What this test measures
GeneXpert MTB/RIF (and the newer Ultra version) is a fully automated cartridge-based real-time PCR test that detects Mycobacterium tuberculosis DNA in sputum (or other body fluids) and identifies the most common rifampicin-resistance mutations in the rpoB gene. The entire process — sample loading, DNA extraction, amplification and result — happens inside a single cartridge in about 2 hours.
The Xpert MTB/RIF Ultra version has higher sensitivity than the original Xpert MTB/RIF, especially in smear-negative and paediatric TB, and is now the WHO-preferred molecular front-line test.
Why it matters
CBNAAT (the Indian programmatic name for GeneXpert) is the single most important diagnostic advance in India's TB programme over the past decade. It allows same-day diagnosis of TB and rifampicin resistance at thousands of sites across the country, dramatically shortening the time from suspicion to appropriate treatment. NTEP has deployed CBNAAT widely, and it is now the recommended initial test for all presumptive TB cases, especially:
- People living with HIV (TB is the leading cause of death). - Pediatric TB suspects (where AFB smear is often negative). - Extra-pulmonary TB (CSF, lymph node, pleural fluid). - Retreatment and follow-up cases.
Same-day rifampicin resistance detection means a patient with MDR-TB can start the right regimen days to weeks earlier than with culture-based methods — saving lives and reducing transmission.
How to prepare
Sputum: collect a deep early-morning sample (5–10 mL). Other accepted samples include bronchoalveolar lavage, pleural fluid, CSF, lymph node aspirate, gastric aspirate (children), and tissue homogenates. Avoid eating, drinking or brushing teeth for 1 hour before sputum collection. The sample should reach the lab within 24 hours, refrigerated.
Markers & reference ranges
Reference ranges below are typical adult values. Your lab's reported range may differ slightly based on the assay platform and patient demographics — always read your report against the range printed on it.
| Marker | Normal range | If low | If high |
|---|---|---|---|
| M. tuberculosis (MTB) (—)[1][2] | Not detected | — | Detected — confirms TB. The result also reports a semi-quantitative load (very low, low, medium, high). High loads correlate with smear-positive disease and higher infectiousness. |
| Rifampicin Resistance (—) | Not detected | — | Detected — rifampicin resistance is present. Treat as MDR-TB; refer to PMDT immediately for full second-line workup. Indeterminate results occur with very low DNA loads — repeat the test or use phenotypic DST. |
CBNAAT vs other front-line TB tests
| Feature | AFB smear | CBNAAT (this test) | MGIT culture |
|---|---|---|---|
| Time to result | 24 h | 2 h | 1–3 weeks |
| Sensitivity (pulmonary TB) | 50–60% | 85–90% | 85–95% |
| Detects rifampicin resistance | No | Yes | Yes (after DST) |
| Use in paediatric TB | Limited | Strong recommendation | Yes |
| Cost (per test) | Lowest | Moderate | Higher |
Frequently asked questions
What does CBNAAT stand for?
Cartridge-Based Nucleic Acid Amplification Test. It is the Indian programmatic name for the GeneXpert MTB/RIF (or Ultra) test — a fully automated PCR that detects TB DNA and rifampicin resistance in 2 hours.
How accurate is CBNAAT?
Very accurate. Sensitivity for pulmonary TB is 85–90% (higher with Ultra in smear-negative cases). Specificity is >98%. Rifampicin resistance detection is >95% accurate.
How is CBNAAT different from culture?
CBNAAT detects DNA — dead or alive. Culture grows a viable organism, which is needed for full drug susceptibility testing. They are complementary, not interchangeable.
Why does WHO prefer Ultra over the original Xpert?
Ultra has higher sensitivity for paucibacillary TB (paediatric, HIV, extra-pulmonary) and clearer rifampicin resistance reporting. NTEP is progressively transitioning to Ultra.
Can CBNAAT be done on samples other than sputum?
Yes — bronchoalveolar lavage, pleural fluid, CSF, lymph node aspirate, gastric aspirate (in children), and tissue homogenates. Performance varies by sample type.
Is CBNAAT available free under NTEP?
Yes — for diagnostic use under NTEP, CBNAAT is free of charge at designated centres. Private testing is also widely available.
What if my CBNAAT is "trace" or "very low"?
Ultra reports "trace" for the lowest detection level. In some clinical contexts (e.g. previously treated patients), trace results need careful clinical correlation. Your TB specialist will interpret.
Related Tuberculosis / Mycobacterial tests
Tests commonly ordered alongside GENEXPERT, or that help interpret an unexpected result.
Sources & references
- WHO — Use of Xpert MTB/RIF Ultra for TB Diagnosis · accessed 2026-05-30T00:00:00.000Z
- NTEP CBNAAT Operational Guidelines · accessed 2026-05-30T00:00:00.000Z
- CDC — TB Laboratory Diagnostics · accessed 2026-05-30T00:00:00.000Z
- India TB Report 2024 · accessed 2026-05-30T00:00:00.000Z
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