Tuberculosis diagnostics: from smear to sequencing

Tuberculosis diagnosis is algorithmic: no single test answers every question.

The stepped pathway 1. **Smear microscopy** — fast and cheap, but insensitive and unable to identify species or resistance. 2. **Rapid molecular testing (e.g., Xpert MTB/RIF)** — detects M. tuberculosis complex and rifampicin resistance (rpoB) in about two hours; WHO-recommended as an initial test. 3. **Line probe assay** — extends molecular resistance detection to isoniazid (katG, inhA) and, with second-line LPA, fluoroquinolones and injectables. 4. **Culture (MGIT)** — the most sensitive routine method; proves viability and yields the isolate needed for full drug susceptibility testing. 5. **Phenotypic DST** — the reference for designing MDR/XDR-TB regimens. 6. **Whole genome sequencing** — comprehensive resistance and strain characterisation for selected cases and outbreak investigation.

Key principles Molecular tests detect DNA — they do not prove viability. Molecular resistance detection and phenotypic resistance are related but not always identical. Rapid molecular tests do not replace culture or phenotypic DST: each step adds information the others cannot provide.