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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. Operationalising targeted next-generation sequencing for routine diagnosis of drug-resistant TB. Public Health Action 2023; 13:43-49. [PMID: 37359066 PMCID: PMC10290261 DOI: 10.5588/pha.22.0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/24/2023] [Indexed: 06/28/2023] Open
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.
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Affiliation(s)
- A Iyer
- Médecins Sans Frontières (MSF), Mumbai, India
| | - Z Ndlovu
- 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
| | - J Sharma
- Médecins Sans Frontières (MSF), Mumbai, India
| | - H Mansoor
- Médecins Sans Frontières (MSF), Mumbai, India
| | - M Bharati
- Médecins Sans Frontières (MSF), Mumbai, India
| | - S Kolan
- Médecins Sans Frontières (MSF), Mumbai, India
| | - M Morales
- Médecins Sans Frontières (MSF), Mumbai, India
| | - M Das
- Médecins Sans Frontières (MSF), Mumbai, India
| | - P Issakidis
- MSF, Southern African Medical Unit, Cape Town, South Africa
| | - G Ferlazzo
- MSF, Southern African Medical Unit, Cape Town, South Africa
| | - N Hirani
- Department of Mycobacteriology, Sir JJ Group of Hospitals, Mumbai, India
| | - A Joshi
- Department of Mycobacteriology, Sir JJ Group of Hospitals, Mumbai, India
| | - P Tipre
- National Tuberculosis Elimination Programme, Mumbai, India
| | - N Sutar
- National Tuberculosis Elimination Programme, Mumbai, India
| | - K England
- Independent Consultant, Honolulu, HI, USA
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