Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 May 12;20(1):20251074.
doi: 10.1515/biol-2025-1074. eCollection 2025.

Metagenomic next-generation sequencing of alveolar lavage fluid improves the detection of pulmonary infection

Ziyu Meng  1 , Dong Li  2 , Wei Yang  3 , Jihong Tang  3
Affiliations

Metagenomic next-generation sequencing of alveolar lavage fluid improves the detection of pulmonary infection

Ziyu Meng et al. Open Life Sci. .

Abstract

This study evaluated the effectiveness of metagenomic next-generation sequencing (mNGS) in detecting pathogens in patients with pulmonary infections, comparing a low-data-volume, human-depleted quantitative (Q) method and a high-data-volume, non-human-depleted pathogen capture engine (PACE) method. A total of 133 patients were enrolled, comprising 59 in a control group (traditional culture) and 74 in an mNGS group (51 Q and 23 PACE). Bronchoalveolar lavage fluid samples were collected for pathogen detection. Mycobacterium tuberculosis was predominantly detected via general mNGS, whereas Candida albicans and Epstein-Barr virus were more frequently identified by PACE and Q, respectively. Among participants, 22.97% had bacterial mono-infections, and 2.70% had viral mono-infections; the most common co-infection involved bacteria and viruses (25.68%). Patients with fever, abnormal white blood cell, neutrophil percentage, and D-dimer levels exhibited higher detection rates. PACE showed consistently high sensitivity (decreasing from 100 to 92% as thresholds became more stringent) and specificity and accuracy that peaked at 100 and 96%, respectively. The Q method maintained 100% sensitivity at the lowest threshold but showed variable specificity (0.52-0.67) and accuracy (71-75%). These findings highlight the need for caution in clinical applications when using low-data-volume, human-depleted approaches, especially for complex pulmonary infection cases.

Keywords: diagnostic methods; metagenomic next-generation sequencing; pathogen detection; pulmonary infection.

PubMed Disclaimer

Conflict of interest statement

Conflict of interest: Authors state no conflict of interest.

Figures

Figure 1
Figure 1
Genus distribution of bacteria (a), fungi (b), and virus (c) detected by different mNGS methods.
Figure 2
Figure 2
Percentage of patients with infections with different types of pathogens (a), or co-infections (b) detected by mNGS PACE and Q method.
Figure 3
Figure 3
(a) The influence of fever, hypoproteinemia, and empyema on the detection rate of mNGS in pulmonary infections. Positive/negative represent cases with/without these symptoms, respectively. Chi-squared test. (b) Proportion of infection type of pulmonary infection with hypoproteinemia detected using mNGS PACE and Q methods. (c) The influence of WBC, NEUT%, and D-dimer on the detection rate of mNGS in pulmonary infections. Chi-squared Test. (d) Proportion of infection type of pulmonary infection with abnormal level of NEUT% and D-dimer detected using mNGS. WBC, white blood cell; NEUT, neutrophil. *P < 0.05.
Figure 4
Figure 4
The comparisons of WBC, neutrophil, and D-dimer across mNGS groups. *P < 0.05.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Adjemian J, Olivier KN, Seitz AE, Holland SM, Prevots DR. NTM infections; A rising global health problem/clinical characteristics and outcomes of patients with non-tuberculous mycobacterial infections at two tertiary academic medical centers. Open Forum Infect Dis. 2021;8(11):ofab466. https://www.ncbi.nlm.nih.gov/pmc/articles/8644936.
    1. Alemu A, Bitew ZW, Worku T, Gamtesa DF. Hepatitis B and C virus infections and associated factors among HIV-positive and HIV-negative tuberculosis patients in public health facilities, Northeast Ethiopia: A comparative cross-sectional study. PLoS One. 2023;18(1):e0279172. https://pubmed.ncbi.nlm.nih.gov/37123386. - PMC - PubMed
    1. Chowdhary A, Sharma C, Meis JF. Candida auris: An emerging fungus that presents a serious global health threat. J Fungi. 2023;9(3):239. https://pubmed.ncbi.nlm.nih.gov/36891046. - PMC - PubMed
    1. Widdifield J, Bernatsky S, Paterson JM, Gunraj N, Thorne JC. Mortality burden associated with all-cause pneumonia among adults with autoimmune inflammatory rheumatic diseases, human immunodeficiency virus infection, and malignancies: a population-based comparative study for informed decision-making in public health policies. BMC Infect Dis. 2020;20(1):203. https://pubmed.ncbi.nlm.nih.gov/32180041. - PubMed
    1. Cureus. The impact of pulmonary rehabilitation in a case of acute respiratory distress syndrome with bronchopneumonia: A case report. Cureus. 2022;14(12):e31583. https://pubmed.ncbi.nlm.nih.gov/36686089. - PMC - PubMed

LinkOut - more resources