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ORIGINAL RESEARCH article

Front. Cell. Infect. Microbiol.
Sec. Clinical Microbiology
Volume 14 - 2024 | doi: 10.3389/fcimb.2024.1398190
This article is part of the Research Topic Targeted metagenomics in pathogen detection View all 10 articles

The value of metagenomic next-generation sequencing with different nucleic acid extracting methods of cell-free DNA or whole-cell DNA in the diagnosis of non-neutropenic pulmonary aspergillosis

Provisionally accepted
Xiaomin Cai Xiaomin Cai 1,2Chao Sun Chao Sun 2Huanhuan Zhong Huanhuan Zhong 2,3Yuchen Cai Yuchen Cai 2Min Cao Min Cao 1Li Wang Li Wang 4Wenkui Sun Wenkui Sun 5Yujian Tao Yujian Tao 6Guoer Ma Guoer Ma 7Baoju Huang Baoju Huang 4Shengmei Yan Shengmei Yan 8Jinjin Zhong Jinjin Zhong 8Jiamei Wang Jiamei Wang 9Yajie Lu Yajie Lu 8Yuanlin Guan Yuanlin Guan 10Mengyue Song Mengyue Song 9Yujie Wang Yujie Wang 8Yuanyuan Li Yuanyuan Li 8Xin Su Xin Su 11,8*
  • 1 Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
  • 2 Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
  • 3 The Second Affiliated Hospital of Suzhou University, Suzhou, China
  • 4 Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Liaoning Province, China
  • 5 Department of Respiratory and Critical Care Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
  • 6 Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Yangzhou University, Yangzhou, Jiangsu Province, China
  • 7 Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
  • 8 Department of Respiratory and Critical Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Liaoning Province, China
  • 9 Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing medical university, Nanjing, China
  • 10 Department of Research and Development, Hugobiotech Co. Ltd., Beijing, China
  • 11 Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Liaoning Province, China

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

    Purpose:Metagenomic next-generation sequencing(mNGS) is a novel molecular diagnostic technique. For nucleic acid extraction methods, both whole-cell DNA (wcDNA) and cell-free DNA (cfDNA) are widely applied with the sample of bronchoalveolar lavage fluid (BALF). We aim to evaluate the clinical value of mNGS with cfDNA and mNGS with wcDNA for the detection of BALF pathogens in non-neutropenic pulmonary aspergillosis.Methods: mNGS with BALF-cfDNA, BALF-wcDNA and conventional microbiological tests (CMTs) were performed in suspected non-neutropenic pulmonary aspergillosis. The diagnostic value of different assays for pulmonary aspergillosis was compared.Results: BALF-mNGS (cfDNA, wcDNA) outperformed CMTs in terms of microorganisms detection. Receiver operating characteristic (ROC) analysis indicated BALF-mNGS (cfDNA, wcDNA) was superior to culture and BALF-GM. Combination diagnosis of either positive for BALF-mNGS (cfDNA, wcDNA) or CMTs is more sensitive than CMTs alone in the diagnosis of pulmonary aspergillosis (BALF-cfDNA+CMTs/BALF-wcDNA+CMTs vs. CMTs : ROC analysis : 0.813 vs.0.66, P=0.0142/0.796 vs.0.66, P=0.0244; Sensitivity : 89.47% vs. 47.37%, P=0.008/84.21% vs. 47.37%, P=0.016). BALF-cfDNA showed a significantly greater reads per million (RPM) than BALF-wcDNA. The area under the ROC curve (AUC) for RPM of Aspergillus detected by BALF-cfDNA, used to predict "True positive" pulmonary aspergillosis patients, was 0.779, with a cut-off value greater than 4.5.Conclusion:We propose that the incorporation of BALF-mNGS (cfDNA, wcDNA) with CMTs improves diagnostic precision in the identification of non-neutropenic pulmonary aspergillosis when compared to CMTs alone. BALF-cfDNA outperforms BALF-wcDNA in clinical value.

    Keywords: Metagenomic next-generation sequencing (mNGS), cell-free DNA, whole-cell DNA, non-neutropenic pulmonary aspergillosis, Pulmonary Aspergillosis

    Received: 09 Mar 2024; Accepted: 09 Jul 2024.

    Copyright: © 2024 Cai, Sun, Zhong, Cai, Cao, Wang, Sun, Tao, Ma, Huang, Yan, Zhong, Wang, Lu, Guan, Song, Wang, Li and Su. 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: Xin Su, Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Liaoning Province, China

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