197
Views
1
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

A Paired Comparison of Plasma and Bronchoalveolar Lavage Fluid for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Suspected Severe Pneumonia

, , , , , , & show all
Pages 4369-4379 | Published online: 09 Aug 2022

References

  • Jain S, Self WH, Wunderink RG, et al. Community-acquired pneumonia requiring hospitalization among U.S. adults. N Engl J Med. 2015;373(5):415–427. doi:10.1056/NEJMoa1500245
  • Magill SS, Edwards JR, Bamberg W, et al. Multistate point-prevalence survey of health care-associated infections. N Engl J Med. 2014;370(13):1198–1208. doi:10.1056/NEJMoa1306801
  • Laporte L, Hermetet C, Jouan Y, et al. Ten-year trends in intensive care admissions for respiratory infections in the elderly. Ann Intensive Care. 2018;8(1):84. doi:10.1186/s13613-018-0430-6
  • Ferreira-Coimbra J, Sarda C, Rello J. Burden of community-acquired pneumonia and unmet clinical needs. Adv Ther. 2020;37(4):1302–1318. doi:10.1007/s12325-020-01248-7
  • Ieven M, Coenen S, Loens K, et al. Aetiology of lower respiratory tract infection in adults in primary care: a prospective study in 11 European countries. Clin Microbiol Infect. 2018;24(11):1158–1163. doi:10.1016/j.cmi.2018.02.004
  • Xie Y, Du J, Jin W, et al. Next generation sequencing for diagnosis of severe pneumonia: china, 2010–2018. J Infect. 2019;78(2):158–169. doi:10.1016/j.jinf.2018.09.004
  • Li Y, Sun B, Tang X, et al. Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients. Eur J Clin Microbiol Infect Dis. 2020;39(2):369–374. doi:10.1007/s10096-019-03734-5
  • Chen Y, Feng W, Ye K, et al. Application of metagenomic next-generation sequencing in the diagnosis of pulmonary infectious pathogens from bronchoalveolar lavage samples. Front Cell Infect Microbiol. 2021;11:541092. doi:10.3389/fcimb.2021.541092
  • Zhou H, Larkin PMK, Zhao D, et al. Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage in the diagnosis and management of pneumonia: a multicenter prospective observational study. J Mol Diagn. 2021;23(10):1259–1268. doi:10.1016/j.jmoldx.2021.06.007
  • Simner PJ, Miller S, Carroll KC. Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases. Clin Infect Dis. 2018;66(5):778–788. doi:10.1093/cid/cix881
  • Kalantar KL, Moazed F, Christenson SC, et al. Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota. Am J Physiol Lung Cell Mol Physiol. 2019;316(3):L578–L584. doi:10.1152/ajplung.00476.2018
  • Azar MM, Schlaberg R, Malinis MF, et al. Added diagnostic utility of clinical metagenomics for the diagnosis of pneumonia in immunocompromised adults. Chest. 2020. doi:10.1016/j.chest.2020.11.008
  • Wang Q, Wu B, Yang D, et al. Optimal specimen type for accurate diagnosis of infectious peripheral pulmonary lesions by mNGS. BMC Pulm Med. 2020;20(1):268. doi:10.1186/s12890-020-01298-1
  • Blauwkamp TA, Thair S, Rosen MJ, et al. 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
  • Benamu E, Gajurel K, Anderson JN, et al. Plasma microbial cell-free DNA next generation sequencing in the diagnosis and management of febrile neutropenia. Clin Infect Dis. 2021. doi:10.1093/cid/ciab324
  • Hogan CA, Yang S, Garner OB, et al. Clinical impact of metagenomic next-generation sequencing of plasma cell-free DNA for the diagnosis of infectious diseases: a multicenter retrospective cohort study. Clin Infect Dis. 2021;72(2):239–245. doi:10.1093/cid/ciaa035
  • Zanella MC, Cordey S, Laubscher F, et al. Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease. Microbiome. 2021;9(1):28. doi:10.1186/s40168-020-00953-3
  • Goggin KP, Gonzalez-Pena V, Inaba Y, et al. Evaluation of plasma microbial cell-free DNA sequencing to predict bloodstream infection in pediatric patients with relapsed or refractory cancer. JAMA Oncol. 2020;6(4):552–556. doi:10.1001/jamaoncol.2019.4120
  • Chen J, Zhao Y, Shang Y, et al. The clinical significance of simultaneous detection of pathogens from bronchoalveolar lavage fluid and blood samples by metagenomic next-generation sequencing in patients with severe pneumonia. J Med Microbiol. 2021;70(1). doi:10.1099/jmm.0.001259
  • Jiang J, Bai L, Yang W, et al. Metagenomic next-generation sequencing for the diagnosis of pneumocystis jirovecii pneumonia in non-HIV-infected patients: a retrospective study. Infect Dis Ther. 2021;10(3):1733–1745. doi:10.1007/s40121-021-00482-y
  • Xie F, Duan Z, Zeng W, et al. Clinical metagenomics assessments improve diagnosis and outcomes in community-acquired pneumonia. BMC Infect Dis. 2021;21(1):352. doi:10.1186/s12879-021-06039-1
  • Chen X, Ding S, Lei C, et al. Blood and bronchoalveolar lavage fluid metagenomic next-generation sequencing in pneumonia. Can J Infect Dis Med Microbiol. 2020;2020:6839103. doi:10.1155/2020/6839103
  • Hill JA, Dalai SC, Hong DK, et al. Liquid biopsy for invasive mold infections in hematopoietic cell transplant recipients with pneumonia through next-generation sequencing of microbial cell-free DNA in plasma. Clin Infect Dis. 2020. doi:10.1093/cid/ciaa1639
  • Yang H, Haidar G, Al-Yousif NS, et al. Circulating microbial cell-free DNA is associated with inflammatory host-responses in severe pneumonia. Thorax. 2021;76(12):1231–1235. doi:10.1136/thoraxjnl-2020-216013
  • Langelier C, Fung M, Caldera S, et al. Detection of pneumonia pathogens from plasma cell-free DNA. Am J Respir Crit Care Med. 2020;201(4):491–495. doi:10.1164/rccm.201904-0905LE
  • Cao B, Huang Y, She DY, et al. Diagnosis and treatment of community-acquired pneumonia in adults: 2016 clinical practice guidelines by the Chinese Thoracic Society, Chinese Medical Association. Clin Respir J. 2018;12(4):1320–1360. doi:10.1111/crj.12674
  • Shi Y, Huang Y, Zhang TT, et al. Chinese guidelines for the diagnosis and treatment of hospital-acquired pneumonia and ventilator-associated pneumonia in adults (2018 Edition). J Thorac Dis. 2019;11(6):2581–2616. doi:10.21037/jtd.2019.06.09
  • Metlay JP, Waterer GW, Long AC, et al. Diagnosis and treatment of adults with community-acquired pneumonia. An official clinical practice guideline of the American Thoracic Society and Infectious Diseases Society of America. Am J Respir Crit Care Med. 2019;200(7):e45–e67. doi:10.1164/rccm.201908-1581ST
  • Shankar-Hari M, Phillips GS, Levy ML, et al. Developing a new definition and assessing new clinical criteria for septic shock: for the third international consensus definitions for sepsis and septic shock (sepsis-3). JAMA. 2016;315(8):775–787. doi:10.1001/jama.2016.0289
  • Ramirez JA, Musher DM, Evans SE, et al. Treatment of community-acquired pneumonia in immunocompromised adults: a consensus statement regarding initial strategies. Chest. 2020;158(5):1896–1911. doi:10.1016/j.chest.2020.05.598
  • Zhou F, Wang Y, Liu Y, et al. Disease severity and clinical outcomes of community-acquired pneumonia caused by non-influenza respiratory viruses in adults: a multicentre prospective registry study from the CAP-China Network. Eur Respir J. 2019;54(2). doi:10.1183/13993003.02406-2018
  • Mu S, Hu L, Zhang Y, et al. Prospective evaluation of a rapid clinical metagenomics test for bacterial pneumonia. Front Cell Infect Microbiol. 2021;11:684965. doi:10.3389/fcimb.2021.684965
  • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120. doi:10.1093/bioinformatics/btu170
  • Zaharia M, Bolosky WJ, Curtis K, et al. Faster and more accurate sequence alignment with SNAP; 2011. Available from: https://arxiv.org/abs/1111.5572. Accessed 23 November, 2011.
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–1760. doi:10.1093/bioinformatics/btp324
  • Li H, Gao H, Meng H, et al. Detection of pulmonary infectious pathogens from lung biopsy tissues by metagenomic next-generation sequencing. Front Cell Infect Microbiol. 2018;8:205. doi:10.3389/fcimb.2018.00205
  • Qian YY, Wang HY, Zhou Y, et al. Improving pulmonary infection diagnosis with metagenomic next generation sequencing. Front Cell Infect Microbiol. 2020;10:567615. doi:10.3389/fcimb.2020.567615
  • Zhang F, Chen J, Huang H, et al. Application of metagenomic next-generation sequencing in the diagnosis and treatment guidance of Pneumocystis jirovecii pneumonia in renal transplant recipients. Eur J Clin Microbiol Infect Dis. 2021;40(9):1933–1942. doi:10.1007/s10096-021-04254-x
  • Peng JM, Du B, Qin HY, Wang Q, Shi Y. Metagenomic next-generation sequencing for the diagnosis of suspected pneumonia in immunocompromised patients. J Infect. 2021;82(4):22–27. doi:10.1016/j.jinf.2021.01.029
  • Qu J, Zhang J, Chen Y, et al. 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. doi:10.1080/22221751.2022.2035194
  • Zhan Y, Xu T, He F, et al. Clinical evaluation of a metagenomics-based assay for pneumonia management. Front Microbiol. 2021;12:751073. doi:10.3389/fmicb.2021.751073
  • Gu W, Deng X, Lee M, et al. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med. 2021;27(1):115–124. doi:10.1038/s41591-020-1105-z
  • Kowarsky M, Camunas-Soler J, Kertesz M, et al. Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA. Proc Natl Acad Sci U S A. 2017;114(36):9623–9628. doi:10.1073/pnas.1707009114
  • Fang X, Xu M, Fang Q, et al. Real-time utilization of metagenomic sequencing in the diagnosis and treatment monitoring of an invasive adenovirus B55 infection and subsequent herpes simplex virus encephalitis in an immunocompetent young adult. Open Forum Infect Dis. 2018;5(6):ofy114. doi:10.1093/ofid/ofy114
  • Rezahosseini O, Drabe CH, Sorensen SS, et al. Torque-Teno virus viral load as a potential endogenous marker of immune function in solid organ transplantation. Transplant Rev. 2019;33(3):137–144. doi:10.1016/j.trre.2019.03.004
  • Doberer K, Schiemann M, Strassl R, et al. Torque teno virus for risk stratification of graft rejection and infection in kidney transplant recipients-A prospective observational trial. Am J Transplant. 2020;20(8):2081–2090. doi:10.1111/ajt.15810