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

• Published in: Public health action Vol. 13; no. 2; pp. 43 - 49
• Main Authors: Iyer, A., 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.
• Format: Journal Article
• Language: English
• Published: France International Union Against Tuberculosis and Lung Disease 21.06.2023
• Subjects: Deeplex-Myctb; Mdr-Tb; Original; Resistotyping; Tngs; resistotyping; MDR-TB; tNGS; Deeplex-MycTB
• ISSN: 2220-8372; 2220-8372
• DOI: 10.5588/pha.22.0041

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.