ddPCR provides a sensitive test compared with GeneXpert MTB/RIF and mNGS for suspected Mycobacterium tuberculosis infection

Dan Zhang; Fei Yu; Dongsheng Han; Weizhen Chen; Lingjun Yuan; Mengxiao Xie; Jieyuan Zheng; Jingchao Wang; Bin Lou; Shufa Zheng; Yu Chen

doi:10.3389/fcimb.2023.1216339

ddPCR provides a sensitive test compared with GeneXpert MTB/RIF and mNGS for suspected Mycobacterium tuberculosis infection

Front Cell Infect Microbiol. 2023 Dec 1:13:1216339. doi: 10.3389/fcimb.2023.1216339. eCollection 2023.

Authors

Dan Zhang^#^{1

2

3}, Fei Yu^#^{1

2

3}, Dongsheng Han^{1

2

3}, Weizhen Chen^{1

2

3}, Lingjun Yuan¹, Mengxiao Xie¹, Jieyuan Zheng¹, Jingchao Wang¹, Bin Lou^{1

2

3}, Shufa Zheng^{1

2

3}, Yu Chen^{1

2

3}

Affiliations

¹ Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
² Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.
³ Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China.

^# Contributed equally.

Abstract

Introduction: The Metagenomics next-generation sequencing (mNGS) and GeneXpert MTB/RIF assay (Xpert) exhibited a sensitivity for tuberculosis (TB) diagnostic performance. Research that directly compared the clinical performance of ddPCR analysis, mNGS, and Xpert in mycobacterium tuberculosis complex (MTB) infection has not been conducted.

Methods: The study aimed to evaluate the diagnostic performance of ddPCR compared to mNGS and Xpert for the detection of MTB in multiple types of clinical samples. The final clinical diagnosis was used as the reference standard.

Results: Out of 236 patients with suspected active TB infection, 217 underwent synchronous testing for tuberculosis using ddPCR, Xpert, and mNGS on direct clinical samples. During follow-up, 100 out of 217 participants were diagnosed with MTB infection. Compared to the clinical final diagnosis, ddPCR produced the highest sensitivity of 99% compared with mNGS (86%) and Xpert (64%) for all active MTB cases.

Discussion: Twenty-two Xpert-negative samples were positive in mNGS tests, which confirmed the clinical diagnosis results from ddPCR and clinical manifestation, radiologic findings. Thirteen mNGS-negative samples were positive in ddPCR assays, which confirmed the clinical final diagnosis.ddPCR provides a higher sensitive compared to Xpert and mNGS for MTB diagnosis, as defined by the high concordance between ddPCR assay and clinical final diagnosis.

Keywords: GeneXpert MTB/RIF; ddPCR; latent TB infection; metagenomics next-generation sequencing; tuberculosis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Antibiotics, Antitubercular* / therapeutic use
High-Throughput Nucleotide Sequencing
Humans
Mycobacterium tuberculosis* / genetics
Rifampin
Sensitivity and Specificity
Tuberculosis* / microbiology
Tuberculosis, Pulmonary* / diagnosis

Substances

Rifampin
Antibiotics, Antitubercular

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by a grant from the National Natural Science Foundation of China (82300007).