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

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.

Exploring the Clinical Utility of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infection

“…Body Fluid Sample: Sample Processing and DNA Extraction A body fluid sample (1.5-3 mL of BALF, pleural effusion, or sputum) was collected from each patient according to standard procedures [5]. A 1.5-mL microcentrifuge tube containing 0.6 mL sample, enzyme, and 1 g of 0.5-mm glass beads was agitated by a vortex mixer, and a 0.3-mL sample was separated into a 1.5-mL microcentrifuge tube and DNA was extracted using the TIANamp Micro DNA Kit (DP316, Tiangen Biotech) following the manufacturer's operational manual.…”

Metagenomic Next-Generation Sequencing for Pathogenic Diagnosis and Antibiotic Management of Severe Community-Acquired Pneumonia in Immunocompromised Adults

“…For SCAP patients, the pathogen positivity rate was 90.3% for mNGS versus 39.5% for conventional methods ( Wu et al., 2020 ). The feasibility of mNGS for bronchoalveolar lavage fluid (BALF), blood, sputum, transbronchial lung biopsy (TBLB) and even lung biopsy tissues ( Li et al., 2018 ; Liu et al., 2019 ; Chen et al., 2020 ; Li et al., 2020 ; Wu et al., 2020 ) in patients with respiratory infections has been demonstrated in many literatures. However, the high cost affects the wide application of mNGS in CAP patients.…”

Diagnostic Accuracy of Metagenomic Next-Generation Sequencing in Sputum-Scarce or Smear-Negative Cases with Suspected Pulmonary Tuberculosis

“…For example, Huang et al used mNGS to detect microbes related to human diseases in 94.49% of samples from patients with pulmonary infections who had received negative results from traditional pathogen detection methods, indicating that the accuracy and sensitivity of mNGS are higher than those of standard pathogen detection techniques [ 28 ]. Similarly, Wang et al found that mNGS was more sensitive than traditional methods in mixed pulmonary infections [ 13 ] whereas Chen et al found that the results obtained using mNGS in BALF of patients with severe disease were highly consistent with those of culture [ 29 ].…”