TY - JOUR T1 - Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs. JF - Eur Respir J Y1 - 2020 A1 - Agathe Jouet A1 - Cyril Gaudin A1 - Nelly Badalato A1 - Allix-Béguec, Caroline A1 - Stéphanie Duthoy A1 - Alice Ferré A1 - Maren Diels A1 - Yannick Laurent A1 - Sandy Contreras A1 - Silke Feuerriegel A1 - Stefan Niemann A1 - Emmanuel André A1 - Michel K Kaswa A1 - Elisa Tagliani A1 - Andrea Cabibbe A1 - Vanessa Mathys A1 - Daniela Cirillo A1 - Bouke C de Jong A1 - Rigouts, Leen A1 - Supply, Philip AB -

Conventional molecular tests for detecting complex (MTBC) drug resistance on clinical samples cover a limited set of mutations. Whole genome sequencing (WGS) typically requires culture. Here, we evaluated the Deeplex Myc-TB targeted deep sequencing assay for prediction of resistance to 13 anti-tuberculous drugs/drug classes, directly applicable on sputum. With MTBC DNA tests, the limit of detection was 100-1000 genome copies for fixed resistance mutations. Deeplex Myc-TB captured in silico 97.1-99.3% of resistance phenotypes correctly predicted by WGS from 3651 MTBC genomes. On 429 isolates, the assay predicted 92.2% of 2369 first- and second-line phenotypes, with a sensitivity of 95.3% and specificity of 97.4%. Fifty-six of 69 (81.2%) residual discrepancies with phenotypic results involved pyrazinamide, ethambutol, and ethionamide, and low-level rifampicin- or isoniazid-resistance mutations, all notoriously prone to phenotypic testing variability. Only 2 of 91 (2.2%) resistance phenotypes undetected by Deeplex Myc-TB had known resistance-associated mutations by WGS analysis outside Deeplex Myc-TB targets. Phenotype predictions from Deeplex Myc-TB analysis directly on 109 sputa from a Djibouti survey matched those of MTBSeq/PhyResSE/Mykrobe, fed with WGS data from subsequent cultures, with a sensitivity of 93.5/98.5/93.1% and specificity of 98.5/97.2/95.3%. Most residual discordances involved gene deletions/indels and 3-12% heteroresistant calls undetected by WGS analysis, or natural pyrazinamide resistance of globally rare " strains then unreported by Deeplex Myc-TB. On 1494 arduous sputa from a Democratic Republic of the Congo survey, 14 902 of 19 422 (76.7%) possible susceptible or resistance phenotypes could be predicted culture-free. Deeplex Myc-TB may enable fast, tailored tuberculosis treatment.

M3 - 10.1183/13993003.02338-2020 ER -