Comprehensive molecular drug resistance profiles derived from stool-based targeted sequencing of Mycobacterium tuberculosis complex: a cross-sectional observational study. tNGS of stool MTBC

BackgroundStool is an important diagnostic specimen for tuberculosis in populations who struggle to provide sputum, such as children or people living with HIV. However, as culture of M tuberculosis complex strains from stool performs poorly, drug resistance testing is currently limited.MethodsWe evaluated the performance of targeted next-generation sequencing (NGS, Deeplex® Myc-TB) for the detection of mutations associated with M tuberculosis complex drug resistance on DNA isolated from stool specimens provided by patients with tuberculosis from a prospective cohort in Eswatini, and an independent German validation cohort. FindingsAnalysis of the Eswatini cohort included specimens from 56 unique participants with and 10 participants without M tuberculosis complex DNA detected in stool by real-time quantitative PCR. The Deeplex® Myc-TB assay detected M tuberculosis complex DNA in 38 of 56 (68%) samples, and for 28 of 38 (74%) samples, a full M tuberculosis complex drug resistance prediction report was obtained. The ability to predict resistance was concentration dependent; and successful in 7/10 (70%), 18/25 (72%) and 3/21 (14%) of samples with stool PCR concentration thresholds of 100 fg/l, respectively (p = 0.0004). The German cohort confirmed these results and demonstrated a high concordance between stool NGS and sputum phenotypic drug susceptibility results ( = 0.84). InterpretationThe Deeplex® Myc-TB assay can identify drug resistance via targeted NGS from stool provided by tuberculosis patients. This discovery affords the opportunity to obtain critical diagnostic information for tuberculosis patients who struggle to provide respiratory specimens.