Diagnostic value of DNA or RNA-based metagenomic next-generation sequencing in lower respiratory tract infections

Jiafu Song; Suxia Liu; Yongpeng Xie; Chen Zhang; Caiyun Xu

doi:10.1016/j.heliyon.2024.e30712

Diagnostic value of DNA or RNA-based metagenomic next-generation sequencing in lower respiratory tract infections

Heliyon. 2024 May 3;10(9):e30712. doi: 10.1016/j.heliyon.2024.e30712. eCollection 2024 May 15.

Authors

Jiafu Song¹, Suxia Liu², Yongpeng Xie², Chen Zhang³, Caiyun Xu²

Affiliations

¹ Department of Respiratory and Critical Care Medicine, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, Jiangsu, China.
² Department of Critical Care Medicine, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, Jiangsu, China.
³ Department of Medicine, Dinfectome Inc., Nanjing, Jiangsu, China.

Abstract

Objectives: We aimed to evaluate and compare the diagnostic performance of RNA-mNGS and DNA-mNGS workflow in bacterial pneumonia, fungal pneumonia and tuberculosis.

Methods: A total of 134 cases suspected pneumonia undergoing both DNA and RNA based mNGS of bronchoalveolar lavage fluid (BALF) and also traditional etiological examination were evaluated retrospectively.Sensitivity, specificity, PPV, NPV and accuracy rate of DNA and RNA based mNGS were estimated.

Results: In the diagnosis performance of bacterial pathogens in LRTIs,the specificity of RNA-mNGS was higher than that of DNA-mNGS(82.3 % vs. 61.9 %, P < 0.01). There was no significant difference of sensitivity between the two process(71.4 % vs. 85.7 %, P = 0.375).In the diagnosis performance of fungal pathogens in LRTIs,the specificity of RNA-mNGS was higher than that of DNA-mNGS (72.3 % vs. 27.3 %,p < 0.001). There was no significant difference of sensitivity between the two process(96.5 % vs. 98.8 %,p = 0.125).In the diagnosis performance of tuberculosis in LRTIs,the sensitivity of DNA-mNGS was higher than that of RNA-mNGS (91.7 % vs. 33.3 %,p = 0.016),the specificity was similar in the two process (100 %).

Conclusions: RNA-mNGS may reduced the misdiagnosis rate of bacterial and fungal pathogens in LRTIs.Compared to RNA-mNGS, DNA-mNGS may could improve the diagnostic rate of tuberculosis.

Keywords: Bacterial pneumonia; DNA-mNGS; Fungal pneumonia; RNA-mNGS; Tuberculosis.