Evaluation of Nanopore Sequencing for Diagnosing Pulmonary Tuberculosis Using Negative Smear Clinical Specimens

Guocan Yu; Yanqin Shen; Liwei Yao; Xudong Xu

doi:10.2147/IDR.S442229

Evaluation of Nanopore Sequencing for Diagnosing Pulmonary Tuberculosis Using Negative Smear Clinical Specimens

Infect Drug Resist. 2024 Feb 19:17:673-682. doi: 10.2147/IDR.S442229. eCollection 2024.

Authors

Guocan Yu¹, Yanqin Shen², Liwei Yao², Xudong Xu¹

Affiliations

¹ Zhejiang Tuberculosis Diagnosis and Treatment Center, Hangzhou Red Cross Hospital, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China.
² Department of Nursing, Hangzhou Red Cross Hospital, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China.

Abstract

Purpose: This study aimed to evaluate the efficacy of nanopore sequencing for diagnosing pulmonary tuberculosis (PTB) using smear-negative clinical specimens.

Methods: We conducted a retrospective study based on a review of patient medical records to assess the accuracy of nanopore sequencing as a diagnostic tool for smear-negative PTB. Compared with clinical diagnosis, we determined the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the curve (AUC) of nanopore sequencing.

Results: A total of 647 patients were evaluated. Nanopore sequencing demonstrated an overall sensitivity of 91.7%, specificity of 85.3%, PPV of 95.1%, NPV of 76.4%, and AUC of 0.88. Notably, the overall diagnostic accuracy of nanopore sequencing was significantly higher than that of Mycobacterium tuberculosis (MTB) culture technique.

Conclusion: Nanopore sequencing exhibited satisfactory overall diagnostic accuracy for smear-negative PTB, regardless of MTB culture status. Therefore, if conditions permit, nanopore sequencing is recommended as a diagnostic method for smear-negative PTB.

Keywords: diagnostic accuracy; nanopore sequencing; pulmonary tuberculosis; smear-negative specimens.

Grants and funding

This work was supported by Hangzhou Science and Technology Bureau, http://kj.hangzhou.gov.cn. Guocan Yu, 20201203B183. The funder does not have a role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.