Targeted next-generation sequencing of Mycobacterium tuberculosis from patient samples: lessons learned from high drug-resistant burden clinical settings in Bangladesh.

IF 8.4 2区 医学 Q1 IMMUNOLOGY Emerging Microbes & Infections Pub Date : 2024-12-01 Epub Date: 2024-08-26 DOI:10.1080/22221751.2024.2392656
Mohammad Khaja Mafij Uddin, Andrea Maurizio Cabibbe, Rumana Nasrin, Arash Ghodousi, Fahim Alam Nobel, S M Mazidur Rahman, Shahriar Ahmed, Md Fahim Ather, S M Abdur Razzaque, Md Abu Raihan, Pronab Kumar Modak, Jean Luc Berland, Wayne Van Gemert, Sardar Munim Ibna Mohsin, Daniela Maria Cirillo, Sayera Banu
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Abstract

Lack of appropriate early diagnostic tools for drug-resistant tuberculosis (DR-TB) and their incomplete drug susceptibility testing (DST) profiling is concerning for TB disease control. Existing methods, such as phenotypic DST (pDST), are time-consuming, while Xpert MTB/RIF (Xpert) and line probe assay (LPA) are limited to detecting resistance to few drugs. Targeted next-generation sequencing (tNGS) has been recently approved by WHO as an alternative approach for rapid and comprehensive DST. We aimed to investigate the performance and feasibility of tNGS for detecting DR-TB directly from clinical samples in Bangladesh. pDST, LPA and tNGS were performed among 264 sputum samples, either rifampicin-resistant (RR) or rifampicin-sensitive (RS) TB cases confirmed by Xpert assay. Resistotypes of tNGS were compared with pDST, LPA and composite reference standard (CRS, resistant if either pDST or LPA showed a resistant result). tNGS results revealed higher sensitivities for rifampicin (RIF) (99.3%), isoniazid (INH) (96.3%), fluoroquinolones (FQs) (94.4%), and aminoglycosides (AMGs) (100%) but comparatively lower for ethambutol (76.6%), streptomycin (68.7%), ethionamide (56.0%) and pyrazinamide (50.7%) when compared with pDST. The sensitivities of tNGS for INH, RIF, FQs and AMGs were 93.0%, 96.6%, 90.9%, and 100%, respectively and the specificities ranged from 91.3 to 100% when compared with CRS. This proof of concept study, conducted in a high-burden setting demonstrated that tNGS is a valuable tool for identifying DR-TB directly from the clinical specimens. Its feasibility in our laboratory suggests potential implementation and moving tNGS from research settings into clinical settings.

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从患者样本中对结核分枝杆菌进行有针对性的下一代测序:从孟加拉国高耐药性临床环境中汲取的经验教训。
摘要耐药性结核病(DR-TB)缺乏适当的早期诊断工具,而且其药物敏感性测试(DST)分析不完整,这对结核病的控制来说令人担忧。表型 DST(pDST)等现有方法耗时长,而 Xpert MTB/RIF(Xpert)和线探针测定法(LPA)仅限于检测少数药物的耐药性。最近,世卫组织批准了靶向新一代测序(tNGS)作为快速、全面 DST 的替代方法。我们对 264 份经 Xpert 检测确认的利福平耐药(RR)或利福平敏感(RS)肺结核病例的痰液样本进行了 pDST、LPA 和 tNGS 检测。将 tNGS 的耐药型与 pDST、LPA 和复合参考标准(CRS,如果 pDST 或 LPA 显示耐药结果则为耐药)进行了比较。3%)、异烟肼(INH)(96.3%)、氟喹诺酮类(FQs)(94.4%)和氨基糖苷类(AMGs)(100%),但与 pDST 相比,乙胺丁醇(76.6%)、链霉素(68.7%)、乙胺酰胺(56.0%)和吡嗪酰胺(50.7%)的敏感性相对较低。与 CRS 相比,tNGS 对 INH、RIF、FQs 和 AMGs 的敏感性分别为 93.0%、96.6%、90.9% 和 100%,特异性从 91.3% 到 100%不等。这项在高负担环境中进行的概念验证研究表明,tNGS 是直接从临床标本中鉴定 DR-TB 的重要工具。它在我们实验室的可行性表明,tNGS 有可能从研究环境中应用到临床环境中。
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来源期刊
Emerging Microbes & Infections
Emerging Microbes & Infections IMMUNOLOGY-MICROBIOLOGY
CiteScore
26.20
自引率
2.30%
发文量
276
审稿时长
20 weeks
期刊介绍: Emerging Microbes & Infections is a peer-reviewed, open-access journal dedicated to publishing research at the intersection of emerging immunology and microbiology viruses. The journal's mission is to share information on microbes and infections, particularly those gaining significance in both biological and clinical realms due to increased pathogenic frequency. Emerging Microbes & Infections is committed to bridging the scientific gap between developed and developing countries. This journal addresses topics of critical biological and clinical importance, including but not limited to: - Epidemic surveillance - Clinical manifestations - Diagnosis and management - Cellular and molecular pathogenesis - Innate and acquired immune responses between emerging microbes and their hosts - Drug discovery - Vaccine development research Emerging Microbes & Infections invites submissions of original research articles, review articles, letters, and commentaries, fostering a platform for the dissemination of impactful research in the field.
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