Current Landscape of Molecular Diagnostic Tests and Emerging Tools for Tuberculosis and Drug Resistance

This review synthesizes recent advances in WHO-endorsed NAATs for TB diagnosis and drug resistance detection. We examine the principles, genetic targets, diagnostic performance, implementation settings, and programmatic role of assays across the spectrum of technological complexity, from cartridge-based platforms to line probe assays and sequencing-based technologies. In addition, we highlight emerging molecular tools that show promise for future WHO endorsement and may further strengthen decentralized and near-patient testing. Low- and moderate-complexity assays such as Xpert^® MTB/RIF, Xpert^® Ultra, and Truenat^TM MTB/MTB Plus have emerged as essential frontline tools for TB diagnosis and rifampicin resistance detection, especially in decentralized settings. LPAs, including GenoType^® MTBDRplus and MTBDRsl, extend resistance profiling to isoniazid, fluoroquinolones, and second-line injectables, and remain valuable in intermediate and central laboratories. More recent developments, including Xpert^® XDR, Deeplex^® Myc-TB, AmPORE-TB^®, and TBseq^®, enable broader resistance detection and, in the case of targeted sequencing assays, comprehensive characterization of multidrug-resistant and extensively drug-resistant TB (MDR/XDR-TB). Emerging diagnostic innovations-such as CRISPR-based detection systems, streamlined isothermal amplification assays, and portable sequencing technologies-further expand the landscape and may complement existing WHO-endorsed platforms. Importantly, these technologies reduce delays in regimen selection, improve patient outcomes, and provide critical data for surveillance. Nevertheless, performance gaps for rare mutations, limited sensitivity in paucibacillary or extrapulmonary disease, infrastructure requirements, and cost remain barriers to universal adoption. The evolution of TB molecular diagnostics demonstrates a clear shift toward more rapid, accurate, and comprehensive resistance detection. No single assay is universally optimal, yet the combined portfolio, spanning rapid cartridge-based NAATs, LPAs, and next-generation sequencing, forms a complementary framework for improving diagnosis, optimizing treatment, and supporting global TB elimination strategies.