Abstract
Conventional molecular tests for detecting Mycobacterium tuberculosis 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 a specificity of 97.4%. 56 out 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 two out 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 a specificity of 98.5/97.2/95.3%, respectively. Most residual discordances involved gene deletions/indels and 3–12% heteroresistant calls undetected by WGS analysis or natural pyrazinamide resistance of globally rare “Mycobacterium canettii” strains then unreported by Deeplex Myc-TB. On 1494 arduous sputa from a Democratic Republic of the Congo survey, 14 902 out of 19 422 (76.7%) possible susceptible or resistance phenotypes could be predicted culture-free.Deeplex Myc-TB may enable fast, tailored tuberculosis treatment.
Highlights
Important gaps remain for the diagnosis of drug-resistant tuberculosis (TB)
Limit of detection and mycobacterial species identification The major gene targets associated with resistance to 13 first- and second-line anti-tuberculous drugs/drug classes and the databases implemented in the web application are shown in figure 1, and tables 1 and 2
Further details on the assay design are provided in note S2 in the supplementary material, including the additional targets amplified in the single 24-plex PCR for mycobacterial species identification, spoligotyping/single nucleotide polymorphism (SNP) typing and an internal control, and the analysis with the web application
Summary
Important gaps remain for the diagnosis of drug-resistant tuberculosis (TB). Less than a third of the around 484 000 multidrug (MDR)- or rifampicin-resistant TB incident cases estimated in 2018 were diagnosed and treated [1]. Whole-genome sequencing (WGS) can effectively predict drug resistance or susceptibility of Mycobacterium tuberculosis complex (MTBC) strains [3,4,5]. Even if complex DNA enrichment procedures or thermoprotective DNA extraction are used, sequence coverage depths obtained by WGS directly on specimens often remain poor, even on samples with high bacterial loads [7, 8]. This limits the sensitivity and/or the degree of confidence for detecting resistance mutations, especially when borne by minority populations (defining heteroresistance) that can be predictive of treatment failure [9]
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