What is the algorithm for an indeterminate rifampicin (RIF) resistance result from a GeneXpert (Xpert MTB/RIF) test?

Management Algorithm for Indeterminate Rifampicin Resistance on GeneXpert

When GeneXpert returns an indeterminate rifampicin resistance result, immediately repeat the GeneXpert test on a new specimen and simultaneously send samples for phenotypic drug susceptibility testing (DST) via liquid culture, while initiating standard first-line TB treatment pending confirmatory results. 1, 2

Immediate Actions Upon Receiving Indeterminate Result

Step 1: Repeat Testing

• Collect a new sputum specimen and repeat GeneXpert testing immediately 2, 3
• The indeterminate result may indicate uncommon rpoB mutations within the rifampicin-resistance determining region, which increases the post-test probability of rifampicin resistance to an unknown extent 4
• Simultaneously send specimens for liquid culture and phenotypic DST, as molecular results must always be confirmed by culture-based methods 1, 2

Step 2: Assess Bacillary Load

• Check the semi-quantitative bacillary load from the initial GeneXpert result 3
• Very low bacillary load ("trace" or "very low") is strongly associated with false-positive rifampicin resistance results (adjusted OR 63.6), making indeterminate results more likely to represent technical issues rather than true resistance 3
• If the initial test showed very low bacillary load, the indeterminate result is more likely a technical artifact 3

Treatment Decisions While Awaiting Confirmatory Results

If Repeat GeneXpert Shows Rifampicin Susceptible:

• Start standard first-line therapy (rifampicin, isoniazid, pyrazinamide, ethambutol) and monitor closely 1, 2
• Continue treatment until phenotypic DST confirms susceptibility 1
• Perform baseline culture and additional GeneXpert testing during treatment monitoring 3

If Repeat GeneXpert Shows Rifampicin Resistant:

• Do NOT start MDR-TB treatment until rifampicin resistance is confirmed on phenotypic DST 3
• Begin standard first-line therapy with close monitoring, as 47% of initial rifampicin-resistant GeneXpert results may be false positives, particularly with low bacillary loads 3
• Add ethambutol at 15 mg/kg as a fourth drug for additional protection 1

If Repeat GeneXpert Remains Indeterminate:

• Treat as rifampicin-susceptible TB with standard four-drug therapy while awaiting phenotypic DST 1, 2
• The sensitivity and specificity of GeneXpert for rifampicin resistance are both >97% when results are definitive, but indeterminate results fall outside this performance range 1
• Indeterminate results on repeat testing suggest uncommon mutations (such as at codon 432, Lys446Gln, or Pro439Leu) that may or may not confer true resistance 4

Risk Stratification for Drug Resistance

Assess the patient's pretest probability of rifampicin resistance to guide clinical decision-making while awaiting confirmatory results 1:

• High-risk patients (previous TB treatment, born in/lived ≥1 year in country with MDR-TB prevalence ≥2%, contact of MDR-TB patient, HIV-infected) warrant more aggressive monitoring 1
• However, high pretest probability does NOT decrease the odds of false rifampicin resistance results (adjusted OR 6.0 for new patients vs. retreatment cases), so confirmation remains essential 3

Critical Pitfalls to Avoid

Do Not Start MDR-TB Treatment Based on Single Indeterminate Result

• Starting MDR-TB treatment without confirmation can cause unnecessary toxicity and is not recommended 1, 3
• Only 53% of initial rifampicin-resistant GeneXpert results are confirmed as true resistance after comprehensive testing 3
• False-positive rifampicin resistance results are particularly common (86%) when bacillary load is very low 3

Do Not Ignore Mixed Infections

• Mixed infections with both drug-sensitive and drug-resistant strains occur in 10% of cases and are associated with false-negative GeneXpert results for rifampicin resistance 5
• GeneXpert fails to detect rifampicin resistance when <90% of organisms in the sample are resistant 5
• False-negative results are strongly associated with poor clinical outcomes (adjusted OR 6.6) 5

Do Not Rely Solely on Molecular Testing

• Rapid molecular DST is an adjunct, not a replacement for culture-based DST 1
• All molecular results require phenotypic confirmation, as GeneXpert only evaluates rifampicin (and occasionally isoniazid) susceptibility 1
• Quality-assured phenotypic DST confirmation is mandatory for all molecular results 2

Monitoring During Treatment

• Perform monthly sputum smear and culture while awaiting final DST results 1
• If sputum remains positive at 2 months, repeat molecular testing and comprehensive DST 1
• Assess clinical response objectively (weight, inflammatory markers, repeat imaging) 1

When Phenotypic DST Results Return

If Confirmed Rifampicin Susceptible:

• Continue standard 6-month regimen (2 months HRZE, then 4 months HR) 1

If Confirmed Rifampicin Resistant:

• Refer immediately to a physician with substantial experience in managing drug-resistant TB 1
• Rifampicin resistance is a marker for MDR-TB in approximately 90% of cases 1
• Treatment requires individualized regimens with minimum 5 effective drugs for at least 20 months, or 9-11 months if eligible for shorter MDR-TB regimen 1