Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

Xu Chen; Shuizi Ding; Cheng Lei; Jieli Qin; Ting Guo; Danhui Yang; Min Yang; Jie Qing; Wenlong He; Min Song; Yan Zhang; Huihui Zeng; Qingwu Qin; Lizhen Yang; Yingjiao Long; Yan Chen; Bingyin Ma; Ruoyun Ouyang; Ping Chen; Hong Luo

doi:10.1155/2020/6839103

Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

Can J Infect Dis Med Microbiol. 2020 Aug 12:2020:6839103. doi: 10.1155/2020/6839103. eCollection 2020.

Authors

Xu Chen^{1

2

3}, Shuizi Ding^{1

2

3}, Cheng Lei^{1

2

3}, Jieli Qin^{1

2

3}, Ting Guo^{1

2

3}, Danhui Yang^{1

2

3}, Min Yang^{1

2

3}, Jie Qing^{1

2

3}, Wenlong He^{1

2

3}, Min Song^{1

2

3}, Yan Zhang^{1

2

3}, Huihui Zeng^{1

2

3}, Qingwu Qin^{1

2

3}, Lizhen Yang^{1

2

3}, Yingjiao Long^{1

2

3}, Yan Chen⁴, Bingyin Ma⁵, Ruoyun Ouyang^{1

2

3}, Ping Chen^{1

2

3}, Hong Luo^{1

2

3}

Affiliations

¹ Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.
² Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China.
³ Hunan Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, Hunan 410011, China.
⁴ BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
⁵ Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China.

Abstract

Background: Metagenomic next-generation sequencing (mNGS) has made a revolution in the mode of pathogen identification. We decided to explore the diagnostic value of blood and bronchoalveolar lavage fluid (BALF) as mNGS samples in pneumonia.

Methods: We retrospectively reviewed 467 mNGS results and assessed the diagnostic performance of paired blood and BALF mNGS in 39 patients with pneumonia.

Results: For bacteria and fungi, 16 patients had culture-confirmed pathogen diagnosis, while 13 patients were culture-negative. BALF mNGS was more sensitive than blood mNGS (81.3% vs. 25.0%, p=0.003), and the specificity in BALF and blood mNGS was not statistically significant different (76.9% vs. 84.6%, p=0.317). For 10 patients without culture test, treatments were changed in 2 patients. For viruses, Epstein-Barr virus was positive in blood mNGS in 9 patients. Human adenovirus was detected in both BALF and blood mNGS in 3 patients.

Conclusion: Our study suggests that BALF mNGS is more sensitive than blood mNGS in detecting bacteria and fungi, but blood also has advantages to identify the pathogens of pneumonia, especially for some viruses.