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ORIGINAL RESEARCH article

Front. Cell. Infect. Microbiol.
Sec. Clinical Infectious Diseases
Volume 14 - 2024 | doi: 10.3389/fcimb.2024.1432446
This article is part of the Research Topic Multi-Omics Approaches in Disease Microbiology: From Biomarkers to Therapeutic Interventions View all articles

Diagnostic value of third-generation nanopore sequencing in extrapulmonary tuberculosis

Provisionally accepted
Chang Song Chang Song 1,2Chuanyan Zhao Chuanyan Zhao 1,2Yanrong Lin Yanrong Lin 3Yingxing Nong Yingxing Nong 1*Aichun Huang Aichun Huang 1*Shaoyong Xi Shaoyong Xi 4*Xiaoying Wei Xiaoying Wei 1*Chunmei Zeng Chunmei Zeng 1*Shixiong Yang Shixiong Yang 5*Zhu Qingdong Zhu Qingdong 1*
  • 1 Department of Tuberculosis, Nanning No.4 People's Hospital, Nanning, Guangxi Zhuang Region, China
  • 2 Guangxi Medical University, Nanning, Guangxi Zhuang Region, China
  • 3 Department of Medical, Nanning No.4 People's Hospital, Nanning, Guangxi Zhuang Region, China
  • 4 Department of Clinical Laboratory, Nanning No.4 People's Hospital, Nanning, Guangxi Zhuang Region, China
  • 5 Administrative Office, Nanning No.4 People's Hospital, Nanning, Guangxi Zhuang Region, China

The final, formatted version of the article will be published soon.

    Background: This study aimed to explore the accuracy of third-generation nanopore sequencing to diagnose extrapulmonary tuberculosis (EPTB).Methods: Samples were collected from the lesions of 67 patients with suspected EPTB admitted between April 2022 and August 2023. Nanopore sequencing, acid-fast bacilli (AFB) staining, DNA testing, and Xpert and mycobacterial cultures were performed. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and area under the receiver operating characteristic curve (AUC) were calculated for different diagnostic methods, and their diagnostic accuracies were compared.Results: Nanopore sequencing demonstrated the highest correct diagnosis rate among 50 positive EPTB cases, independently diagnosing 19 positive cases missed by conventional methods. Its sensitivity (62.00%), specificity (94.10%), PPV (96.90%), NPV (45.70%) and AUC (0.781, 95% CI: 0.67-0.89) were superior to those of conventional methods, such as AFB staining, DNA testing, Xpert, and solid culture, indicating its significantly efficient advantage in EPTB detection.Nanopore sequencing technology significantly outperforms conventional methods such as AFB staining, DNA testing, Xpert, and mycobacterial culture to diagnose EPTB, promising to improve the diagnosis of EPTB.

    Keywords: nanopore sequencing, Extrapulmonary tuberculosis, diagnostic value, Conventional methods, clinical microbiology

    Received: 14 May 2024; Accepted: 25 Nov 2024.

    Copyright: © 2024 Song, Zhao, Lin, Nong, Huang, Xi, Wei, Zeng, Yang and Qingdong. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Yingxing Nong, Department of Tuberculosis, Nanning No.4 People's Hospital, Nanning, 530001, Guangxi Zhuang Region, China
    Aichun Huang, Department of Tuberculosis, Nanning No.4 People's Hospital, Nanning, 530001, Guangxi Zhuang Region, China
    Shaoyong Xi, Department of Clinical Laboratory, Nanning No.4 People's Hospital, Nanning, 530001, Guangxi Zhuang Region, China
    Xiaoying Wei, Department of Tuberculosis, Nanning No.4 People's Hospital, Nanning, 530001, Guangxi Zhuang Region, China
    Chunmei Zeng, Department of Tuberculosis, Nanning No.4 People's Hospital, Nanning, 530001, Guangxi Zhuang Region, China
    Shixiong Yang, Administrative Office, Nanning No.4 People's Hospital, Nanning, 530001, Guangxi Zhuang Region, China
    Zhu Qingdong, Department of Tuberculosis, Nanning No.4 People's Hospital, Nanning, 530001, Guangxi Zhuang Region, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.