Perez‐Risco 2018.

Study characteristics
Patient Sampling	Study design unclear, manner of patient selection not reported, retrospective
Patient characteristics and setting	Presenting signs and symptoms: Smear‐negative extrapulmonary patients Age: adult Sex, female: not reported Children: 0% HIV infection: not reported Clinical setting: laboratory‐based evaluation Past history of TB: not reported Participants on anti‐TB treatment: not reported Number of specimens evaluated: CSF 3; pleural fluid 24; urine 24; bone or joint fluid 24 Laboratory level: central Country: Spain World Bank Income Classification: high High TB burden: no High TB/HIV burden: no High MDR‐TB burden: no
Index tests	Xpert Ultra WHO SOP or manufacturer's protocol followed: yes
Target condition and reference standard(s)	Target condition: TB meningitis, pleural TB, genitourinary TB, bone or joint TB Reference standard TB detection: MGIT and LJ culture Speciation: yes Decontamination: no
Flow and timing
Comparative
Notes	The specimens were collected between May 1999 and May 2017; frozen specimens
Methodological quality
Item	Authors' judgement	Risk of bias	Applicability concerns
DOMAIN 1: Patient Selection
Was a consecutive or random sample of patients enrolled?	Unclear
Was a case‐control design avoided?	Unclear
Did the study avoid inappropriate exclusions?	No
Could the selection of patients have introduced bias?		High risk
Are there concerns that the included patients and setting do not match the review question?			Unclear
DOMAIN 2: Index Test (Xpert MTB/RIF)
DOMAIN 2: Index Test (Xpert Ultra)
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 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?	Unclear
For rifampicin resistance testing, were the reference standard results interpreted without knowledge of the results of the index test?
Could the reference standard, its conduct, or its interpretation have introduced bias?		Unclear risk
Are there concerns that the target condition as defined by the reference standard does not match the question?			Low concern
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