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

IF 1.3 Q4 RESPIRATORY SYSTEM

Public Health Action Pub Date : 2023-06-21 DOI:10.5588/pha.22.0041

A Iyer, Z Ndlovu, J Sharma, H Mansoor, M Bharati, S Kolan, M Morales, M Das, P Issakidis, G Ferlazzo, N Hirani, A Joshi, P Tipre, N Sutar, K England

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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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用于耐药结核病常规诊断的靶向新一代测序的运作。

背景:结核分枝杆菌的表型药敏试验(pDST)可能需要长达8周的时间，而传统的分子试验鉴定出一组有限的耐药突变。靶向下一代测序(tNGS)为预测全面耐药性提供了快速结果，本研究试图在印度孟买的一个公共卫生实验室探索其操作可行性。方法:采用常规方法和tNGS对Xpert mtb阳性患者肺标本进行耐药检测。下面分享了研究小组成员的实验室操作和后勤实施经验。结果:在接受检测的患者总数中，70%(113/161)没有结核病史或治疗史;然而，88.2% (n = 142)患有利福平耐药/耐多药结核病(RR/MDR-TB)。对于大多数药物，tNGS和pDST的耐药预测之间存在高度一致性，tNGS总体上更准确地识别耐药。将tNGS整合并适应到实验室工作流程中;然而，批量样品导致结果周转时间明显延长，最快为24天。人工DNA提取效率低下;因此，执行了协议优化。分析无特征的突变和解释报告模板需要技术专门知识。每个样品的tNGS成本为230美元，而pDST的成本为119美元。结论:在参比实验室实施tNGS是可行的。它可以快速识别耐药性，应被视为pDST的潜在替代品。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Public Health Action RESPIRATORY SYSTEM-

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期刊介绍： Launched on 1 May 2011, Public Health Action (PHA) is an official publication of the International Union Against Tuberculosis and Lung Disease (The Union). It is an open access, online journal available world-wide to physicians, health workers, researchers, professors, students and decision-makers, including public health centres, medical, university and pharmaceutical libraries, hospitals, clinics, foundations and institutions. PHA is a peer-reviewed scholarly journal that actively encourages, communicates and reports new knowledge, dialogue and controversy in health systems and services for people in vulnerable and resource-limited communities — all topics that reflect the mission of The Union, Health solutions for the poor.