review question B: Yes, if persons suspected of having pulmonary
TB were consecutively enrolled in an outpatient setting or persons
suspected of MDR-TB who presented for resistance detection
No if patients were not consecutively or randomly enrolled.
Unclear if patient characteristics or setting are inadequately de-
scribed
Acceptable reference standard? Yes for all studies. Review question A: The reference standard for
detection of pulmonary TB is culture, solid or liquid. Although
imperfect (culture may miss culture-negative TB cases), mycobac-
terial culture is considered to be the optimal reference standard
for pulmonary TB and is a criterion for inclusion of studies in the
review
Review question B: The refe rence standard for rifampicin suscep-
tibility testing is 1) solid culture or 2) a commercial liquid culture
system (BACTEC 460, MGIT 960, and MGIT Manual System,
Becton Dickinson, USA; BacT/ALERT MP, Biomerieux, France;
VersaTREK, Trek Diagnostic Systems, USA)
Acceptable delay between tests? Yes if index test and reference standards are collected on the same
patients at the same time or within 30 days of each other. (Ideally
19Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
(Continued)
specimens for Xpert and culture are collected on the same patients
at the same time. However, if this is not possible and a delay of
several weeks occurs between results, misclassification is unlikely,
as TB is a chronic disease and little change in disease status is

expected during this time)
No if the time period between index test and reference standard
collection is > 30 days
Unclear if the time period between index test and reference stan-
dard collection is not described
Partial verification avoided? Yes if all participants who received Xpert also received the reference
test
No if not all participants received both index and reference tests
Unclear if not enough information is provided.
Differential verification avoided? Yes if all participants received the same reference test regardless of
Xpert results
Noif diffe rent reference tests were used depending on Xpert results
Unclear if not enough information is provided for judgment.
Incorporation avoided Yes for all studies. Xpert does not form part of the reference stan-
dard for studies in this review
Were th e reference standard results interpreted without knowledge
of Xpert results
Answer separately for review question A and B.
Yes if stated that the person reading the reference test result did
not know the results of Xpert or if the two tests were carried out
in different places
No if stated that the same person performed both tests or Xpert
results were known to the person undertaking the reference test
Unclear if not enough information is provided for judgment.
Were the Xpert results interpreted without knowledge of reference
standard results
Yes for all studies. Xpert is a fully automated system that provides
a print out of test results
Relevant clinical information Yes for all studies. In this review the availability or absence of clin-
ical information such as age and presence and severity of symp-

toms should not affect test performance f or the index test (fully
automated system) or reference standard
Were uninterpretable results reported? Answer separately for review question A and B.
Yes if the numbers in 2x2 table =number enroll ed or if explanation
is pr ovided for any discrepancy
No if the numbers in 2x2 table number enrolled and there is
insufficient explanation as to why
Unclear if not enough information is provided for judgment.
Withdrawals explained? Yes if a flow diagram or statement was included making it clear
what happened to all participants in the study
No if participants are excluded and no reason is provided.
20Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
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Unclear if not enough information is provided for judgment.
H I S T O R Y
Protocol first published: Issue 1, 2012
C O N T R I B U T I O N S O F A U T H O R S
MP had the original idea for the review. The protocol was written by KRS and MP, with input from HS and N D. The search strategy
was written by LAK. HS and KRS will review articles for relevance, and extract and analyse data. HS, MP, ND, CCB, and KRS will
interpret data and write the manuscript.
D E C L A R A T I O N S O F I N T E R E S T
KRS serves as Co-ordinator of the Evidence Synthesis and Policy Subgroup of Stop TB Partnership’s New Diagnostics Working Group.
MP is a recipient of a New Investigator Award from the Canadian Institutes of Health Research (CIHR). MP serves as an external
consultant for the Bill & Melinda Gates Foundation. CCB is employed by the Foundation for Innovative New Diagnostics FIND) and
has conducted studies and published on Xpert MTB/RIF as part of a collaborative project between FIND, a Swiss non-profit, Cepheid,
a US company, and academic partners. The product developed through this partnership was developed under a contract that obligated
FIND to pay for development costs and trial costs and that obligated Cepheid to make the test available at specified preferential pricing
to the public sector in developing countries. The authors h ave no financial involvement with any organization or entity with a financial
interest in or financial conflict with the subject matter or materials discussed in the protocol apart from those disclosed.

21Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance (Protocol)
Copyright © 2012 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.