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Closing the diagnostic gap for the BPaLM treatment regimen with tNGS: Deeplex Myc-TB XL

N Badalato(1) E Lenoir(1) A Ferré(1) M Clément(1) Y Laurent(1) P Supply(2)

1:GenoScreen; 2:Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France

The targeted next generation sequencing (tNGS)-based Deeplex Myc-TB assay has been recently endorsed by WHO for rapid diagnosis of tuberculosis (TB) drug resistance, with performance criteria outstandingly met for 10/10 drugs evaluated. However, pretomanid (or delamanid), part of the BPaLM regimen now recommended as the first choice, near-universal treatment for multidrug resistant TB, is not covered. To close the existing BPaLM diagnostic gap, we therefore developed Deeplex Myc-TB XL, based on a single 42-plex PCR amplification (vs 24-plex with Deeplex Myc-TB) followed by deep Illumina sequencing. The test includes all the targets that harbor mutations associated with resistance/resistance- Interim to recommended anti-TB drugs in the latest WHO mutation catalogue. This comprises a total of 15 targets for BPaLM drugs, with e.g. 6 and 5 full genes for pretomanid/delamanid and bedaquiline, respectively, - and accounting also for known epistasis between mutations in bedaquiline resistance-associated genes -, in addition to optimized design of previous targets. In order to increase culture-free applicability on paucibacillary samples, representing challenges especially for pediatric TB, TB/HIV and TB meningitis, we also worked to improve the limit of detection, with a resulting analytical sensitivity measured at ~10 extracted genome copies. Last but not least, we substantially simplified the DNA library preparation, resulting in a reduction of more than half of the manipulations and hands-on time. This novel, augmented tNGS tool may thus further enable fast, comprehensive diagnosis to guide critical clinical decision-making for treatment of TB, including under its most challenging forms.

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