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Rapid Diagnosis of MDR-TB and XDR-TB

1. Definitions (Essential Foundation)

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2. Why Rapid Diagnosis?

• Increase transmission to contacts
• Allow amplification of resistance (progression from MDR → Pre-XDR → XDR)
• Delay appropriate treatment initiation
• Worsen mortality (XDR-TB: 98% mortality in HIV co-infected patients in early South African cohorts)

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3. Rapid Diagnostic Methods

A. Nucleic Acid Amplification Tests (NAAT) - PRIMARY RAPID TOOLS

i. Xpert MTB/RIF (CBNAAT)

• Fully automated real-time PCR platform (GeneXpert)
• Detects M. tuberculosis complex AND rifampicin resistance simultaneously
• Turn-around time: <2 hours
• Sensitivity for pulmonary TB: 85% overall (98% smear-positive, ~70% smear-negative)
• Sensitivity for RIF resistance: 96%; Specificity: 98%
• Minimal biosafety requirements; battery-operated versions available for peripheral settings
• WHO-recommended first-line diagnostic test for all adults and children with signs/symptoms of TB
• Preferred initial test for PLHIV

ii. Xpert MTB/RIF Ultra (Ultra)

• Next-generation cartridge on same GeneXpert platform
• Overall sensitivity: 90% (including trace calls); without trace calls: 86%
• Largest gains: smear-negative culture-positive cases (+17%), PLHIV (+12%)
• Specificity slightly lower (2%) due to detection of DNA from non-viable bacilli
• RIF resistance: sensitivity 94%, specificity 99%
• Extrapulmonary TB: sensitivity varies - pleural fluid 71%, synovial fluid 97%, lymph node biopsy 100%
• "Trace calls" in high-risk groups (children, PLHIV, extrapulmonary TB) should be treated as true positives

iii. CBNAAT M.tb/XDR Test (NEW - NTEP 2024)

• Introduced by NTEG in August 2024 under NTEP
• Detects resistance to H, fluoroquinolones (FQ), second-line injectables (SLI), and ethionamide (Eto) simultaneously
• Used at C&DST laboratories equipped with the technology
• Key addition enabling rapid molecular detection of XDR-TB pattern

iv. Truenat MTB / MTB Plus / MTB-RifDx

• Battery-operated chip-based PCR tests - portable, used at peripheral settings
• Truenat MTB: sensitivity 73%, specificity 98%
• Truenat MTB Plus: sensitivity 80%, specificity 96%
• Truenat MTB-RifDx: detects rifampicin resistance; sensitivity 84%, specificity 97%
• Can replace smear microscopy at primary care level

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B. Line Probe Assays (LPA) - MOLECULAR DST

i. First-Line LPA (FL-LPA)

• Detects mutations in rpoB (rifampicin resistance), katG and inhA (isoniazid resistance)
• Applicable to smear-positive specimens or culture isolates
• Clinical interpretation:
  • katG mutation = associated with high-level isoniazid resistance (KatG-Hh resistance)
  • inhA mutation = associated with low-level isoniazid resistance AND ethionamide (Eto) resistance
• WHO-recommended for detecting H and R resistance when smear-positive specimens or cultured isolate available

ii. Second-Line LPA (SL-LPA)

• Detects mutations associated with fluoroquinolone resistance (gyrA, gyrB) and second-line injectable resistance (rrs, eis)
• Applied as initial test when RR-TB or MDR-TB is confirmed by FL-LPA/NAAT
• Guides classification as Pre-XDR-TB or XDR-TB
• WHO recommends SL-LPA as initial rapid test for resistance to fluoroquinolones and second-line injectables

1. All presumptive TB → NAAT for MTB/RIF (Xpert or Truenat)
2. If M.tb detected → NAAT for H and FQ resistance (where available) OR FL-LPA for H resistance
3. If H/R resistance found → SL-LPA for FQ and SLI resistance detection
4. If discordance between NAAT and LPA → Repeat NAAT at C&DST lab; use "best of three" rule (2/3 concordant = final result)

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C. Other Molecular Platforms (High-Throughput / Reference Labs)

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D. Targeted Next-Generation Sequencing (tNGS)

• WHO-recommended to detect drug resistance after TB diagnosis to guide treatment decisions
• Directly from sputum specimens - no culture required (unlike WGS)
• Provides comprehensive resistance profile including drugs for which LPA/DST is not routinely available
• Particularly useful for patients requiring comprehensive DST
• Faster results than conventional phenotypic culture-based DST
• Currently being scaled up; available at specialized reference centers

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E. Phenotypic Culture-Based DST (Reference Standard)

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4. NTEP Diagnostic Algorithm Summary (2024-25)

Presumptive TB
      ↓
NAAT (Xpert MTB/RIF or Truenat) on sputum/EP specimen
      ↓
MTB Detected?
  ├─ RIF Resistant → NAAT for H+FQ resistance (or SL-LPA for FQ+SLI)
  │        ↓
  │   FQ Sensitive → MDR-TB → BPaLM or 9-11 month regimen
  │   FQ Resistant → Pre-XDR-TB → 18-20 month longer oral regimen
  │   FQ + Bdq/Lzd Resistant → XDR-TB → Individualized longer regimen
  │
  ├─ RIF Sensitive + H Resistant (FL-LPA) → Hr-TB → 6-month Hr-TB regimen
  └─ Both Sensitive → DS-TB → Standard 6-month HRZE regimen
      ↓
Baseline LC-DST for all MDR-TB patients
(Bdq, Lzd, Pa, Dlm, Z, Mfx) - modify regimen as results available

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5. Specimens Used for Rapid Diagnosis

• Pulmonary TB: Sputum (2 specimens), induced sputum, gastric lavage (GL), bronchoalveolar lavage (BAL)
• Extra-pulmonary TB:
  • FNAC of peripheral lymph nodes
  • CSF (TB meningitis - Xpert/Ultra is initial test of choice)
  • Pleural fluid (sensitivity low - 50-71%)
  • Synovial fluid (sensitivity high - 97%)
  • Fine needle aspirates, biopsies
• Note: All EP specimens except FNAC of peripheral LNs and CSF should preferably be sent directly to C&DST laboratory for further processing.

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6. Rapid Diagnosis in Special Situations

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7. Key Mutations and Their Clinical Significance

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8. Comparative Summary of Rapid Diagnostic Tests

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9. Key Points for Examination

1. NAAT (Xpert MTB/RIF) is the WHO and NTEP-endorsed first-line test for all presumptive TB; it detects both MTB and RIF resistance in under 2 hours.
2. RIF resistance = proxy for MDR-TB - Universal DST mandated for all TB patients.
3. FL-LPA detects H and R resistance (rpoB, katG, inhA); SL-LPA detects FQ and SLI resistance (gyrA/B, rrs/eis) - essential for classifying Pre-XDR vs XDR-TB.
4. CBNAAT M.tb/XDR (introduced NTEP 2024) enables single-step molecular detection of XDR-TB pattern.
5. tNGS is the newest WHO-recommended tool for comprehensive resistance profiling from sputum directly.
6. Liquid culture DST (MGIT) for Bdq, Lzd, Pa, Dlm, Z, Mfx remains mandatory at baseline for all MDR-TB patients to guide and modify regimens.
7. "Trace calls" in Xpert Ultra = treat as true positive in PLHIV, children, and extrapulmonary TB.
8. Discordant NAAT vs LPA = repeat NAAT at C&DST; best-of-three concordance rule determines final result.
9. Diagnosis of XDR-TB requires demonstration of MDR/RR + FQ resistance + resistance to at least one of Bdq or Lzd.
10. All confirmed RR/MDR-TB patients should have rapid FQ resistance testing before treatment initiation (maximum within 15 days) to enable appropriate regimen selection.

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• National Guidelines for Management of Drug Resistant TB, NTEP/CTD, Ministry of Health and Family Welfare, Government of India, November 2024 (updated March 2025)
• Harrison's Principles of Internal Medicine, 22nd Edition, 2025 (McGraw Hill) - Chapter on Tuberculosis
• Medical Microbiology, 9th Edition - Chapter on Drug-Resistant M. tuberculosis