From mutation detection to treatment decisions: CRISPR-enabled diagnostics for drug-resistant tuberculosis

Abstract

Effective management of drug-resistant tuberculosis requires molecular assays that not only detect Mycobacterium tuberculosis but also identify resistance-associated variants, support drug-level interpretation, and indicate when broader confirmatory testing is needed. This narrative review applies a mutation-to-drug-to-decision framework to distinguish assay validity, exact-variant detection, drug-level inference, and decision impact. We synthesize evidence on target accessibility, minority-allele preservation, multiplexing, direct-specimen testing, and sequencing enrichment, emphasizing how these factors shape clinical interpretability. Current evidence remains dominated by analytical studies, isolate-based evaluations, and small direct-specimen investigations, with prospective multicenter treatment-impact validation still lacking. Population-level benchmarks indicate incomplete biological coverage for compact target regions, reaching approximately 92.6% for rpoB RRDR-based rifampicin detection, 85.4% for katG codon 315 plus the inhA promoter for isoniazid, and 84.7%–88.2% for gyrA/gyrB-based fluoroquinolone detection. Allele-specific CRISPR is therefore best suited to rapid rule-in of selected resistance-associated variants, while dispersed or heterogeneous mechanisms require broader molecular or phenotypic assessment. CRISPR should complement WHO-recommended rapid molecular testing and targeted next-generation sequencing rather than replace established molecular or phenotypic methods.