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Open Access Operationalising targeted next-generation sequencing for routine diagnosis of drug-resistant TB

This article is Open Access under the terms of the Creative Commons CC BY licence.

BACKGROUND: Phenotypic drug susceptibility testing (pDST) for Mycobacterium tuberculosis can take up to 8 weeks, while conventional molecular tests identify a limited set of resistance mutations. Targeted next-generation sequencing (tNGS) offers rapid results for predicting comprehensive drug resistance, and this study sought to explore its operational feasibility within a public health laboratory in Mumbai, India.

METHODS: Pulmonary samples from consenting patients testing Xpert MTB-positive were tested for drug resistance by conventional methods and using tNGS. Laboratory operational and logistical implementation experiences from study team members are shared below.

RESULTS: Of the total number of patients tested, 70% (113/161) had no history of previous TB or treatment; however, 88.2% (n = 142) had rifampicin-resistant/multidrug-resistant TB (RR/MDR-TB). There was a high concordance between resistance predictions of tNGS and pDST for most drugs, with tNGS more accurately identifying resistance overall. tNGS was integrated and adapted into the laboratory workflow; however, batching samples caused significantly longer result turnaround time, fastest at 24 days. Manual DNA extraction caused inefficiencies; thus protocol optimisations were performed. Technical expertise was required for analysis of uncharacterised mutations and interpretation of report templates. tNGS cost per sample was US$230, while for pDST this was US$119.

CONCLUSIONS: Implementation of tNGS is feasible in reference laboratories. It can rapidly identify drug resistance and should be considered as a potential alternative to pDST.

Keywords: Deeplex-MycTB; MDR-TB; resistotyping; tNGS

Document Type: Research Article

Affiliations: 1: Médecins Sans Frontières (MSF), Mumbai, India 2: MSF, Southern African Medical Unit, Cape Town, South Africa, Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa 3: MSF, Southern African Medical Unit, Cape Town, South Africa 4: Department of Mycobacteriology, Sir JJ Group of Hospitals, Mumbai, India 5: National Tuberculosis Elimination Programme, Mumbai, India 6: Independent Consultant, Honolulu, HI, USA

Publication date: June 21, 2023

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