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BORSTELFZBhttps://www.ebi.ac.uk/ena/browser/view/PRJEB82439Background (68) The rpoB I491F multidrug resistant tuberculosis strain was characterized in 2009 in Eswatini. This mutation, undetectable by GeneXpert® MTB/RIF Ultra (Xpert Ultra) and the GenoType MTBDRplus line probe assay (LPA), increased in prevalence from 30% to 58% by 2018. In response, the Ministry of Health developed a targeted next-generation sequencing (tNGS) program in 2019. Here we detail the program's development, early implementation, and advantages over traditional diagnostic methods. Methods (61) tNGS was performed on all samples with resistance detected to isoniazid or rifampicin by Xpert Ultra, LPA, or phenotypic drug susceptibility testing. Patient specimens were tested first by Xpert Ultra and second by LPA, liquid culture and tNGS, using the Deeplex® Myc-TB assay, at the Eswatini National Tuberculosis Reference Lab. Clinical data was collected through programmatic structures developed to support implementation. Results (71) Implementation started in March 2022, following partner coordination, training, and tuberculosis guideline revisions. A Clinical Advisory Committee was established to guide clinicians on tNGS interpretation. tNGS testing identified rpoB I491F mutations in 46% (17/37) of initial samples tested and a high prevalence of bedaquiline resistance in the rpoB I491F strain (64%, 11/17). tNGS results led to regimen changes in 73% (27/37) of patients contributing to an 84% (31/37) treatment success rate. Interpretation (46) Our experience underscores the potential of tNGS to improve TB management in high-burden settings like Eswatini. Our findings raise concerns regarding the efficacy of BPaL(M) regimens as bedaquiline resistance emerges and highlight the need for new classifications to capture strains with bedaquiline but no fluoroquinolone resistance.ENAfalsetNGS of M. tuberculosis compleyx strains from EswatiniProgrammatic and Clinical Impact of Targeted Next-Generation Sequencing for Tuberculosis Care in Eswatini: A Health Policy and Descriptive Study2024-11-112024-11-11PRJEB82439