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Using targeted Next Generation Sequencing directly from sputum for comprehensive drug resistance prediction of Mycobacterium tuberculosis strains in Namibia

L Mhuulu(1) V Dreyer(2) H Ekandjo(1) A Diergaardt(1) O Shavuka(1) L de Araujo(2) N Ruswa(4) T Niemann(1,2) G Günther(1,5) M Claassens(1) E Nepolo(1) S Niemann(1,2)

1:Department of Human, Biological & Translational Sciences, School of Medicine, University of Namibia, Namibia; 2:Research Center Borstel - Leibniz Lung Center, Germany; 3:Namibia Institute of Pathology, Namibia; 4:National Tuberculosis and Leprosy Program, Ministry of Health and Social Services, Namibia; 5:Department of Pulmonology and Allergology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland

In high tuberculosis (TB) burden countries access to drug susceptibility testing is a major bottleneck. Targeted Next Generation Sequencing (tNGS) is a promising technology for rapid resistance detection. This study assessed the performance of tNGS for detection of drug-resistant TB (DR-TB) directly from sputum in a university lab in Namibia. A total of 34 sputum samples (13 rifampicin resistant [RR] and 21 sensitive based on Xpert® MTB/RIF) from confirmed TB patients were subjected to tNGS using the Deeplex® Myc-TB kit and sequenced using the Illumina iSeq100 platform. Data were analysed on the Deeplex Myc-TB web application. 20 out of 34 (59%) were successfully sequenced, of which 19 had a complete resistance profile for all 13 anti-TB drugs evaluated by Deeplex® assay and one sample was reported as NTM. Of the successfully sequenced samples, tNGS identified 9 pan-susceptible, 3 mono-resistant, 6 multi-drug resistant TB and one extensively drug resistant (XDR)-TB strain. Seven out of 13 RR by Xpert® MTB/RIF were confirm using tNGS, of this 6 had additional resistance to one or more first-line drugs. With tNGS, resistance to bedaquiline was detected in one sample, resulting in an XDR-TB re-classification, which would have been missed by the current diagnostic tools in the country. Moreover, three samples that were initially defined as rifampicin sensitive, had mutations conferring resistance to Isoniazid, Pyrazinamide and Streptomycin. In conclusion, our data show that tNGS can be used to complement in the diagnosis of DR-TB and for the design of a timely introduced individualised treatment regimen.

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