Metagenomic Next‑generation Sequencing of BALF for the Clinical Diagnosis of Severe Community‑acquired Pneumonia in Immunocompromised Patients: A Single‑center Study

Overview

Journal Exp Ther Med

Specialty Pathology

Date 2023 Apr 3

PMID 37006881

Authors

Xiaohui Zhang

Yuhong Qin

Wei Lei

Jian-An Huang

Affiliations

Soon will be listed here.

Abstract

The diagnostic methods of conventional microbiological tests (CMTs) for severe community-acquired pneumonia (SCAP) may be too complicated or impossible to use in polymicrobial infections, and it may be difficult to identify unexpected pathogens. CMTs are also limited due to the early application of broad-spectrum or prophylactic antimicrobial drugs and the fastidious or slow-growing pathogenic microorganisms. The present study aimed to investigate the value of mNGS compared with CMTs in the clinical diagnosis of SCAP in immunocompromised individuals. Therefore, 37 patients diagnosed with SCAP in immunocompromised adult patients were enrolled from the Respiratory Intensive Care Unit of the First Affiliated Hospital of Soochow University (Soochow, China) between May 1, 2019, and March 30, 2022. A bronchoalveolar lavage fluid sample from each individual was divided in half. Half was sent to the microbiology laboratory directly for examination, and the other one was sent for DNA extraction and sequencing. In addition, other relevant specimens (such as blood) were sent for CMTs, including culture or smear, T-spot, acid-fast stain, antigen detection, multiplex PCR and direct microscopic examination. Based on a composite reference standard, the diagnostic outcomes were compared between CMTs and mNGS. Among the enrolled patients, 31 patients were diagnosed with microbiologically confirmed pneumonia, with 16 (43.2%) having monomicrobial infections, while 15 (40.5%) had polymicrobial infections. Fungi were the most common etiologic pathogens in immunosuppressive individuals. (45.9%) and spp. (18.9%) were the most common etiologic pathogens. Initial screening test validity of mNGS [sensitivity=96.8%; specificity=33.3%; positive predictive value (PPV)=88.2%; negative predictive value (NPV)=66.6%; likelihood ratio (LR)+, 1.45; LR-, 0.10) was higher compared with that of CMTs (sensitivity=38.7%; specificity=82.3; PPV=92.3%; NPV=20.8%; LR+, 2.3; LR-, 0.74). The total diagnostic accuracy of mNGS was superior to CMTs and it was statistically significantly different [86.5% (32/37) vs. 45.9% (17/37); P<0.001]. In conclusion, the total diagnostic accuracy of mNGS was superior to CMTs for SCAP in immunocompromised patients as an important diagnostic method.

Citing Articles

Validation of metagenomic next-generation sequencing of bronchoalveolar lavage fluid for diagnosis of suspected pulmonary infections in patients with systemic autoimmune rheumatic diseases receiving immunosuppressant therapy.

Wen S, Peng S, Hu X, Jiang N, Li B, Chen B Front Med (Lausanne). 2023; 10:1161661.

PMID: 37484860 PMC: 10359889. DOI: 10.3389/fmed.2023.1161661.

References

Duan H, Li X, Mei A, Li P, Liu Y, Li X . The diagnostic value of metagenomic next⁃generation sequencing in infectious diseases. BMC Infect Dis. 2021; 21(1):62. PMC: 7805029. DOI: 10.1186/s12879-020-05746-5. View

Han D, Li Z, Li R, Tan P, Zhang R, Li J . mNGS in clinical microbiology laboratories: on the road to maturity. Crit Rev Microbiol. 2019; 45(5-6):668-685. DOI: 10.1080/1040841X.2019.1681933. View

Goldberg B, Sichtig H, Geyer C, Ledeboer N, Weinstock G . Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics. mBio. 2015; 6(6):e01888-15. PMC: 4669390. DOI: 10.1128/mBio.01888-15. View

Wu X, Gu S, Cai Y, Zhai T, Zhan Q . [Etiology of severe community-acquired pneumonia in immunocompromised patients]. Zhonghua Jie He He Hu Xi Za Zhi. 2021; 44(10):892-896. DOI: 10.3760/cma.j.cn112147-20210131-00087. View

Wilson M, Sample H, Zorn K, Arevalo S, Yu G, Neuhaus J . Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis. N Engl J Med. 2019; 380(24):2327-2340. PMC: 6764751. DOI: 10.1056/NEJMoa1803396. View

Quah J, Jiang B, Tan P, Siau C, Tan T . Impact of microbial Aetiology on mortality in severe community-acquired pneumonia. BMC Infect Dis. 2018; 18(1):451. PMC: 6122562. DOI: 10.1186/s12879-018-3366-4. View

Montull B, Menendez R, Torres A, Reyes S, Mendez R, Zalacain R . Predictors of Severe Sepsis among Patients Hospitalized for Community-Acquired Pneumonia. PLoS One. 2016; 11(1):e0145929. PMC: 4699794. DOI: 10.1371/journal.pone.0145929. View

Pan T, Tan R, Qu H, Weng X, Liu Z, Li M . Next-generation sequencing of the BALF in the diagnosis of community-acquired pneumonia in immunocompromised patients. J Infect. 2018; 79(1):61-74. PMC: 7133759. DOI: 10.1016/j.jinf.2018.11.005. View

Zhang P, Chen Y, Li S, Li C, Zhang S, Zheng W . Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study. PeerJ. 2020; 8:e9623. PMC: 7395598. DOI: 10.7717/peerj.9623. View

10.

Sun T, Wu X, Cai Y, Zhai T, Huang L, Zhang Y . Metagenomic Next-Generation Sequencing for Pathogenic Diagnosis and Antibiotic Management of Severe Community-Acquired Pneumonia in Immunocompromised Adults. Front Cell Infect Microbiol. 2021; 11:661589. PMC: 8204719. DOI: 10.3389/fcimb.2021.661589. View

11.

Bateman C, Kesson A, Powys M, Wong M, Blyth E . Cytomegalovirus Infections in Children with Primary and Secondary Immune Deficiencies. Viruses. 2021; 13(10). PMC: 8538792. DOI: 10.3390/v13102001. View

12.

Lopardo G, Fridman D, Raimondo E, Albornoz H, Lopardo A, Bagnulo H . Incidence rate of community-acquired pneumonia in adults: a population-based prospective active surveillance study in three cities in South America. BMJ Open. 2018; 8(4):e019439. PMC: 5898349. DOI: 10.1136/bmjopen-2017-019439. View

13.

Spasovska K, Grozdanovski K, Milenkovic Z, Bosilkovski M, Cvetanovska M, Kuzmanovski N . Evaluation of severity scoring systems in patients with severe community acquired pneumonia. Rom J Intern Med. 2021; 59(4):394-402. DOI: 10.2478/rjim-2021-0025. View

14.

Wilson M, ODonovan B, Gelfand J, Sample H, Chow F, Betjemann J . Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing. JAMA Neurol. 2018; 75(8):947-955. PMC: 5933460. DOI: 10.1001/jamaneurol.2018.0463. View

15.

Abril M, Barnett A, Wegermann K, Fountain E, Strand A, Heyman B . Diagnosis of Sepsis by Whole-Genome Next-Generation Sequencing. Open Forum Infect Dis. 2016; 3(3):ofw144. PMC: 5047422. DOI: 10.1093/ofid/ofw144. View

16.

Burnham P, Dadhania D, Heyang M, Chen F, Westblade L, Suthanthiran M . Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract. Nat Commun. 2018; 9(1):2412. PMC: 6010457. DOI: 10.1038/s41467-018-04745-0. View

17.

Li Y, Sun B, Tang X, Liu Y, He H, Li X . Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients. Eur J Clin Microbiol Infect Dis. 2019; 39(2):369-374. PMC: 7102353. DOI: 10.1007/s10096-019-03734-5. View

18.

Qu J, Zhang J, Chen Y, Huang Y, Xie Y, Zhou M . Aetiology of severe community acquired pneumonia in adults identified by combined detection methods: a multi-centre prospective study in China. Emerg Microbes Infect. 2022; 11(1):556-566. PMC: 8843176. DOI: 10.1080/22221751.2022.2035194. View

19.

Ivy M, Thoendel M, Jeraldo P, Greenwood-Quaintance K, Hanssen A, Abdel M . Direct Detection and Identification of Prosthetic Joint Infection Pathogens in Synovial Fluid by Metagenomic Shotgun Sequencing. J Clin Microbiol. 2018; 56(9). PMC: 6113468. DOI: 10.1128/JCM.00402-18. View

20.

Blauwkamp T, Thair S, Rosen M, Blair L, Lindner M, Vilfan I . Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol. 2019; 4(4):663-674. DOI: 10.1038/s41564-018-0349-6. View