Iram 2015.

Study characteristics
Patient Sampling	Cross‐sectional, consecutive, prospective
Patient characteristics and setting	Presenting signs and symptoms: patients with clinical presentation, radiological findings, and histopathological evidence of extrapulmonary TB Age: mean 37 years, range 10 to 80 years Sex, female: 41% Children: 3% HIV infection: 2% Clinical setting: teaching hospital Past history of TB: 53% Patients on anti‐TB treatment: yes, 3% Number of specimens evaluated: 18 Laboratory level: intermediate Country: Pakistan World Bank Income Classification: middle income High TB burden: yes High TB/HIV burden: no High MDR‐TB burden: yes
Index tests	Xpert MTB/RIF WHO SOP or manufacturer's protocol followed: yes Manufacturer's involvement: no
Target condition and reference standard(s)	Target condition: pleural TB, peritoneal TB Reference standard for TB detection: LJ Reference standard for rifampicin resistance: LJ‐DST Speciation: not reported Decontamination: no
Flow and timing
Comparative
Notes
Methodological quality
Item	Authors' judgement	Risk of bias	Applicability concerns
DOMAIN 1: Patient Selection
Was a consecutive or random sample of patients enrolled?	Yes
Was a case‐control design avoided?	Yes
Did the study avoid inappropriate exclusions?	Yes
Could the selection of patients have introduced bias?		Low risk
Are there concerns that the included patients and setting do not match the review question?			Unclear
DOMAIN 2: Index Test (Xpert MTB/RIF)
Were the index test results interpreted without knowledge of the results of the reference standard?	Yes
If a threshold was used, was it pre‐specified?	Yes
Could the conduct or interpretation of the index test have introduced bias?		Low risk
Are there concerns that the index test, its conduct, or interpretation differ from the review question?			Low concern
DOMAIN 2: Index Test (Xpert Ultra)
DOMAIN 3: Reference Standard
Is the reference standards likely to correctly classify the target condition?	Yes
Were the reference standard results interpreted without knowledge of the results of the index tests?	Yes
For rifampicin resistance testing, were the reference standard results interpreted without knowledge of the results of the index test?	Yes
Could the reference standard, its conduct, or its interpretation have introduced bias?		Low risk
Are there concerns that the target condition as defined by the reference standard does not match the question?			Unclear
DOMAIN 4: Flow and Timing
Was there an appropriate interval between index test and reference standard?	Yes
Did all patients receive the same reference standard?	Yes
Were all patients included in the analysis?	Yes
Could the patient flow have introduced bias?		Low risk