What this test measures
The second-line LPA (e.g. Hain GenoType MTBDRsl) detects M. tuberculosis DNA and key resistance mutations to fluoroquinolones (gyrA, gyrB) and injectables (rrs, eis promoter). Some platforms also detect ethambutol resistance (embB).
The related WHO-endorsed Xpert MTB/XDR cartridge extends this to additionally cover isoniazid (katG, inhA, fabG1, oxyR-ahpC) and amikacin/kanamycin/capreomycin resistance, all in a 90-minute automated workflow.
Together these molecular tests give rapid identification of pre-XDR and XDR-TB resistance patterns — critical because XDR-TB regimens differ markedly from MDR-TB regimens.
Why it matters
NTEP's drug-resistance algorithm in MDR-TB cases moves to second-line LPA / Xpert MTB/XDR as soon as rifampicin resistance is confirmed. Detecting fluoroquinolone or injectable resistance within days (versus weeks for phenotypic DST) allows:
- Earlier individualisation of MDR-TB regimens. - Earlier detection of pre-XDR / XDR-TB so that bedaquiline + linezolid + pretomanid regimens are started without delay. - Better outcomes and lower transmission of highly resistant strains.
This matters particularly in Mumbai, where MDR and pre-XDR TB rates are higher than the national average due to historical incomplete treatment cycles.
How to prepare
Smear-positive sputum or a positive M. tuberculosis culture is required. Inform the lab of any second-line TB drug already taken.
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 |
|---|---|---|---|
| Fluoroquinolone resistance (gyrA / gyrB) (—)[1] | Wild-type — sensitive | — | Mutation detected — fluoroquinolone resistance. High-confidence mutations (e.g. D94G) confer high-level resistance; low-confidence mutations (e.g. A90V) may retain susceptibility at high-dose moxifloxacin. Triggers pre-XDR / XDR pathway when combined with MDR. |
| Injectable resistance (rrs / eis promoter) (—)[1] | Wild-type — sensitive | — | Mutation detected — resistance to amikacin / kanamycin / capreomycin. The specific gene mutation predicts the drug pattern. Triggers pre-XDR / XDR pathway when combined with MDR. |
TB resistance categories and corresponding tests
| Category | Definition | Detected by |
|---|---|---|
| Drug-sensitive | Sensitive to all 1st-line | CBNAAT, LPA 1st-line |
| MDR | Resistant to H + R | CBNAAT + LPA 1st-line |
| Pre-XDR (FQ) | MDR + fluoroquinolone resistance | LPA 2nd-line / Xpert MTB/XDR |
| Pre-XDR (injectable) | MDR + injectable resistance | LPA 2nd-line / Xpert MTB/XDR |
| XDR | MDR + FQ + linezolid or bedaquiline | Phenotypic DST + Xpert MTB/XDR |
Frequently asked questions
When is the second-line LPA done?
As soon as rifampicin resistance is confirmed on CBNAAT or LPA first-line, the isolate is reflexed to second-line LPA to identify pre-XDR or XDR-TB rapidly.
What if fluoroquinolone resistance is detected?
The regimen avoids levofloxacin / moxifloxacin and shifts to a bedaquiline + linezolid + pretomanid backbone (with or without delamanid), guided by your TB specialist.
Does it detect bedaquiline or linezolid resistance?
Not directly. Second-line LPA covers fluoroquinolones and injectables. Bedaquiline and linezolid resistance is assessed by phenotypic DST and (where available) sequencing of Rv0678, atpE (bedaquiline) and rrl, rplC (linezolid).
How long does the test take?
About 1–2 days from a smear-positive sample. From smear-negative cases, the bacteria need to be cultured first.
Is the test available under NTEP?
Yes — at NTEP intermediate and national reference labs, and increasingly through the new Xpert MTB/XDR cartridge. Private NABL-accredited labs also offer it.
Why is rapid second-line resistance detection so important?
Without it, an MDR-TB patient may be started on a fluoroquinolone-based regimen that will fail because they actually have pre-XDR or XDR-TB. Phenotypic DST takes weeks; the LPA / Xpert MTB/XDR gives the same information in 1–2 days.
Should phenotypic DST still be done?
Yes — for confirmation and to test drugs the molecular test does not cover. LPA and phenotypic DST are complementary.
Related Tuberculosis / Mycobacterial tests
Tests commonly ordered alongside TB XDR SCREEN (LPA), or that help interpret an unexpected result.
Sources & references
- WHO — Line Probe Assays for second-line TB drugs · accessed 2026-05-30T00:00:00.000Z
- NTEP LPA Operational Guidelines · accessed 2026-05-30T00:00:00.000Z
- India TB Report 2024 · accessed 2026-05-30T00:00:00.000Z
- CDC — TB Laboratory Diagnostics · accessed 2026-05-30T00:00:00.000Z
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