Online annexes MTBDRsl - WHO...4 Footnotes. 1. Eight studies used a cross-sectional study design and...

1

2016

Online Annexes (5-8)

to

WHO Policy guidance: The use of molecular line

probe assay for the detection of resistance to

second-line anti-tuberculosis drugs

2

Contents:

Annex 5: GRADE summary of findings tables……………………………………………………………………………………………………………………………………….3

Annex 6: Evidence to recommendations tables………………………………..……………………………………………………………………………………….……….15

Annex 7. Drug concentrations used in culture-based DST for each included study…………………………………………………………………………..…51

Annex 8. References to studies excluded from the review of the diagnostic accuracy of MTBDRsl assay……………………………………………56

THIS IS THE FINAL VERSION OF THE WHO POLICY DOCUMENT APPROVED

BY THE WHO GUIDELINES REVIEW COMMITTEE.

THE FINAL FORMATTED VERSION OF THE GUIDELINES AND APPENDICES 5,6,7 AND 8

WILL BE AVAILABLE ONLINE IN EARLY JUNE 2016 AT :

www.who.int/tb/areas-of-work/laboratory/policy_statements/en/

3

Annex 5. GRADE summary of findings tables

Table 1. Accuracy of MTBDRsl by direct testing for detection of fluoroquinolone resistance in patients with rifampicin-resistant or MDR-TB

Question: What is the diagnostic accuracy of MTBDRsl by direct testing for detection of FQ resistance in patients with rifampicin-resistant or MDR-TB?

Participants: patients with rifampicin-resistant or MDR-TB

Prior testing: Patients who received MTBDRsl testing will first have received smear microscopy, Xpert MTB/RIF or other nucleic acid amplification test, and culture to diagnose TB

detection and Xpert MTB/RIF, MTBDRplus (version 2.0) or an alternative line-probe assay to detect first-line drug resistance

Role: Replacement test for culture-based drug susceptibility testing

Settings: Intermediate or central level laboratories

Index (new) test: MTBDRsl (version 1.0).5 The test was performed by direct testing on smear-positive specimens

Reference standard: Culture-based drug susceptibility testing

Studies: Mainly cross-sectional studies

Sensitivity 0.86 (95% CI: 0.75 to 0.93)

Specificity 0.99 (95% CI: 0.97 to 0.99)

Prevalences 5% 10% 15%

Outcome

Number of studies

(Number of patients)

Study design

Factors that may decrease quality of evidence Effect per 1000 patients tested

Test accuracy QoE

Risk of bias Indirectness Inconsistency Imprecision Publication

bias

Pre-test probability of

5%


10%


15%

True positives (patients with FQ resistance)

9 studies 519 patients

cross-sectional (cohort type accuracy study)

1

not serious 2 not serious

3 serious

4 not serious none 43 (37 to 47) 86 (75 to 93) 129 (112 to

140) ⨁⨁⨁◯

MODERATE

False negatives (patients incorrectly classified as not having FQ resistance)

7 (3 to 13) 14 (7 to 25) 21 (10 to 38)

True negatives (patients without FQ resistance)



1

not serious 2 not serious

3 not serious not serious none 937 (921 to

944) 887 (872 to 895)

838 (824 to 845)

⨁⨁⨁⨁ HIGH

False positives (patients incorrectly classified as having FQ resistance)

13 (6 to 29) 13 (5 to 28) 12 (5 to 26)

4

Footnotes.

1. Eight studies used a cross-sectional study design and one study used a case-control study design.

2. The QUADAS-2 tool was used to assess the risk of bias. All studies used consecutive sampling. In seven studies, the reader of the index test was blinded to results of the

reference standard and in two studies information about blinding to the reference standard was not reported. Several studies used critical concentrations for the

phenotypic culture-based reference standard that differed from the concentrations recommended by WHO. This may have lowered specificity, but this was not observed.

The evidence was not downgraded.

3. There was low concern for applicability. Given that the test's high specificity and ability to provide results within a matter of days, the test might improve patient

outcomes by enabling earlier initiation of appropriate therapy. The evidence was not downgraded.

4. For individual studies, sensitivity estimates ranged from 33% to 100%. One small study with the lowest sensitivity only included three fluoroquinolone-resistant patients.

However, the remaining heterogeneity could not be explained by study quality or other factors. The evidence was downgraded one point

5. This systematic review mainly evaluated MTBDRsl (version 1.0), which has recently been replaced with version 2.0. The addition of new probes targeting more known

resistance-conferring mutations in the MTBDRsl (version 2.0) would be expected to yield a diagnostic accuracy at least the same as or higher than that of MTBDRsl

(version 1.0). Therefore the findings in this review should be considered applicable to the test.

5

Table 2. Accuracy of MTBDRsl by direct testing for detection of SLID resistance in patients with rifampicin-resistant or MDR-TB

Question: What is the diagnostic accuracy of MTBDRsl by direct testing for detection of SLID resistance in patients with rifampicin-resistant or MDR-TB?






Index (new) test: MTBDRsl (version 1.0).5 The test was performed by direct testing on smear-positive specimens


Studies: Mainly cross-sectional studies




Outcome Number of studies


Study design

Factors that may decrease quality of evidence Effect per 1000 patients tested Test

accuracy QoE

Risk of bias

Indirectness

Inconsistency Imprecision Publication

bias


5%


10%


15%

True positives (patients with SLID resistance)



serious 1

not serious 2

not serious 3 serious

4 none 44 (19 to 49) 87 (38 to 99) 131 (57 to 148) ⨁⨁◯◯

LOW

False negatives (patients incorrectly classified as not having SLID resistance)

6 (1 to 31) 13 (1 to 62) 19 (2 to 93)

True negatives (patients without SLID resistance)



serious 1

not serious 2

not serious not serious none 945 (889 to 950)

896 (842 to 900)

846 (796 to 850)

⨁⨁⨁◯

MODERATE

False positives (patients incorrectly classified as having SLID resistance)

5 (0 to 61) 4 (0 to 58) 4 (0 to 54)

6

Footnotes

1. The QUADAS-2 was used to assess the risk of bias. All studies used consecutive or random sampling. In six studies, the reader of the index test was blinded to results of

the reference standard in two studies information about blinding to the reference standard was not reported. Fifty percent of the studies used critical concentrations for

the phenotypic culture-based reference standard that differed from the concentrations recommended by WHO. The evidence was downgraded by one point.

2. There was low concern for applicability. Given the test's high specificity and ability to provide results within a matter of days, the test might improve patient outcomes by

enabling earlier initiation of appropriate therapy. The evidence was not downgraded.

3. For individual studies, sensitivity estimates ranged from 9% to 100%. The variability was explained in part by the use of different drugs, critical concentrations, and types

of culture media in the reference standard and likely presence of eis resistance-conferring mutations in patients in Eastern European countries. The evidence was not

downgraded and considered this in the context of other factors, in particular imprecision.

4. The wide confidence interval around true positives and false negatives may lead to different decisions depending on which confidence limits are assumed. The evidence

was downgraded by one point.




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Table 3. Accuracy of MTBDRsl by indirect testing for detection of FQ resistance in patients with rifampicin-resistant or MDR-TB

Question: What is the diagnostic accuracy of MTBDRsl by indirect testing for detection of FQ resistance in patients with rifampicin-resistant or MDR-TB?






Index (new) test: MTBDRsl (version 1.0).5 The test was performed by indirect testing on culture isolates


Studies: Cross-sectional and case-control studies






Study design


accuracy QoE

Risk of bias

Indirectness Inconsistency Imprecision Publication

bias


5%


10%


15%

True positives (patients with FQ resistance)


cohort & case-control type studies

1

not serious

2

serious 3 serious

4 not serious none 43 (40 to 45) 86 (79 to 90) 128 (119 to

136) ⨁◯◯◯

VERY LOW

False negatives (patients incorrectly classified as not having FQ resistance)

7 (5 to 10) 14 (10 to 21) 22 (14 to 31)

True negatives (patients without FQ resistance)



1

not serious

2

serious 3 not serious not serious none 937 (921 to

944) 887 (872 to 895)

838 (824 to 845)

⨁⨁◯◯

LOW

False positives (patients incorrectly classified as having FQ resistance)

13 (6 to 29) 13 (5 to 28) 12 (5 to 26)

8

Footnotes

1. Thirteen studies used a cross-sectional study design and six studies used a case-control design. A sensitivity analysis that only included cross-sectional studies found sensitivity

and specificity estimates similar to those for all studies.

2. The QUADAS-2 tool was used to assess the risk of bias. Fourteen studies used consecutive or random sampling. In 12 studies, the reader of the test was blinded to results of

the reference standard. The majority of studies used critical concentrations for the phenotypic culture-based reference standard that differed from the concentrations

recommended by WHO. The evidence was downgraded by one point.

3. Several studies included patients (such as known drug-susceptible patients) that did not match the review question. Indirectness was considered in the context of other

factors, including the different critical concentrations used for culture-based drug susceptibility testing. The evidence was downgraded by one point.

4. For individual studies, sensitivity estimates ranged from 57% to 100%. Some of the variability in sensitivity might be explained by the use of different drugs, different critical

concentrations, and different types of culture media in the reference standard. However, some of the variability remained unexplained. The evidence was downgraded by one

point.


resistance-conferring mutations in the MTBDRsl (version 2.0) would be expected to yield a diagnostic accuracy at least the same as or higher than that of MTBDRsl (version

1.0). Therefore the findings in this review should be considered applicable to the test.

9

Table 4. Accuracy of MTBDRsl by indirect testing for detection of SLID resistance in patients with rifampicin-resistant or MDR-TB

Question: What is the diagnostic accuracy of MTBDRsl by indirect testing for detection of SLID resistance in patients with rifampicin-resistant or MDR-TB?


Prior testing: Patients who received MTBDRsl testing will first have received smear microscopy, Xpert MTB/RIF or other nucleic acid amplification test, and culture

to diagnose TB detection and Xpert MTB/RIF, MTBDRplus (version 2.0) or an alternative line-probe assay to detect first-line drug resistance











Study design


accuracy QoE

Risk of bias


bias

pre-test probability of

5%


10%


15%

True positives (patients with SLID resistance )



1

serious 2 serious

3 serious

4 not serious none 38 (32 to 43) 77 (63 to 86) 115 (95 to 129) ⨁◯◯◯

VERY LOW

False negatives (patients incorrectly classified as not having SLID resistance)

12 (7 to 18) 23 (14 to 37) 35 (21 to 55)

True negatives (patients without SLID resistance)



1

serious 2 serious

3 not serious not serious none 941 (924 to

947) 892 (876 to 897)

842 (827 to 847)

⨁⨁◯◯

LOW

False positives (patients incorrectly classified as having SLID resistance)

9 (3 to 26) 8 (3 to 24) 8 (3 to 23)

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Footnotes

1. Ten studies were cross-sectional design and six studies were case-control design. A sensitivity analysis that only included cross-sectional studies found sensitivity and

specificity estimates similar to those for all studies.

2. The QUADAS-2 tool was used to assess the risk of bias. Eleven studies used consecutive or random sampling. In ten studies, the reader of the test was blinded to results of the

reference standard. The majority of studies used critical concentrations for the phenotypic culture-based reference standard that differed from the concentrations

recommended by WHO. The evidence was downgraded by one point.

3. Several studies included patients (drug-susceptible) that did not match the review question. Indirectness was considered in the context of other factors, including the different

critical concentrations used for culture-based drug susceptibility testing. The evidence was downgraded by one point.

4. For individual studies, sensitivity estimates ranged from 25% to 100%. Some of the variability could be explained by the use of different drugs, critical concentrations, and

types of culture media in the reference standard and by presence of the eis mutation in patients from Eastern Europe. eis gene is not targeted by version 1.0 of the test, which

may lead to lower sensitivity among Eastern European strains. However, some of the variability remained unexplained. The evidence was downgraded by one point.




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Table 5. Accuracy of MTBDRsl by direct testing for the diagnosis of XDR-TB in patients with rifampicin-resistant or MDR-TB

Question: What is the diagnostic accuracy of MTBDRsl by direct testing for the diagnosis of XDR-TB in patients with rifampicin-resistant or MDR-TB?














Study design

Factors that may decrease quality of evidence Effect per 1000 patients tested

Test accuracy QoE Risk of

bias Indirectness Inconsistency Imprecision

Publication bias


1%


5%


10%

True positives (patients with XDR-TB)



serious 1 not serious

2

not serious 3 serious

4 none 7 (4 to 9) 35 (19 to 45) 69 (39 to 89) ⨁⨁◯◯

LOW

False negatives (patients incorrectly classified as not having XDR-TB)

3 (1 to 6) 15 (5 to 31) 31 (11 to 61)

True negatives (patients without XDR-TB)



serious 1 not serious

2

not serious not serious none 980 (941 to 983)

941 (903 to 943)

891 (855 to 894)

⨁⨁⨁◯

MODERATE

False positives (patients incorrectly classified as having XDR-TB)

10 (7 to 49) 9 (7 to 47) 9 (6 to 45)

12

Footnotes

1. The QUADAS-2 tool was used to assess the risk of bias. All studies used consecutive sampling. In four studies, the reader of the test was blinded to results of the reference

standard and in two studies information about blinding was not reported. The majority of studies used critical concentrations for the phenotypic culture-based reference

standard that differed from the concentrations recommended by WHO. The evidence was downgraded by one point.

2. There was low concern for applicability. Given the test's high specificity and ability to provide results within a matter of days, the test might improve patient outcomes by

enabling earlier initiation of appropriate therapy. The evidence was not downgraded.

3. For individual studies, sensitivity estimates ranged from 14% to 92%. We thought variability could be explained in part by the use of different drugs, critical concentrations,

and types of culture media in the reference standard and likely presence of eis mutation in patients in Eastern European countries. The evidence was not downgrade and

considered this in the context of other factors, in particular imprecision.

4. The very wide 95% CI for true positives and false negatives may lead to different decisions depending on which confidence limits are assumed. The evidence was downgraded

by one point.




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Table 6. Accuracy of MTBDRsl by indirect testing for the diagnosis of XDR-TB in patients with rifampicin-resistant or MDR-TB

Question: What is the diagnostic accuracy of MTBDRsl by indirect testing for the diagnosis of XDR-TB in patients with rifampicin-resistant or MDR-TB?












Outcome № of studies (№

of patients) Study design


accuracy QoE

Risk of bias


bias


1%


5%


10%

True positives (patients with XDR-TB)



1

serious 2 serious

3 serious

4 not serious

5

none 7 (4 to 9) 35 (19 to 45) 69 (39 to 89) ⨁◯◯◯

VERY LOW

False negatives (patients incorrectly classified as not having XDR-TB)

3 (1 to 6) 15 (5 to 31) 31 (11 to 61)

True negatives (patients without XDR-TB)



1

serious 2 serious

3 not serious

4 not serious none 980 (941 to

983) 941 (903 to 943)

891 (855 to 894) ⨁⨁◯◯

LOW

False positives (patients incorrectly classified as having XDR-TB)

10 (7 to 49) 9 (7 to 47) 9 (6 to 45)

14

Footnotes

1. Four studies were cross-sectional design and four were case-control design.

2. The QUADAS-2 tool was used to assess the risk of bias. Six studies used consecutive sampling. In six studies, the reader of the test was blinded to results of the reference

standard. All studies used critical concentrations for the phenotypic culture-based reference standard that differed from the concentrations recommended by WHO. The

evidence was downgraded one point.

3. Several studies included patients (drug-susceptible) that did not match the review question. Indirectness was considered in the context of other factors, including the

different critical concentrations used for culture-based drug susceptibility testing. The evidence was downgraded one point.

4. For individual studies, sensitivity estimates ranged from 20% to 100%. Some of the variability could be explained by the use of different drugs, critical concentrations, and

types of culture media in the reference standard and by presence of the eis mutation in patients in Eastern Europe. eis gene is not targeted by version 1.0 of the test,

which may lead to lower sensitivity in Eastern European strains. However, some of the variability remained unexplained. The evidence was downgraded one point.

5. The wide confidence interval around true positives and false negatives may lead to different decisions depending on which confidence limits are assumed. The evidence

was not further downgraded as one point was deducted for inconsistency.




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Annex 6. Evidence to recommendations Table 1: Evidence to recommendation: Accuracy of MTBDRsl by direct testing for detection of fluoroquinolone resistance in patients with rifampicin-resistant or

MDR-TB

JUDGEMENT RESEARCH EVIDENCE

ADDITIONAL

CONSIDERATIONS

PROBLEM

Is the problem a priority? ○ No ○ Probably no ○ Probably yes

● Yes ○ Varies

○ Don't know

In 2014 WHO has estimated that 9.7% of the 480,000 cases of MDR-TB , were actually XDR TB, i.e. MDR TB

with added resistance to at least one FQ and one SLID. Genotypic (molecular) methods have considerable advantages for scaling up programmatic management and surveillance of drug-resistant TB, offering speed of diagnosis, standardised testing, potential for high through-put, and fewer requirements for laboratory biosafety. Molecular tests for detecting drug resistance such as the MTBDRsl assay have shown promise for the diagnosis of drug-resistant tuberculosis (TB).

The MTBDRsl assay incorporates probes to detect mutations within genes (gyrA and rrs for version 1.0 and, in addition, gyrB and the eis promoter for version 2.0), which are associated with resistance to the class of fluoroquinolones or the class of second-line injectable drugs (SLID).

Additional regions

associated with resistance to FQ and SLIDs are included in the version 2.0 assay. Accuracy of version 2.0 assay is expected to be no worse than

version 1.0 and should have improved sensitivity for detection of resistance for these drug classes.

TEST ACCURACY

How accurate is the test? ○ Very inaccurate

○ Inaccurate ○ Accurate ○ Very accurate

● Varies ○ Don't know

In this review – data from the 9 studies, 1771 patients, reference standard: culture based DST

Test accuracy MTBDRsl by direct testing for fluoroquinolones: Sensitivity: 86% (95% CI: 75% to 93%) Specificity: 99% (95% CI: 97% to 99%)

More data is needed to better understand the correlation of the presence of certain fluoroquinolone resistance conferring mutations with phenotypic DST resistance for moxifloxacin and patient outcomes.

The presence of mutations in these

regions does not necessarily imply resistance to all the drugs within that class. Although specific mutations within these regions

may be associated with different levels of resistance to each drug within these classes, the extent of this is not completely understood.

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DESIRABLE EFFECTS How substantial are the

desirable anticipated effects? ○ Trivial

○ Small ○ Moderate

● Large ○ Varies ○ Don't know

The anticipated desirable effect is the correct diagnosis of fluoroquinolone (FQ) resistant cases (TP) as well as FQ susceptible cases (TN). MTBDRsl would correctly identify 43 cases out of 50 per 1000 individuals

tested if the pre-test probability of TB with FQ resistance is 5%. For 10-15% there would be 86 and 129 patients respectively (see table below). Correct identification of FQ resistant cases should lead to higher cure rates, less sequelae to the individual patient, and less transmission in the community.

Similarly MTBDRsl would correctly identify 937 FQ-susceptible (TN) out of 950 per 1000 individuals tested if the pre-test probability of TB with FQ resistance is 5%. For 10-15% prevalence’s there would be 887 and 838 patients respectively (see table below). Correct identification of FQ susceptible cases should lead to avoiding unnecessary treatment with additional drugs with increased risk of severe adverse events and greater costs.

The anticipated undesirable effect is the incorrect identification of an individual as a FQ susceptible or FQ resistant case (FN or FP). MTBDRsl would misclassify 7 cases as FN per 1000 individuals tested if the pre-test probability of TB with FQ resistance is 5%, and 14 to 21 cases under pre-test probabilities of 10-15%. Incorrect identification of an individual as FQ susceptible may have a potential increased risk of patient morbidity and mortality, continued risk of community transmission of drug-resistant TB. However, the harm may be lessened as patients without resistance detected to fluoroquinolones may be

eligible for an MDR-TB regimen which would include either moxifloxacin or gatifloxacin.

MTBDRsl had misclassified 13 cases as FP per 1000 individuals tested if the pre-test probability of TB with FQ resistance is 5%, and 13 to 12 cases under pre-test probabilities of 10-15%. Incorrect identification of an individual as FQ resistant may lead to patient anxiety, possible delays in further diagnostic evaluation, prolonged and unnecessary treatment with drugs that may have additional serious adverse effects.

Should MTBDRsl by direct testing be used to diagnose FQ resistance in patients with RR or MDR TB?

Test result

Number of results per 1000 patients

tested (95% CI) Number of

participants

(studies)

Quality of the

Evidence (GRADE) Prevalence

5%

Prevalence

10%

Prevalence

15%

True positives

(patients with FQ resistance )

43 (37 to 47)

86 (75 to 93)

129 (112 to 140)

519

(9)

⨁⨁⨁◯ MODERATE

False negatives

(patients incorrectly classified as not having FQ resistance )

7 (3 to 13) 14 (7 to 25) 21 (10 to

38)

Desirable anticipated effects

MTBDRsl can be performed in a single day to allow the initiation of an appropriate treatment regimen. Phenotypic

DST more difficult to

perform.

UNDESIRABLE EFFECTS

How substantial are the undesirable anticipated effects? ○ Large

● Moderate ○ Small ○ Trivial

○ Varies ○ Don't know

Undesirable anticipated effects per drug: FN results are of main concern as patients may not be given an

effective treatment regimen. Less concern for FP results. Conventional phenotypic DST should be used in the

follow-up evaluation of patients with a negative result especially in settings with a high pre-test probability for resistance to

fluoroquinolones. Two GDG members

thought that the undesirable effects were large. Physicians should

be guided by the MTBDRsl assay in their initial choice of an MDR-TB treatment regimen.

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True negatives

(patients without FQ

resistance )

937 (921 to

944)

887 (872 to

895)

838 (824 to

845)

1252

(9)

⨁⨁⨁⨁

HIGH

False positives

(patients incorrectly classified

as having FQ resistance )

13 (6 to 29) 13 (5 to 28) 12 (5 to 26)

Implications for the detection of FQ conferring mutations among RR-TB persons

TP: Test result suggests modification of a WHO recommended MDR-TB regimen. No additional harms. Patient receive optimal regimen. FP: Test result suggests modification of a WHO recommended MDR-TB regimen. Increased risk of serious

adverse effects. Patient receive optimal regimen. FN: Test result do not suggests modification of a WHO recommended MDR-TB regimen. Patient receive

suboptimal regimen. No benefits. TN: Test result do not suggests modification of a WHO recommended MDR-TB regimen. No additional harms. Patient receive optimal regimen.

CERTAINTY OF THE

EVIDENCE OF TEST

ACCURACY

What is the overall certainty of the evidence of test accuracy?

○ Very low ○ Low ● Moderate ○ High ○ No included studies

In this review the risk of bias was not serious

Indirectness was considered not serious

Inconsistency was considered serious for test sensitivity and not serious for test specificity

Imprecision was considered not serious for both sensitivity and specificity

Publication bias – none for all studies.

Quality of evidence for test accuracy is: Sensitivity –moderate quality of evidence Specificity – high

quality of evidence

CERTAINTY OF THE

EVIDENCE OF TEST'S

EFFECTS

What is the overall certainty of

the evidence for any critical or important direct benefits, adverse effects or burden of the test? ○ Very low ○ Low

○ Moderate ○ High

● No included studies

The test is labour-intensive and presents certain burden for the health worker. There is a need for

appropriate infrastructure with separate rooms and biosafety requirements, which assumes a considerable investment. The burden and adverse effects are potentially insignificant for the patient.

CE

OF

M A NWhat is the overall certainty if Ideally test results should guide management decisions, provided use of test is adopted by national policy. A

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the evidence of effects of the management that is guided by

the test results? ○ Very low

○ Low ○ Moderate ○ High


positive test result should be sufficient for a patient to start treatment.

CERTAINTY OF THE

EVIDENCE OF TEST

RESULT/M

ANAGEMENT

How certain is the link between test results and management decisions? ○ Very low ○ Low ○ Moderate ○ High


The link between test results and management decisions may be uncertain in various settings. In some occasions clinicians use empirical treatment for TB. In others capacity of health system may be insufficient to provide the patient with necessary treatment.

Turnaround time would be faster than for conventional DST

The need for sample referral may cause delays

CERTAINTY OF EFFECTS

What is the overall certainty of the evidence of effects of the test? ○ Very low

○ Low

● Moderate ○ High

○ No included studies

This question is intended to summarize previous four questions on the certainty of the evidence.

VALUES

Is there important uncertainty about or variability in how much people value the main outcomes? ○ Important uncertainty or

variability ○ Possibly important uncertainty or

variability ● Probably no important uncertainty or variability ○ No important uncertainty or

variability ○ No known undesirable outcomes

There is no important uncertainty about or variability in how much people value the main outcomes.

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BALANCE OF EFFECTS

Does the balance between desirable and undesirable

effects favor the intervention or the comparison? ○ Favors the comparison

○ Probably favors the comparison ○ Does not favor either the

intervention or the comparison ● Probably favors the intervention ○ Favors the intervention


FN results increase with increasing pre-test probability for FQ resistance. Conventional phenotypic DST should be used in the follow-up evaluation of patients with a negative result especially in settings with a high

pre-test probability for resistance to fluoroquinolones.

RESOURCES REQUIRED

How large are the resource requirements (costs)? ○ Large costs ○ Moderate costs

○ Negligible costs and savings ○ Moderate savings ○ Large savings

○ Varies

● Don't know

No research evidence was identified.

CERTAINTY OF EVIDENCE OF

REQUIRED RESOURCES

What is the certainty of the evidence of resource requirements (costs)? ○ Very low ○ Low




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COST EFFECTIVENESS

Does the cost-effectiveness of the intervention favor the

intervention or the comparison? ○ Favors the comparison


intervention or the comparison ○ Probably favors the intervention ○ Favors the intervention

○ Varies



EQUITY

What would be the impact on health equity? ○ Reduced ○ Probably reduced ○ Probably no impact

● Probably increased ○ Increased


System incorporating molecular methods provides more equity.

ACCEPTABILITY

Is the intervention acceptable to

key stakeholders? ○ No ○ Probably no

● Probably yes ○ Yes

○ Varies

○ Don't know

The test may be acceptable to be implemented in reference settings, where infrastructure and qualified staff

to perform MTBDRsl exist. If MTBDRsl is implemented for first-line DST the MTBDRsl assay could be performed on the same specimen for rifampicin-resistant TB or MDR-TB cases.

FEASIBILITY

Is the intervention feasible to implement? ○ No ○ Probably no



Implementation of the test would require additional funding and technical support for the infrastructure upgrade, training of staff and procuring the equipment.

21 | P a g e

Summary of judgments

JUDGEMENT IMPLICATIONS

PROBLEM No Probably no Probably yes Yes

Varies Don't know

TEST ACCURACY Very inaccurate Inaccurate Accurate Very accurate

Varies Don't know

DESIRABLE EFFECTS Trivial Small Moderate Large

Varies Don't know

UNDESIRABLE

EFFECTS Large Moderate Small Trivial

Varies Don't know

CERTAINTY OF THE

EVIDENCE OF TEST

ACCURACY

Very low Low Moderate High

No included studies

CERTAINTY OF THE

EVIDENCE OF TEST'S

EFFECTS


No included studies

CERTAINTY OF THE

EVIDENCE OF

MANAGEMENT'S

EFFECTS


No included studies

CERTAINTY OF THE

EVIDENCE OF TEST

RESULT/MANAGEMENT


No included studies

CERTAINTY OF

EFFECTS Very low Low Moderate High

No included studies

VALUES

Important uncertainty or variability

Possibly important

uncertainty or variability

Probably no important


No important uncertainty or variability

No known undesirable outcomes

BALANCE OF EFFECTS Favors the comparison

Probably favors the comparison

Does not favor either the

Probably favors the

Favors the intervention

Varies Don't know

22 | P a g e


intervention or the comparison

intervention

RESOURCES

REQUIRED Large costs Moderate costs

Negligible costs and savings

Moderate savings Large savings Varies Don't know

CERTAINTY OF

EVIDENCE OF

REQUIRED

RESOURCES


No included studies

COST EFFECTIVENESS Favors the comparison




Probably favors the intervention


Varies No included

studies

EQUITY Reduced Probably reduced

Probably no impact

Probably increased

Increased Varies Don't know

ACCEPTABILITY No Probably no Probably yes Yes

Varies Don't know

FEASIBILITY No Probably no Probably yes Yes

Varies Don't know

Conclusions


TYPE OF RECOMMENDATION

Strong recommendation against the intervention

Conditional recommendation against

the intervention

Conditional recommendation for either the intervention or the

comparison

Conditional recommendation for the

intervention

Strong recommendation for the intervention

○ ○ ○ ● ○

RECOMMENDATION For patients with confirmed rifampicin-resistant TB or MDR-TB, the WHO guideline development group suggests using direct testing of patient specimens with the MTBDRsl assay as the initial test, over culture and phenotypic DST, to detect resistance to FQ (Conditional recommendation, Moderate certainty in the evidence for test accuracy).

JUSTIFICATION

SUBGROUP Accuracy of version 2.0 assay is expected to be no worse than version 1.0 and should have improved sensitivity for detection of resistance for these

23 | P a g e

CONSIDERATIONS drug classes.

IMPLEMENTATION CONSIDERATIONS

Adoption of the MTBDRsl assay does not eliminate the need for conventional culture and DST capability. Despite good specificity of the MTBDRsl for the detection of resistance to FQs, culture and phenotypic DST is required to completely exclude resistance to this drug class. However, the demand for

conventional culture and DST capacity may change, based on the prevalence of resistance to second-line anti-TB drugs in patients with confirmed RR-TB or MDR-TB. The following implementation considerations apply:

• MTBDRsl cannot determine resistance to individual drugs in the class of fluoroquinolones. Phenotypic resistance to ofloxacin and levofloxacin is highly correlated with resistance conferring mutations detected by the MTBDRsl assay. Uncertainty remains about the susceptibility to moxifloxacin and gatifloxacin for such strains with mutations;

• MTBDRsl assay should be used in the direct testing of sputum samples irrespective of whether samples are smear-negative or smear-positive from patients with confirmed rifampicin-resistant TB or MDR-TB;

• MTBDRsl assay is designed to TB and resistance to second-line injectable drugs from processed sputum samples. Other respiratory samples (e.g. bronchoalveolar lavage and gastric aspirates) or extrapulmonary samples (tissue samples, CSF or other body fluids) have not been adequately evaluated;

• Culture and phenotypic DST plays a critical role in the monitoring of patients’ response to treatment and for detecting additional resistance to second-line drugs during treatment. Patients with false negative resistance results using the MTBDRsl can be identified and captured through treatment monitoring. Patients with false positive results might benefit from the addition of other drugs;

• The availability of additional second-line drugs is critical.

MONITORING AND

EVALUATION

System of quality assurance is necessary.

RESEARCH PRIORITIES

Current recommendations on the MTBDRsl assay should not prevent or restrict further research on new rapid molecular DST tests, especially for assays that can be used as close as possible to where patients are initially diagnosed with RR-TB and MDR-TB and where treatment can be initiated. Further operational research on the MTBDRsl test should focus on the following priorities:

• Develop and improved understanding of the correlation between the detection of resistance conferring mutations with phenotypic DST results and patient outcomes;

• Develop improved knowledge of the presence of specific mutations detected with the MTBDRsl assay correlated with MICs for individual drugs within the class of fluoroquinolones;

• Review evidence to confirm or revise different critical concentrations used in phenotypic DST methods; • Determine the limit of detection of MTBDRsl for the detection of heteroresistance; • Determine training, competency, and quality assurance needs; • Gather more evidence on the impact on appropriate MDR-TB treatment initiation and mortality; • Meet “Standards for Reporting Diagnostic accuracy studies” (STARD) for future studies; • Perform country-specific cost-effectiveness and cost-benefit analyses of MTDDRsl assay use in different programmatic settings.

24 | P a g e

Table 2: Evidence to recommendation: Accuracy of MTBDRsl by direct testing for detection of SLID resistance in patients with rifampicin-resistant or MDR-TB


ADDITIONAL

CONSIDERATIONS

PROBLEM


● Yes ○ Varies ○ Don't know




Additional regions



TEST ACCURACY


○ Inaccurate ○ Accurate

○ Very accurate



Test accuracy MTBDRsl by direct testing for SLID: Sensitivity: 87% (95% CI: 38% to 99%) Specificity: 99% (95% CI: 94% to 100%)

MTBDRsl by direct testing for Amikacin: Sensitivity: 92% (95% CI: 71% to 98%) Specificity: 100% (95% CI: 95% to 100%) MTBDRsl by direct testing for Kanamycin: Sensitivity: 79% (95% CI: 12% to 99%) Specificity: 100% (95% CI: 94% to 100%) MTBDRsl by direct testing for Capreomycin: Sensitivity: 77% (95% CI: 61% to 87%7) Specificity: 98% (95% CI: 93% to 100%)

The accuracy varies with the different

SLID. The variability is explained in part by the use of different drugs, critical concentrations, types of culture media in the reference

standard and likely presence of eis resistance-conferring mutations in patients in Eastern European countries.

DESIRABLE

EFFECTS

How substantial are the desirable anticipated effects? ○ Trivial ○ Small ○ Moderate

● Large

The anticipated desirable effect is the correct diagnosis of SLID resistant cases (TP) as well as SLID susceptible cases (TN). MTBDRsl would correctly identify 44 cases out of 50 per 1000 individuals tested if the pre-test probability of TB is 5%. For 10-15% there would be 87 and 131 patients respectively (see table below). Correct identification of SLID resistant cases should lead to higher cure rates, less sequelae to the individual patient, and less transmission in the community.

Desirable anticipated effects per drug: Amikacin – Large desirable effects Capreomycin – Large

desirable effects

25 | P a g e

○ Varies

○ Don't know

Similarly MTBDRsl would correctly identify 945 TB-free cases (TN) out of 950 per 1000 individuals tested if the pre-test probability of TB is 5%. For 10-15% prevalence’s there would be 896 and 846 patients

respectively (see table below). Correct identification of SLID susceptible cases should lead to avoiding unnecessary treatment with additional drugs with increased risk of severe adverse events and greater costs.

The anticipated undesirable effect is the incorrect identification of an individual as a SLID susceptible or resistant case (FN or FP).

MTBDRsl would misclassify 6 cases as FN per 1000 individuals tested if the pre-test probability of TB with SLID resistance is 5%, and 13 to 19 cases under pre-test probabilities of 10-15%. Incorrect identification

of an individual as SLID susceptible may have a potential increased risk of patient morbidity and mortality, and continued risk of community transmission of drug-resistant TB as well initiation of an MDR-TB regimen which includes a SLID with doubtful efficacy.

MTBDRsl had misclassified 5 cases as FP per 1000 individuals tested if the pre-test probability of TB is 5%, and 4 cases under pre-test probabilities of 10-15%. Incorrect identification of an individual as SLID resistant may lead to patient anxiety, possible delays in further diagnostic evaluation, prolonged and unnecessary treatment with drugs that may have additional serious adverse effects.

Should MTBDRsl by direct testing be used to diagnose SLID resistance in patients with RR or MDR TB?

Test result



participants

(studies)

Quality of the


5%

Prevalence

10%

Prevalence

15%

True positives

(patients with SLID resistance )

44 (19 to 49)

87 (38 to 99)

131 (57 to 148)

348

(8)

⨁⨁◯◯ LOW 1,2,3,4

False negatives

(patients incorrectly classified as not having SLID

resistance )

6 (1 to 31) 13 (1 to 62) 19 (2 to 93)

True negatives

(patients without SLID resistance )

945 (889 to 950)

896 (842 to 900)

846 (796 to 850)

1291

(8)

⨁⨁⨁◯ MODERATE 1,2,5

False positives

(patients incorrectly classified as having SLID resistance )

5 (0 to 61) 4 (0 to 58) 4 (0 to 54)

Kanamycin – Large desirable effects

UNDESIRABLE EFFECTS


○ Moderate ○ Small

○ Trivial


Undesirable anticipated effects per drug:

Amikacin – Small undesirable effects Capreomycin and kanamycin – moderate undesirable effects

Two GDG members thought that the undesirable effects were large. Physicians should be guided by the

MTBDRsl assay in

their initial choice of an MDR-TB treatment regimen. Conventional phenotypic DST

should be used in the follow-up evaluation of patients with a negative result especially in settings with a high pre-test probability for

resistance to SLIDs.

26 | P a g e

Implications for the detection of SLID conferring mutations among RR-TB persons

TP: Test result suggests modification of a WHO recommended MDR-TB regimen. No additional harms.

Patient receive optimal regimen. FP: Test result suggests modification of a WHO recommended MDR-TB regimen. Increased risk of serious adverse effects. Patient receive optimal regimen. FN: Test result do not suggests modification of a WHO recommended MDR-TB regimen. Patient receive suboptimal regimen. No benefits. TN: Test result do not suggests modification of a WHO recommended MDR-TB regimen. No additional harms. Patient receive optimal regimen.

CERTAINTY OF THE EVIDENCE

OF TEST ACCURACY


○ Very low ● Low ○ Moderate ○ High ○ No included studies

In this review the risk of bias was serious

Indirectness was considered not serious

Inconsistency was considered not serious

Imprecision was considered serious for sensitivity and not serious for specificity

Publication bias – none for all studies

Quality of evidence for test accuracy is: Sensitivity –low

quality of evidence Specificity – moderate quality of evidence Kanamycin-low certainty Capreomycin-low certainty

Amikacin – moderate certainty

CERTAINTY OF THE

EVIDENCE OF TEST'S

EFFECTS

What is the overall certainty of the evidence for any critical or important direct benefits, adverse effects or burden of the test? ○ Very low

○ Low



The test is labour-intensive and presents certain burden for the health worker. There is a need for appropriate infrastructure with separate rooms and biosafety requirements, which assumes a considerable investment. The burden and adverse effects are potentially insignificant for the patient.

CERTAINTY OF THE

EVIDENCE OF

MANAGEMENT'S

EFFECTS

What is the overall certainty if the evidence of effects of the management that is guided by the test results? ○ Very low ○ Low ○ Moderate ○ High

Ideally test results should guide management decisions, provided use of test is adopted by national policy. A positive test result should be sufficient for a patient to start treatment.

27 | P a g e


CERTAINTY OF THE

EVIDENCE OF TEST

RESULT/M

ANAGEMENT

How certain is the link between test results and management decisions? ○ Very low ○ Low








● Low ○ Moderate

○ High


This question is intended to summarize previous four questions on the certainty of the evidence. Kanamycin and Capreomycin – low certainty


VALUES






28 | P a g e

BALANCE OF EFFECTS






Desirable (Amikacin, Kanamycin, Capreomycin) - Large, Large, Large

Undesirable (Amikacin, Kanamycin, Capreomycin) - Small, Moderate, Moderate

Concern - FN

Accuracy for

detecting amikacin resistance is better than for capreomycin or kanamycin.

RESOURCES REQUIRED



○ Varies

● Don't know



REQUIRED RESOURCES





29 | P a g e

COST EFFECTIVENESS





○ Varies



EQUITY





ACCEPTABILITY




○ Varies

○ Don't know


to perform MTBDRsl exist. If MTBDRsl is implemented for first-line DST the MTBDRsl assay could be performed on the same sample

FEASIBILITY





30 | P a g e




Varies Don't know


Varies Don't know


Varies Don't know

UNDESIRABLE


Varies Don't know

CERTAINTY OF THE

EVIDENCE OF TEST

ACCURACY


No included studies

CERTAINTY OF THE

EVIDENCE OF TEST'S

EFFECTS


No included studies

CERTAINTY OF THE

EVIDENCE OF

MANAGEMENT'S

EFFECTS


No included studies

CERTAINTY OF THE

EVIDENCE OF TEST

RESULT/MANAGEMENT


No included studies

CERTAINTY OF


No included studies

VALUES


Possibly important






BALANCE OF EFFECTS Favors the Probably favors Does not favor Probably favors Favors the Varies Don't know

31 | P a g e


comparison the comparison either the intervention or the comparison

the intervention

intervention

RESOURCES




CERTAINTY OF

EVIDENCE OF

REQUIRED

RESOURCES


No included studies







Varies No included

studies


Probably no impact

Probably increased



Varies Don't know


Varies Don't know

Conclusions


TYPE OF

RECOMMENDATION Strong recommendation against the intervention


the intervention


comparison


intervention


○ ○ ○ ● ○

RECOMMENDATION For patients with confirmed rifampicin-resistant TB or MDR-TB, the WHO guideline development group suggests using direct testing of patient specimens with the MTBDRsl assay as the initial test, over culture and phenotypic DST, to detect resistance to SLID (Conditional recommendation, Low certainty in the evidence for test accuracy).

JUSTIFICATION

32 | P a g e

SUBGROUP CONSIDERATIONS

Accuracy of version 2.0 assay is expected to be no worse than version 1.0 and should have improved sensitivity for detection of resistance for these drug classes.

IMPLEMENTATION

CONSIDERATIONS

Adoption of the MTBDRsl assay does not eliminate the need for conventional culture and DST capability. Despite good specificity of the MTBDRsl for the

detection of resistance to SLIDs, culture and phenotypic DST is required to completely exclude resistance to these drug classes. However, the demand for conventional culture and DST capacity may change, based on the prevalence of resistance to second-line anti-TB drugs in patients with confirmed RR-TB or MDR-TB. The following implementation considerations apply:

• Mutations in some regions (e.g., the eis promoter region) may be responsible for causing resistance to one drug in a class more than other drugs within that class. The eis C14T mutation is associated with kanamycin resistance in strains from Eastern Europe;

• MTBDRsl assay should be used in the direct testing of sputum samples irrespective of whether samples are smear-negative or smear-positive from patients with confirmed rifampicin-resistant TB or MDR-TB;

• MTBDRsl assay is designed to TB and resistance to second-line injectable drugs from processed sputum samples. Other respiratory samples (e.g. bronchoalveolar lavage and gastric aspirates) or extrapulmonary samples (tissue samples, CSF or other body fluids) have not been adequately evaluated;

• Culture and phenotypic DST plays a critical role in the monitoring of patients’ response to treatment and for detecting additional resistance to second-line drugs during treatment. Patients with false negative resistance results using the MTBDRsl can be identified and captured through treatment monitoring. Patients with false positive results might benefit from the addition of other drugs;

• The availability of additional second-line drugs is critical.

MONITORING AND EVALUATION


RESEARCH PRIORITIES


• Develop and improved understanding of the correlation between the detection of resistance conferring mutations with phenotypic DST results and patient outcomes;

• Develop improved knowledge of the presence of specific mutations detected with the MTBDRsl assay correlated with MICs for individual drugs

within the class of SLIDs; • Review evidence to confirm or revise different critical concentrations used in phenotypic DST methods; • Determine the limit of detection of MTBDRsl for the detection of heteroresistance; • Determine training, competency, and quality assurance needs; • Gather more evidence on the impact on appropriate MDR-TB treatment initiation and mortality; • Meet “Standards for Reporting Diagnostic accuracy studies” (STARD) for future studies; • Perform country-specific cost-effectiveness and cost-benefit analyses of MTDDRsl assay use in different programmatic settings.

33 | P a g e

Table 3: Evidence to recommendations: Accuracy of MTBDRsl by indirect testing for detection of fluoroquinolone resistance in patients with rifampicin-resistant

or MDR-TB


ADDITIONAL

CONSIDERATIONS

PROBLEM


● Yes ○ Varies

○ Don't know

In 2014 WHO has estimated that 9.7% of the 480,000 cases of MDR-TB , were actually XDR TB, i.e. MDR TB with added resistance to at least one FQ and one SLID. Genotypic (molecular) methods have considerable advantages for scaling up programmatic management and surveillance of drug-resistant TB, offering speed of diagnosis, standardised testing, potential for high through-put, and fewer requirements for laboratory biosafety. Molecular tests for detecting drug resistance such as the MTBDRsl assay have shown promise for the diagnosis of drug-resistant tuberculosis (TB).


Additional regions associated with resistance to FQ and SLIDs are included in the version 2.0 assay. Accuracy of version

2.0 assay is expected to be no worse than version 1.0 and should have improved sensitivity for detection of resistance for these

drug classes.

TEST ACCURACY

How accurate is the test? ○ Very inaccurate ○ Inaccurate

● Accurate ○ Very accurate

○ Varies

○ Don't know


Test accuracy MTBDRsl by indirect testing for fluoroquinolones: Sensitivity: 86%(95% CI: 79% to 90%) Specificity: 99% (95% CI: 97% to 99%) More data is needed to better understand the correlation of the presence of certain fluoroquinolone resistance conferring mutations with phenotypic DST resistance for moxifloxacin and patient outcomes. The diagnostic accuracy of MTBDRsl is similar when performed using either direct or indirect testing.

The presence of mutations in these regions does not necessarily imply resistance to all the drugs within that class. Although

specific mutations within these regions may be associated with different levels of resistance to each drug within these classes, the extent of

this is not completely understood.

DESIRABLE

EFFECTS How substantial are the

desirable anticipated effects? ○ Trivial ○ Small

● Moderate ○ Large

The anticipated desirable effect is the correct diagnosis of fluoroquinolone (FQ) resistant cases (TP) as well as FQ susceptible cases (TN). MTBDRsl would correctly identify 43 cases out of 50 per 1000 individuals tested if the pre-test probability of TB with FQ resistance is 5%. For 10-15% there would be 86 and 128 patients respectively (see table below). Correct identification of FQ resistant cases should lead to higher cure rates, less sequelae to the individual patient, and less transmission in the community.

Desirable anticipated effects Indirect testing with MTBDRsl can be performed in a single day once the culture

34 | P a g e

○ Varies

○ Don't know

Similarly MTBDRsl would correctly identify 937 FQ-susceptible (TN) out of 950 per 1000 individuals tested if the pre-test probability of TB with FQ resistance is 5%. For 10-15% prevalence’s there would be 887 and

838 patients respectively (see table below). Correct identification of FQ susceptible cases should lead to avoiding unnecessary treatment with additional drugs with increased risk of severe adverse events and greater costs.

The anticipated undesirable effect is the incorrect identification of an individual as a FQ susceptible or FQ resistant case (FN or FP).

MTBDRsl would misclassify 7 cases as FN per 1000 individuals tested if the pre-test probability of TB with FQ resistance is 5%, and 14 to 22 cases under pre-test probabilities of 10-15%. Incorrect identification of an

individual as FQ susceptible may have a potential increased risk of patient morbidity and mortality, continued risk of community transmission of drug-resistant TB. However, the harm may be lessened as patients without resistance detected to fluoroquinolones may be eligible for an MDR-TB

regimen which would include either moxifloxacin or gatifloxacin.

MTBDRsl had misclassified 13 cases as FP per 1000 individuals tested if the pre-test probability of TB with FQ

resistance is 5%, and 13 to 12 cases under pre-test probabilities of 10-15%. Incorrect identification of an

individual as FQ resistant may lead to patient anxiety, possible delays in further diagnostic evaluation, prolonged and unnecessary treatment with drugs that may have additional serious adverse effects. Should MTBDRsl by indirect testing be used to diagnose FQ resistance in patients with RR or MDR TB?

Test result



participants

(studies)

Quality of the


5%

Prevalence

10%

Prevalence

15%

True positives

(patients with FQ resistance )

43 (40 to

45)

86 (79 to

90)

128 (119 to

133)

869

(19)

⨁◯◯◯ VERY LOW

False negatives (patients incorrectly classified

as not having FQ resistance )

7 (5 to 10) 14 (10 to

21)

22 (14 to

31)

True negatives (patients without FQ

resistance )

937 (921 to 944)

887 (872 to 895)

838 (824 to 845)

1354 (19)

⨁⨁◯◯ LOW

False positives

(patients incorrectly classified as having FQ resistance )

13 (6 to 29) 13 (5 to 28) 12 (5 to 26)

is grown. The method is faster and easier to

perform than phenotypic DST.

UNDESIRABLE EFFECTS


● Moderate ○ Small ○ Trivial



FN results are of main concern as patients may not be given an effective treatment regimen. Less concern for FP results.

Conventional phenotypic DST should be used in the follow-up evaluation of patients with a negative result

especially in settings

with a high pre-test probability for resistance to fluoroquinolones.

35 | P a g e

Implications for the detection of FQ conferring mutations among RR-TB persons


Patient receive optimal regimen. FP: Test result suggests modification of a WHO recommended MDR-TB regimen. Increased risk of serious adverse effects. Patient receive optimal regimen. FN: Test result do not suggests modification of a WHO recommended MDR-TB regimen. Patient receive suboptimal regimen. No benefits. TN: Test result do not suggests modification of a WHO recommended MDR-TB regimen. No additional harms. Patient receive optimal regimen.

CERTAINTY OF THE

EVIDENCE OF TEST

ACCURACY


● Very low ○ Low ○ Moderate ○ High ○ No included studies


Indirectness was considered serious

Inconsistency was considered serious for test sensitivity and not serious for test specificity

Imprecision was considered not serious for sensitivity and specificity

Publication bias – none for all studies.

Quality of evidence for test accuracy is: Sensitivity – very low

quality of evidence Specificity – low quality of evidence

CERTAINTY OF THE

EVIDENCE OF TEST'S

EFFECTS

What is the overall certainty of the evidence for any critical or important direct benefits, adverse effects or burden of the test? ○ Very low

○ Low ○ Moderate ○ High



CERTAINTY OF THE

EVIDENCE OF

MANAGEMENT'S EFFECTS

What is the overall certainty if the evidence of effects of the management that is guided by the test results? ○ Very low ○ Low ○ Moderate

○ High



36 | P a g e

CERTAINTY OF THE

EVIDENCE OF TEST

RESULT/M

ANAGEMENT

How certain is the link between test results and management

decisions? ○ Very low ○ Low ○ Moderate

○ High


The link between test results and management decisions may be uncertain in various settings. In some occasions clinicians use empirical treatment for TB. In others capacity of health system may be insufficient to

provide the patient with necessary treatment.




What is the overall certainty of

the evidence of effects of the test? ○ Very low ○ Low

● Moderate ○ High


This question is intended to summarize previous four questions on the certainty of the evidence.

VALUES



variability

● Probably no important uncertainty

or variability ○ No important uncertainty or



37 | P a g e

BALANCE OF EFFECTS






FN results increase with increasing pre-test probability for FQ resistance. Conventional phenotypic DST should be used in the follow-up evaluation of patients with a negative result especially in settings with a high

pre-test probability for resistance to fluoroquinolones.

RESOURCES REQUIRED



○ Varies

● Don't know



REQUIRED RESOURCES





38 | P a g e

COST EFFECTIVENESS





○ Varies



EQUITY





ACCEPTABILITY




○ Varies

○ Don't know


to perform MTBDRsl exist. If MTBDRsl is implemented for first-line DST the MTBDRsl assay could be performed on the same specimen for rifampicin-resistant TB or MDR-TB cases.

FEASIBILITY





39 | P a g e




Varies Don't know


Varies Don't know


Varies Don't know

UNDESIRABLE


Varies Don't know

CERTAINTY OF THE

EVIDENCE OF TEST

ACCURACY


No included studies

CERTAINTY OF THE

EVIDENCE OF TEST'S

EFFECTS


No included

studies

CERTAINTY OF THE

EVIDENCE OF

MANAGEMENT'S

EFFECTS


No included studies

CERTAINTY OF THE

EVIDENCE OF TEST

RESULT/MANAGEMENT


No included studies

CERTAINTY OF


No included

studies

VALUES

Important


Possibly important




No important


No known

undesirable outcomes

BALANCE OF EFFECTS Favors the comparison



Probably favors the


Varies Don't know

40 | P a g e



intervention

RESOURCES




CERTAINTY OF

EVIDENCE OF

REQUIRED

RESOURCES


No included studies







Varies No included

studies


Probably no impact

Probably increased



Varies Don't know


Varies Don't know

Conclusions


TYPE OF RECOMMENDATION

Strong recommendation against the intervention


the intervention


comparison


intervention


○ ○ ○ ● ○

RECOMMENDATION For patients with confirmed rifampicin-resistant TB or MDR-TB, the WHO guideline development group suggests using indirect testing of cultured

isolates of M.tuberculosis with the MTBDRsl assay as the initial test, over culture and phenotypic DST, to detect resistance to FQ (Conditional recommendation, Very low certainty in the evidence for test accuracy).

JUSTIFICATION

SUBGROUP Accuracy of version 2.0 assay is expected to be no worse than version 1.0 and should have improved sensitivity for detection of resistance for these

41 | P a g e

CONSIDERATIONS drug classes.

IMPLEMENTATION CONSIDERATIONS

Adoption of the MTBDRsl assay does not eliminate the need for conventional culture and DST capability. Despite good specificity of the MTBDRsl for the detection of resistance to FQs, culture and phenotypic DST is required to completely exclude resistance to this drug class. However, the demand for

conventional culture and DST capacity may change, based on the prevalence of resistance to second-line anti-TB drugs in patients with confirmed RR-TB or MDR-TB. The following implementation considerations apply:

• MTBDRsl cannot determine resistance to individual drugs in the class of fluoroquinolones. Phenotypic resistance to ofloxacin and levofloxacin is highly correlated with resistance conferring mutations detected by the MTBDRsl assay. Uncertainty remains about the susceptibility to moxifloxacin and gatifloxacin for such strains with mutations;

• Culture and phenotypic DST plays a critical role in the monitoring of patients’ response to treatment and for detecting additional resistance to second-line drugs during treatment. Patients with false negative resistance results using the MTBDRsl can be identified and captured through

treatment monitoring. Patients with false positive results might benefit from the addition of other drugs; • The availability of additional second-line drugs is critical.



RESEARCH PRIORITIES


• Develop and improved understanding of the correlation between the detection of resistance conferring mutations with phenotypic DST results

and patient outcomes; • Develop improved knowledge of the presence of specific mutations detected with the MTBDRsl assay correlated with MICs for individual drugs

within the class of fluoroquinolones; • Review evidence to confirm or revise different critical concentrations used in phenotypic DST methods; • Determine the limit of detection of MTBDRsl for the detection of heteroresistance; • Determine training, competency, and quality assurance needs; • Gather more evidence on the impact on appropriate MDR-TB treatment initiation and mortality;

• Meet “Standards for Reporting Diagnostic accuracy studies” (STARD) for future studies; • Perform country-specific cost-effectiveness and cost-benefit analyses of MTDDRsl assay use in different programmatic settings.

42 | P a g e

Table 4: Accuracy of MTBDRsl by indirect testing for detection of SLID resistance in patients with rifampicin-resistant or MDR-TB


ADDITIONAL

CONSIDERATIONS

PROBLEM


● Yes ○ Varies ○ Don't know




Additional regions



TEST ACCURACY


○ Inaccurate ○ Accurate

○ Very accurate



Test accuracy MTBDRsl by direct testing for SLID: Sensitivity: 76.5% (95% CI: 63.3% to 86.0%) Specificity: 99.1% (95% CI: 97.3% to 99.7%)

MTBDRsl by direct testing for Amikacin: Sensitivity: 84.9% (95% CI: 79.2% to 89.1%) Specificity: 99.1% (95% CI: 97.6% to 99.6%) MTBDRsl by direct testing for Kanamycin: Sensitivity: 66.9% (95% CI: 44.1% to 83.8%) Specificity: 98.6% (95% CI: 96.1% to 99.5%) MTBDRsl by direct testing for Capreomycin: Sensitivity: 79.5% (95% CI: 58.3% to 91.4%) Specificity: 95.8% (95% CI: 93.4% to 97.3%)

The accuracy varies with the different

SLID. The variability is explained in part by the use of different drugs, critical concentrations, types of culture media in the reference

standard and likely presence of eis resistance-conferring mutations in patients in Eastern European countries.

DESIRABLE

EFFECTS

How substantial are the desirable anticipated effects? ○ Trivial ○ Small ○ Moderate

● Large

The anticipated desirable effect is the correct diagnosis of SLID resistant cases (TP) as well as SLID susceptible cases (TN). MTBDRsl would correctly identify 32 cases out of 50 per 1000 individuals tested if the pre-test probability of TB is 5%. For 10-15% there would be 77 and 115 patients respectively (see table below). Correct identification of SLID resistant cases should lead to higher cure rates, less sequelae to the individual patient, and less transmission in the community.

Desirable anticipated effects per drug: Amikacin – Large desirable effects Capreomycin – Large

desirable effects

43 | P a g e

○ Varies

○ Don't know

Similarly MTBDRsl would correctly identify 941 TB cases susceptible to SLID (TN) out of 950 per 1000 individuals tested if the pre-test probability of TB is 5%. For 10-15% prevalence’s there would be 896 and

846 patients respectively (see table below). Correct identification of SLID susceptible cases should lead to avoiding unnecessary treatment with additional drugs with increased risk of severe adverse events and greater costs.

The anticipated undesirable effect is the incorrect identification of an individual as a SLID susceptible or resistant case (FN or FP).

MTBDRsl would misclassify 12 cases as FN per 1000 individuals tested if the pre-test probability of TB with SLID resistance is 5%, and 23 to 35 cases under pre-test probabilities of 10-15%. Incorrect identification

of an individual as SLID susceptible may have a potential increased risk of patient morbidity and mortality, and continued risk of community transmission of drug-resistant TB as well initiation of an MDR-TB regimen which includes a SLID with doubtful efficacy.MTBDRsl had misclassified 9 cases as FP per 1000 individuals tested if the pre-test probability of TB with re

sistance to SLID is 5%, and 8 cases under pre-test probabilities of 10-15%. Incorrect identification of an individual as SLID resistant may lead to patient anxiety, possible delays in further diagnostic evaluation, prolonged and unnecessary treatment with drugs that may have additional serious adverse effects.

Should MTBDRsl by indirect testing be used to diagnose SLID resistance in patients with RR or MDR TB?

Test result



participants

(studies)

Quality of the


5%

Prevalence

10%

Prevalence

15%

True positives

(patients with SLID resistance )

38 (32 to

43)

77 (63 to

86)

115 (95 to

129)

575

(16)

⨁◯◯◯ VERY LOW

False negatives

(patients incorrectly classified

as not having SLID resistance )

12 (7 to 18) 23 (14 to

37)

35 (21 to

55)

True negatives (patients without SLID resistance )

941 (924 to

947)

892 (876 to

897)

842 (827 to

847)

1346 (16)

⨁⨁◯◯ LOW

False positives 9 (3 to 26) 8 (3 to 24) 8 (3 to 23)

Kanamycin – Large desirable effects

UNDESIRABLE EFFECTS


○ Moderate ○ Small

○ Trivial



Amikacin – Small undesirable effects Capreomycin and kanamycin – moderate undesirable effects

Physicians should be guided by the MTBDRsl assay in their initial choice of an MDR-TB treatment regimen.

Conventional

phenotypic DST should be used in the follow-up evaluation of patients with a negative result especially in settings

with a high pre-test probability for resistance to SLIDs.

44 | P a g e

(patients incorrectly classified as having SLID resistance )

Implications for the detection of SLID conferring mutations among RR-TB persons


Patient receive optimal regimen.

FP: Test result suggests modification of a WHO recommended MDR-TB regimen. Increased risk of serious adverse effects. Patient receive optimal regimen. FN: Test result do not suggests modification of a WHO recommended MDR-TB regimen. Patient receive suboptimal regimen. No benefits. TN: Test result do not suggests modification of a WHO recommended MDR-TB regimen. No additional harms. Patient receive optimal regimen.

CERTAINTY OF THE

EVIDENCE OF TEST

ACCURACY


● Very low ○ Low ○ Moderate ○ High ○ No included studies


Indirectness was considered serious

Inconsistency was considered serious for sensitivity and not serious for specificity

Imprecision was considered not serious for sensitivity and specificity

Publication bias – none for all studies (both direct and indirect testing).

Quality of evidence

for test accuracy is: Sensitivity – very low quality of evidence Specificity – low

quality of evidence

CERTAINTY OF THE

EVIDENCE OF TEST'S

EFFECTS

What is the overall certainty of the evidence for any critical or important direct benefits, adverse effects or burden of the

test? ○ Very low ○ Low ○ Moderate ○ High



CERTAINTY OF

THE EVIDENCE OF

MANAGEMENT'S

EFFECTS

What is the overall certainty if the evidence of effects of the

management that is guided by the test results? ○ Very low ○ Low ○ Moderate


45 | P a g e

○ High


CERTAINTY OF THE

EVIDENCE OF TEST

RESULT/M

ANAGEMENT

How certain is the link between test results and management decisions? ○ Very low

○ Low ○ Moderate

○ High







● Low ○ Moderate ○ High


This question is intended to summarize previous four questions on the certainty of the evidence. Kanamycin and Capreomycin – low certainty


VALUES




variability

○ No known undesirable outcomes


46 | P a g e

BALANCE OF EFFECTS






Desirable (Amikacin, Kanamycin, Capreomycin) - Large, Large, Large

Undesirable (Amikacin, Kanamycin, Capreomycin) - Small, Moderate, Moderate

Concern - FN

Accuracy for

detecting amikacin resistance is better than for capreomycin or kanamycin.

RESOURCES REQUIRED



○ Varies

● Don't know



REQUIRED RESOURCES





47 | P a g e

COST EFFECTIVENESS





○ Varies



EQUITY





ACCEPTABILITY




○ Varies

○ Don't know


to perform MTBDRsl exist. If MTBDRsl is implemented for first-line DST the MTBDRsl assay could be performed on the same culture isolate.

FEASIBILITY





48 | P a g e




Varies Don't know


Varies Don't know


Varies Don't know

UNDESIRABLE


Varies Don't know

CERTAINTY OF THE

EVIDENCE OF TEST

ACCURACY


No included studies

CERTAINTY OF THE

EVIDENCE OF TEST'S

EFFECTS


No included studies

CERTAINTY OF THE

EVIDENCE OF

MANAGEMENT'S

EFFECTS


No included studies

CERTAINTY OF THE

EVIDENCE OF TEST

RESULT/MANAGEMENT


No included studies

CERTAINTY OF


No included studies

VALUES


Possibly important






BALANCE OF EFFECTS Favors the Probably favors Does not favor Probably favors Favors the Varies Don't know

49 | P a g e


comparison the comparison either the intervention or the comparison

the intervention

intervention

RESOURCES




CERTAINTY OF

EVIDENCE OF

REQUIRED

RESOURCES


No included studies







Varies No included

studies


Probably no impact

Probably increased



Varies Don't know


Varies Don't know

Conclusions


TYPE OF

RECOMMENDATION Strong recommendation against the intervention


the intervention


comparison


intervention


○ ○ ○ ● ○

RECOMMENDATION For patients with confirmed rifampicin-resistant TB or MDR-TB, the WHO guideline development group suggests using indirect testing of a culture of M.tuberculosis with the MTBDRsl assay as the initial test, over culture and phenotypic DST, to detect resistance to SLID (Conditional recommendation, Very low certainty in the evidence for test accuracy).

JUSTIFICATION

50 | P a g e

SUBGROUP CONSIDERATIONS

Accuracy of version 2.0 assay is expected to be no worse than version 1.0 and should have improved sensitivity for detection of resistance for these drug classes.

IMPLEMENTATION

CONSIDERATIONS

Adoption of the MTBDRsl assay does not eliminate the need for conventional culture and DST capability. Despite good specificity of the MTBDRsl for the

detection of resistance to SLIDs, culture and phenotypic DST is required to completely exclude resistance to these drug classes. However, the demand for conventional culture and DST capacity may change, based on the prevalence of resistance to second-line anti-TB drugs in patients with confirmed RR-TB or MDR-TB. The following implementation considerations apply:

• Mutations in some regions (e.g., the eis promoter region) may be responsible for causing resistance to one drug in a class more than other drugs within that class. The eis C14T mutation is associated with kanamycin resistance in strains from Eastern Europe;

• Culture and phenotypic DST plays a critical role in the monitoring of patients’ response to treatment and for detecting additional resistance to second-line drugs during treatment. Patients with false negative resistance results using the MTBDRsl can be identified and captured through

treatment monitoring. Patients with false positive results might benefit from the addition of other drugs; • The availability of additional second-line drugs is critical.



RESEARCH PRIORITIES


• Develop and improved understanding of the correlation between the detection of resistance conferring mutations with phenotypic DST results

and patient outcomes; • Develop improved knowledge of the presence of specific mutations detected with the MTBDRsl assay correlated with MICs for individual drugs

within the class of SLIDs; • Review evidence to confirm or revise different critical concentrations used in phenotypic DST methods; • Determine the limit of detection of MTBDRsl for the detection of heteroresistance; • Determine training, competency, and quality assurance needs; • Gather more evidence on the impact on appropriate MDR-TB treatment initiation and mortality;

• Meet “Standards for Reporting Diagnostic accuracy studies” (STARD) for future studies; • Perform country-specific cost-effectiveness and cost-benefit analyses of MTDDRsl assay use in different programmatic settings.

51 | P a g e

Annex 7. Drug concentrations used in culture-based DST for each included study

Table 1. Ofloxacin, levofloxacin, and moxifloxacin, drug concentrations used in culture-based drug susceptibility testing in relation to the WHO-recommended

critical concentrations

Study Reference standard Concentration used

(ug/ml)

Met WHO-recommended

critical concentration

Comments

Ajbani 2012 MGIT 960 Ofloxacin: 2.0 Yes

Moxifloxacin: 0.25 No

Barnard 2012 Middlebrook 7H11 (agar

proportion)

Ofloxacin: 2.0

Yes

Brossier 2010 LJ (agar proportion) Ofloxacin: 2.0

No

Catanzaro 2015 MGIT 960 Ofloxacin: 2.0 Yes


Chikamatsu 2012 Ogawa Levofloxacin: 1.0 Not applicable No WHO- recommended concentration

specified for Ogawa media

Fan 2011 MGIT 960 Ofloxacin: 2.0 Yes


Ferro 2013 Middlebrook 7H10 (agar

proportion)

Moxifloxacin: 2.0 Yes

FIND 2016 MGIT 960 Ofloxacin: 2.0 Yes

Levofloxacin: 1.5 Yes

Moxifloxacin: 0.5 No The WHO- recommended low level

concentration was used

Hillemann 2009 MGIT 960 and LJ Ofloxacin: 2.0 for both

media

Yes for MGIT; no for LJ

Huang 2011 MGIT 960 and Middlebrook 7H11 Ofloxacin: 2.0 Yes for both media

Ignatyeva 2012 MGIT 960 Ofloxacin: 2.0 Yes

52 | P a g e

Jin 2013 LJ and BacT/ALERT 3D Ofloxacin: 5.0 (LJ); 50

(BacT/ALERT 3D)

No for LJ; Not applicable

BacT/ALERT 3D

No WHO- recommended concentration

specified for BacT/ALERT 3D media

Kambli 2015a MGIT 960 Ofloxacin: 2.0 Yes


Kambli 2015b MGIT 960 Levofloxacin: 1.5 Yes

Kiet 2010 LJ Ofloxacin: 2.0 No

Kontsevaya 2011 MGIT 960 Ofloxacin: 2.0 Yes


Kontsevaya 2013 MGIT 960 Ofloxacin: 2.0 Yes


Lacoma 2012 BACTEC 460TB Moxifloxacin: 0.5 Not applicable No WHO- recommended concentration

specified for BACTEC 460 media

Lopez-Roa 2012 MGIT 960 and Middlebrook 7H11 Ofloxacin: 2.0 Yes

Miotto 2012 MGIT 960 Ofloxacin: 2.0 Yes

NICD 2015 MGIT 960 Ofloxacin: 2.0 Yes

Said 2012 Middlebrook 7H11 Ofloxacin: 2.0 Yes

Simons 2015 MGIT 960 and Middlebrook 7H10

(agar dilution)

Moxifloxacin: 0.5 for

MGIT and 1.0 for 7H10

No For moxifloxacin using MGIT, the WHO-

recommended low level concentration was

used

Tagliani 2015 MGIT 960 and LJ (agar proportion) Ofloxacin: 2.0 for MGIT

and 4.0 for LJ

Yes

MGIT 960 Moxifloxacin: 0.5 No The WHO- recommended low level

concentration was used

MGIT 960 Levofloxacin: 1.5 Yes

Tomasicchio

2016

MGIT 960 Ofloxacin: 2.0 Yes

Tukvadze 2014 LJ (proportion method) Ofloxacin: 2.0 No

van Ingen 2010 Middlebrook 7H10 (agar Moxifloxacin: 1.0 No

53 | P a g e

proportion)

Zivanovic 2012 MGIT 960 and LJ agar proportion Ofloxacin: 2.0 for both

media


LJ-Löwenstein-Jensen; MGIT –Mycobacterial growth indicator tube

Reference: WHO, Updated interim critical concentrations for first-line and second-line DST (as of May 2012)

http://www.stoptb.org/wg/gli/assets/documents/Updated%20critical%20concentration%20table_1st%20and%202nd%20line%20drugs.pdf

Table 2. Amikacin, kanamycin, and capreomycin, drug concentrations used in culture-based drug susceptibility testing in relation to the WHO-recommended

critical concentrations

Study Reference standard Concentration used

(ug/ml)

Met WHO-recommended

critical concentration

Comments

Ajbani 2012 MGIT 960 Amikacin: 1.0 Yes

Kanamycin: 2.5 Yes

Capreomycin: 2.5 Yes

Barnard 2012 Middlebrook 7H11 (agar

proportion)

Amikacin: 4.0 Not applicable No WHO- recommended concentration

specified for amikacin using 7H11

Brossier 2010 LJ (agar proportion) Amikacin: 20.0 No

Kanamycin: 20.0 No

Capreomycin: 20.0 No

Catanzaro 2015 MGIT 960 Amikacin: 1.0 Yes

Kanamycin: 2.5 Yes


Chikamatsu 2012 Ogawa Amikacin: unknown Not applicable No WHO- recommended concentration

specified for Ogawa media Kanamycin: unknown Not applicable

Capreomycin: unknown Not applicable

Fan 2011 MGIT 960 Amikacin: 1.0 Yes

Ferro 2013 Middlebrook 7H10 (agar

proportion)

Amikacin: 5.0 No

Kanamycin: 5.0 Yes

FIND 2016 MGIT 960 Amikacin: 1.0 Yes

54 | P a g e

Kanamycin: 2.5 Yes


Hillemann 2009 MGIT 960 and LJ (agar

proportion)

Amikacin: 1.0 for MGIT

and 40.0 for LJ


Capreomycin: 2.5 for

MGIT and 40.0 for LJ

Yes Yes for both types of media

Huang 2011 Middlebrook 7H11 and MGIT 960 Amikacin: 1.0 Yes for MGIT; not applicable

for 7H11

No WHO- recommended concentration

specified for amikacin using 7H11

Kanamycin: 6.0 Yes

Capreomycin: 10.0 Not applicable

Ignatyeva 2012 MGIT 960 Amikacin: 1.0 Yes

Kanamycin: 5.0 No


Jin 2013 LJ and BacT/ALERT 3D Kanamycin: 10.0 Not applicable No WHO- recommended concentrations

specified for BacT/ALERT 3D media Capreomycin: unknown Unknown

Kiet LJ Kanamycin: 20.0 No

Kontsevaya 2013 MGIT 960 Amikacin: 1.0 Yes

Kanamycin: 5.0 No


Lacoma 2012 BACTEC 460TB Kanamycin: 5.0 Not applicable No WHO- recommended concentrations

specified for BACTEC 460 media Capreomycin: 1.25 Not applicable

Lopez-Roa 2012 Middlebrook 7H11 and MGIT 960 Amikacin: 4.0

No

Miotto 2012 MGIT 960 Amikacin: 1.0 Yes

Kanamycin: 5.0 No


NICD 2015 MGIT 960 Amikacin: 1.0 Yes

Kanamycin: 2.5 Yes

55 | P a g e


Said 2012 Middlebrook 7H11 Kanamycin: 5.0 No


Simons 2015 MGIT 960 and Middlebrook 7H10

(agar dilution)


and 5.0 for Middlebrook

7H10

Yes for MGIT; no for 7H10


MGIT and 10.0 for

Middlebrook 7H10

Yes for MGIT; no for 7H10

Tagliani 2015 MGIT 960 and LJ (agar

proportion)


and 30.0 for LJ

Yes for both types of media

Kanamycin: 2.5 for






Tomasicchio

2016

MGIT 960 Amikacin: 1.0 Yes

Tukvadze 2014 LJ Kanamycin: 30.0 Yes


van Ingen 2010 Middlebrook 7H10 (agar

proportion)

Amikacin: 5.0 No


Zivanovic 2012 MGIT 960 and LJ agar proportion Amikacin: 1.0 for MGIT

and 40.0 for LJ





LJ-Löwenstein-Jensen; MGIT –Mycobacterial growth indicator tube

Reference: WHO, Updated interim critical concentrations for first-line and second-line DST (as of May 2012)

http://www.stoptb.org/wg/gli/assets/documents/Updated%20critical%20concentration%20table_1st%20and%202nd%20line%20drugs.pdf

56 | P a g e

Annex 8. References to studies excluded from the review of the diagnostic accuracy of MTBDRsl assay

1. Aubry A, Sougakoff W, Bodzongo P, Delcroix G, Armand S, Millot G, et al. First evaluation of drug-resistant Mycobacterium tuberculosis clinical isolates from

Congo revealed misdetection of fluoroquinolone resistance by line probe assay due to a double substitution T80A-A90G in GyrA. PLoS One. 2014;9(4):e95083.

Reason for exclusion: No cases with second-line resistance

2. Babamahmoodi F, Mahdavi MR, Jalali H, Talebi B, Roshan P, Mahdavi M. Evaluation of gene mutations involved in drug resistance in mycobacterium

tuberculosis strains derived from tuberculosis patients in Mazandaran, Iran, 2013. Int J Mol Cell Med. 2014 Summer;3(3):190-5. Reason for exclusion: not a

diagnostic accuracy study

3. Bantouna V, Kontos F, Gitti Z, Spandidos DA. Evaluation of the new GenoType MTBDRs1 (R) assay for rapid detection of resistance in Mycobacterium

tuberculosis isolates at a low-incidence community. In: International Journal of Molecular Medicine. Vol. 28. 2011:S76. Reason for exclusion: Conference abstract

4. Bergvala L, Sengstakea S, Bachyiska E, Brankova N, Tankova K, Levterova V, et al. Evaluation of a new molecular test for the identification of drug resistance in

Mycobacterium tuberculosis clinical isolates. Problems of Infectious and Parasitic Diseases 2010;38(2):27-30. Reason for exclusion: Technical study, not a

diagnostic accuracy study

5. Brossier F, Veziris N, Aubry A, Jarlier V, Sougakoff W. Detection by genotype MTBDRsl test of complex resistance mechanisms to second-line drugs and

ethambutol in multidrug-resistant strains of Mycobacterium tuberculosis. Clinical Microbiology and Infection. 2010 April;Conference: 20th ECCMID Vienna Austria.

Conference Start: 20100410 Conference End: 20100413. Conference Publication: (var.pagings). 16:S53-S4. Reason for exclusion: Conference abstract

6. Choi JH, Lee KW, Kang HR, Hwang YI, Jang S, Kim DG, et al. Clinical efficacy of direct DNA sequencing analysis on sputum specimens for early detection of drug-

resistant Mycobacterium tuberculosis in a clinical setting. Chest 2010;137(2):393-400. Reason for exclusion: not a diagnostic accuracy study

7. Fallico L, Peracchi M, Khalil S, Rassu M, Pascarella M, Manganelli R, et al. Molecular epidemiology and prevalence of mutations in Mycobacterium tuberculosis

strains from an Italian northeastern area. In: Clinical Microbiology and Infection. Vol. 18. 2012:550. Reason for exclusion: Conference abstract

57 | P a g e

8. Felkel M, Exner R, Schleucher R, Lay H, Autenrieth I, Kempf VA, et al. Evaluation Of Mycobacterium tuberculosis drug susceptibility in clinical specimens from

Nigeria using Genotype MTBDRplus and MTBDRsl assays. European Journal of Microbiology and Immunology 2013;3(4):252-7. Reason for exclusion: Technical. No

diagnostic data for FLUOROQUINOLONESs, SLIDs or XDR-TB

9. Festoso I, Mantegani P, Miotto P, Cabibbe AM, Valente I, Borroni E, et al. Clinical evaluation of the GenoType MTBDRsl for the rapid diagnosis of second-line

resistance in Mycobacterium tuberculosis. In: Clinical Microbiology and Infection. Vol. 17. 2011:S592. Reason for exclusion: Conference abstract

10. Gkaravela L, Foka A, Athanassiou M, Lazarou N, Kontos F, Mollaki V, et al. The genetic diversity of Mycobacterium tuberculosis complex in Azerbaijan by 24

MIRU-VNTR loci genotyping in association with susceptibility testing by conventional and molecular methods. In: Clinical Microbiology and Infection. Vol. 18.

2012:829. Reason for exclusion: Conference abstract

11. Gomgnimbou MK, Klotoe BJ, Molina B, Dominguez J, Refrégier G, Sola C. An "all-in-one" solution for simultaneous spoligotyping and drug resistance gene

analysis of Mycobacterium tuberculosis: TB-SPRINT and TB-SPRINTplus. International Journal of Mycobacteriology. 2015. Reason for exclusion: not a diagnostic

accuracy study; no reference standard

12. Iem V, Somphavong S, Buisson Y, Steenkeste N, Breysse F, Chomarat M, et al. Resistance of Mycobacterium tuberculosis to antibiotics in Lao PDR: first

multicentric study conducted in 3 hospitals. BMC Infectious Diseases 2013;13:275. Reason for exclusion: Technical. Only one case of second-line resistance

13. Jang E, Hwang S, Ryoo S. Practical value of the Genotype MTBDRsl assay for XDR testing of Mycobacterium tuberculosis from clinical isolates. In: American

Journal of Respiratory and Critical Care Medicine. Conference: American Thoracic Society International Conference, ATS. Vol. 183. 2011. Reason for exclusion:

Conference abstract

14. Karabela S, Nikolaou S, Kouseris I, Makrigiannis N, Kanavaki S. Extensively drug-resistant tuberculosis (XDR TB) in Athens. In: International Journal of

Antimicrobial Agents. Vol. 29 (Suppl 2). 2007:S574. Reason for exclusion: Conference abstract

15. Kaswa MK, Aloni M, Nkuku L, Bakoko B, Lebeke R, Nzita A, et al. Pseudo-outbreak of pre-extensively drug-resistant (Pre-XDR) tuberculosis in Kinshasa:

collateral damage caused by false detection of fluoroquinolone resistance by GenoType MTBDRsl. J Clin Microbiol. 2014 Aug;52(8):2876-80. Reason for exclusion:

not a diagnostic accuracy study

58 | P a g e

16. Kontos F, Zande M, Mavromanolakis D, Bazigos S, Manidaki A, Gitti Z. Evaluation of the new GenoType MTBDRsl assay for rapid detection of resistance in

Mycobacterium tuberculosis isolates in a low-incidence community. In: Clinical Microbiology and Infection. Vol. 17. 2011:S587. Reason for exclusion: Conference

abstract

17. Kontos F, Bobola M, Mollaki V, Karonis T, Souli M, Dimopoulos G, et al. Tuberculosis: molecular susceptibility testing reveals mixed infections with three strains.

In: Clinical Microbiology and Infection. Vol. 18. 2012:553-4. Reason for exclusion: Conference abstract

18. Lacoma A, Molina-Moya B, Prat C, Pimkina E, Diaz J, Dudnyk A, et al. Pyrosequencing for rapid detection of Mycobacterium tuberculosis second-line drugs and

ethambutol resistance. Diagnostic microbiology and infectious disease. 2015;83(3):263-9 Reason for exclusion: not a diagnostic accuracy study

19. Lemus D, Alvarez Y, Díaz R, Valdés I, Echemendía M, Martin A, et al. Molecular confirmation of resistance to first- and second-line antituberculosis drugs using

GenoType MTBDRplus and GenoType MTBDRsl assays. In: Clinical Microbiology and Infection. Vol. 17. 2011:S729. Reason for exclusion:

20. López Roa P, Ruiz-Serrano MJ, García-Escribano N, García de Viedma D, Bouza E. Rapid testing of susceptibility of multidrug-resistant Mycobacterium

tuberculosis (MDRTB) to second-line drugs using GenoType MTBDRsl. In: Abstracts of the Interscience Conference on Antimicrobial Agents and Chemotherapy. Vol.

50. 2010. Reason for exclusion: Conference abstract

21. Mindru R, Spînu V, Popa C, Botezatu E, Spătaru R.. [Conventional and molecular diagnosis on a group of patients with TB-DR]. Pneumologia (Bucharest,

Romania) 2013;63(3):168-73. Reason for exclusion: Data insufficient for 2x2 tables

22. Molina-Moya B, Lacoma A, Prat C, Diaz J, Dudnyk A, Haba L, et al. AID TB resistance line probe assay for rapid detection of resistant Mycobacterium

tuberculosis in clinical samples. Journal of Infection. 2015;70(4):400-8. Reason for exclusion: Test other than MTBDRsl

23. Niehaus AJ, Mlisana K, Gandhi NR, Mathema B, Brust JC. High Prevalence of inhA Promoter Mutations among Patients with Drug-Resistant Tuberculosis in

KwaZulu-Natal, South Africa. PLoS One. 2015;10(9):e0135003. Reason for exclusion: not a diagnostic accuracy study

24. Ouassa T, Loukou YG, Dotia A, Faye-Kette H. Molecular characterization of the resistance of Mycobacterium tuberculosis to second line drugs in Cote d'ivoire.

Tropical Journal of Pharmaceutical Research. 2014 May;13 (5):727-30. Reason for exclusion: not a diagnostic accuracy study (no reference standard)

59 | P a g e

25. Singh AK, Maurya AK, Kant S, Umrao J, Kushwaha RA, Nag VL, et al. Rapid detection of drug resistance and mutational patterns of extensively drug-resistant

strains by a novel GenoType® MTBDRsl assay. Journal of Postgraduate Medicine 2013;59(3):179-85. Reason for exclusion: Technical. No information on resistance

to the pre-specified FLUOROQUINOLONESs and no cases susceptible to the SLIDs

26. Tessema B, Beer J, Emmrich F, Sack U, Rodloff AC. Analysis of gene mutations associated with isoniazid, rifampicin and ethambutol resistance among

Mycobacterium tuberculosis isolates from Ethiopia. BMC Infectious Diseases 2012;12:37. Reason for exclusion: Technical. No information on resistance to

FLUOROQUINOLONESs, SLIDs or XDR-TB.

27. Tessema B, Beer J, Emmrich F, Sack U, Rodloff AC. First- and second-line anti-tuberculosis drug resistance in Northwest Ethiopia. International Journal of

Tuberculosis and Lung Disease 2012;16(6):805–11. Reason for exclusion: Technical. No information on resistance to FLUOROQUINOLONESs, SLIDs or XDR-TB

28. Totten S, May R, Heifets LB. Comparative study of two diagnostic tools for the rapid detection of Mycobacterium tuberculosis complex from smear positive

respiratory specimens. In: American Journal of Respiratory and Critical Care Medicine. Conference: American Thoracic Society International Conference, ATS. Vol.

183. 2011:A4889 Reason for exclusion: Conference abstract

29. Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, et al. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug

susceptibility and resistance: a retrospective cohort study. Lancet Infect Dis. 2015 Jun 23. Reason for exclusion: not a diagnostic accuracy study

30. Wedajo W, Schon T, Bedru A, Kiros T, Hailu E, Mebrahtu T, et al. A 24-well plate assay for simultaneous testing of first and second line drugs against

Mycobacterium tuberculosis in a high endemic setting. BMC Res Notes. 2014;7:512. Reason for exclusion: not a diagnostic accuracy study, insufficient data for 2x2

table

31. Zhang L, Duo L, Lu X, Xie Y, Song X, Kang M, et al. Molecular epidemiology of multidrug-resistant (MDR) Mycobacterium tuberculosis revealed by GenoType

MTBDR assays in southern China. In: Clinical Microbiology and Infection. Vol. 17. 2011:S599-600. Reason for exclusion: Conference abstract

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