Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex®-MycTB

The emergence of multidrug-resistant (MDR) and extensively-drug-resistant (XDR-TB) Mycobacterium tuberculosis complex (Mtbc) isolates challenges tuberculosis (TB) control worldwide [1] and requires the rapid determination of extensive resistance profiles [2], enabling prompt initiation of effective treatment regimens. Phenotypic drug susceptibility testing (pDST) takes up to six weeks [3], and is unreliable and/or not standardised for several drugs according to WHO guidelines [4]. Molecular DST (mDST) assays, like Xpert MTB/RIF (Cepheid) or MTBDR plus / sl line probe assays (LPAs, Hain Lifesciences) can be performed directly from clinical specimens, but only target a limited number of resistance variants [5]. Footnotes This manuscript has recently been accepted for publication in the European Respiratory Journal . It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article. Conflict of interest: Dr. Andres has nothing to disclose. Conflict of interest: Dr. Badalato reports personal fees from GenoScreen, during the conduct of the study; personal fees from GenoScreen, outside the submitted work. Conflict of interest: Dr. Conteh has nothing to disclose. Conflict of interest: Dr. Feuerriegel has nothing to disclose. Conflict of interest: Dr. Foray has nothing to disclose. Conflict of interest: Dr. Fouad Kamara has nothing to disclose. Conflict of interest: Dr. Heyckendorf has nothing to disclose. Conflict of interest: Dr. Jouet reports personal fees from GenoScreen, during the conduct of the study. Conflict of interest: Dr. Kohl has nothing to disclose. Conflict of interest: Dr. Maurer has nothing to disclose. Conflict of interest: Dr. Niemann reports grants from German Center for Infection Research, grants from Excellenz Cluster Precision Medicine in Chronic Inflammation EXC 2167, grants from Leibniz Science Campus Evolutionary Medicine of the LUNG (EvoLUNG), during the conduct of the study. Conflict of interest: Dr. Supply reports personal fees from Genoscreen, during the conduct of the study. Conflict of interest: Dr. Utpatel has nothing to disclose.