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Line Probe Assay LPA first line second line tuberculosis RIF INH gyrA rrs interpretation India NTEP
Here is a full explanation of this report:
TB Diagnostic Report - Explained
This is a standardized TB laboratory reporting form used under India's National TB Elimination Program (NTEP). It covers three types of tests performed in a cascade manner. Here is what each section means:
1. CBNAAT (Cartridge-Based Nucleic Acid Amplification Test)
Also called GeneXpert MTB/RIF, this is the front-line rapid molecular test.
- Sample A/B: Identifies which sputum sample was tested.
- M. Tuberculosis: Whether TB bacteria were detected or not detected in the sample.
- Rif Resistance Test: Whether the bacteria show resistance to Rifampicin (RIF) - the most important first-line TB drug. Options are: Detected / Not Detected / Indeterminate / N/A.
- A result of "Detected" for both MTB and Rif Resistance = RR-TB (Rifampicin-Resistant TB), which triggers further testing.
2. Culture (LJ / LC)
- LJ = Lowenstein-Jensen solid medium; LC = Liquid Culture (MGIT system).
- Grows actual TB bacteria from the sample - slower but more definitive.
- Results: Negative / Positive, or identifies NTM (Non-Tuberculous Mycobacteria - other species that are NOT M. tuberculosis).
- Contamination is also reported here.
3. Line Probe Assay (LPA) - Lab Serial 2577
This is the most detailed section. LPA is a molecular test that detects specific genetic mutations causing drug resistance. It is done in two levels:
First Line LPA (GenoType MTBDRplus)
Detects resistance to Rifampicin (RIF) and Isoniazid (INH) - the two most important first-line drugs.
RpoB gene (Rifampicin resistance):
- WT (Wild Type) bands 1-8: Normal (sensitive) gene sequences. If a WT band is absent, that region is mutated = resistant.
- MUT (Mutation) bands: Specific known resistance mutations. If a MUT band is present, confirmed resistance.
- WT1-WT8 cover codons in the rifampicin resistance-determining region (RRDR) of the rpoB gene.
- On this report: Most WTs are marked present (normal) with some MUT bands checked.
KatG gene (High-level INH resistance):
- KatG WT (315): If absent = resistance. MUT1 (S315T1/T2): If present = resistance.
- KatG315 mutation causes ~50-80% of high-level INH resistance globally.
InhA gene (Low-level INH resistance, also ethambutol):
- InhA WT bands and MUT bands covering the promoter region.
- Mutations here cause low-level INH resistance and are also associated with ethionamide resistance.
Second Line LPA (GenoType MTBDRsl) - Lab Serial 2577
Done when MDR-TB is confirmed. Detects resistance to fluoroquinolones and injectable agents.
| Gene | Drug Class Tested | Notes |
|---|---|---|
| gyrA | Fluoroquinolones (moxifloxacin, levofloxacin, ofloxacin) | WT1(85-90), WT2(89-93), WT3(90-97) cover QRDR; MUT1(A90V), MUT2(S91P), MUT3 variants = FQ resistance |
| gyrB | Fluoroquinolones | WT1(536-541); MUT1(N538D), MUT2(E540V) |
| rrs | Aminoglycosides - amikacin, kanamycin, capreomycin | WT1(1401-02); MUT1(A1401G) = high-level resistance to all three |
| eis | Kanamycin (low-level) | WT1(37), WT2(14,12,10), WT3(2); MUT1(C-14T) |
4. Final LPA Interpretation (filled in)
This is the key result:
| Parameter | Result | Meaning |
|---|---|---|
| MTB Result | MTB Positive | TB confirmed |
| RIF | Inferred (resistance) | Rifampicin resistant - based on mutation pattern |
| INH | High-level resistant | High-level Isoniazid resistance (likely KatG315 mutation) |
| Quinolone (SLID) | Indeterminate | Fluoroquinolone/injectable result unclear |
| Date Result | 7/5/2026 | Reported on 7 May 2026 |
| Reported by | Dr. Shraddhā Dāki (+ signature) | TB-C DST Laboratory, GGMC & Sir J.J. Hospital, Mumbai - 400 008 |
5. Drug Susceptibility Test (DST) Results
This section (blank here) would show phenotypic (culture-based) susceptibility to a full panel of drugs:
- 1st line drugs: R (Rifampicin), H (INH), Z (Pyrazinamide), E (Ethambutol), S (Streptomycin)
- SLI (Second-line injectables): Km (Kanamycin), Cm (Capreomycin), Am (Amikacin)
- FQ (Fluoroquinolones): Lfx (Levofloxacin), Mfx (Moxifloxacin at 0.5 and 2 mcg)
- Other drugs: Eto (Ethionamide), PAS, Lzd (Linezolid), Cfz (Clofazimine), Clr (Clarithromycin), Azi (Azithromycin)
This section is marked "Not done" on this form.
Clinical Summary
This patient has confirmed MDR-TB (Multidrug-Resistant TB), meaning resistance to both Rifampicin AND high-level Isoniazid. The fluoroquinolone/injectable result is indeterminate, which means a definitive classification as pre-XDR-TB cannot be made yet. The sample was processed at GGMC & Sir J.J. Hospital Mumbai, a designated NTEP DST laboratory.
Under NTEP guidelines, this patient would be referred for an all-oral longer MDR-TB regimen (likely containing bedaquiline, linezolid, and clofazimine), with repeat phenotypic DST recommended if the indeterminate result cannot be resolved.
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