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Journal Article
|Research

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

Iyer AS, Ndlovu Z, Sharma J, Mansoor H, Bharati M, Kolan S, Morales M, Das M, Issakidis P, Ferlazzo G, Hirani N, Joshi A, Tipre P, Sutar N, England K
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Operationalising targeted next-generation sequencing for routine diagnosis of drug-resistant TB | Journal Article / Research | MSF Science Portal
Abstract
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.

Countries

India

Subject Area

antibiotic resistancetuberculosisdiagnosticsgenetics & genomicsantimicrobial resistance

Languages

English
French
DOI
10.5588/pha.22.0041
Published Date
21 Jun 2023
PubMed ID
37359066
Journal
Public Health Action
Volume | Issue | Pages
Volume 13, Issue 2, Pages 43-49
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