A cartridge-based assay for improved detection of multidrug-resistant <i>Mycobacterium tuberculosis</i> directly from sputum

The Xpert MTB/RIF Ultra assay (Ultra) is a gold standard test for rapidly diagnosing tuberculosis (TB) as well as resistance to rifampicin directly from sputum samples. However, the Ultra assay does not detect certain rifampicin resistance mutations, which are observed clinically and cannot detect resistance to isoniazid, another key drug against TB. We modified the Ultra assay, creating a prototype MDRmDx assay designed for 10-color instruments that detects isoniazid resistance, which can be a precursor of potential rifampicin resistance and has improved ability to detect rifampicin resistance. In both analytic and retrospectively collected clinical sputum samples, we found that the MDRmDx assay performed at least as well as the Ultra assay with the additional advantage of detecting isoniazid resistance and <i>rpoB</i> I491F mutations with high sensitivity and specificity. The MDRmDx assay's improved performance should improve detection of drug-resistant TB and facilitate the selection of effective treatment.