1887

Journal of Medical Microbiology logo

Volume 70, Issue 1

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 Open Access

Abstract

Bloodstream infection is a common complication in patients with severe pneumonia and is regarded as an independent risk factor for prediction of poor outcome. Metagenomic next-generation sequencing (mNGS) has been widely applied for pathogen determination of various clinical specimens from patients with infectious diseases. However, the clinical significance of and necessity for simultaneous pathogen detection of both blood samples and bronchoalveolar lavage fluid (BALF) by mNGS in patients with severe pneumonia remains unclear.

. Simultaneous detection of pathogens from both BALF and blood samples in patients with severe pneumonia helps to determine the complication of the bloodstream infection.

This study aimed to elucidate the clinical significance and necessity of pathogen detection simultaneously in both blood samples and BALF samples with the application of mNGS in patients with severe pneumonia.

In this study, 20 patients with severe pneumonia were enrolled and the potential pathogens in both BALF and blood samples were detected simultaneously by conventional microbial examination and mNGS tests. Moreover, multiple consecutive microbial detections were undertaken to investigate the dynamic variation of pathogens during the course of disease progression in two of the 20 patients.

In 85 % (17/20) of the patients with severe pneumonia, various pathogens were determined positively in the BALF by mNGS, including 10 cases with bacterial infection, five cases with viral infection and two cases with fungal infection. By contrast, pathogens in 50 % (10/20) of cases could be detected positively in the BALF by conventional microbial tests. Among 17 severe pneumonia patients with mNGS-positive BALF, pathogens were also identified in 10 cases with mNGS-positive blood samples. By contrast, only one patient complicated with a bloodstream infection could be found by conventional bacterial culture. Moreover, the pathogens from BALF were highly consistent with that from blood samples detected by mNGS in the early stage of the disease. With disease progression and after recurrent antibiotic treatment, significant dynamic changes of the microbial species from the BALF and blood samples could be clearly found by mNGS.

This study emphasizes the utility of mNGS in the rapid simultaneous detection of pathogens from both BALF and blood samples in patients with severe pneumonia, and could allow determination of bloodstream infection and guide clinicians regarding antimicrobial treatments.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bloodstream infection , bronchoalveolar lavage fluid , metagenomic next-generation sequencing and severe pneumonia
Funding
This study was supported by the:
  • College of Dentistry, University of Tennessee (US) (Award NO.B2017019, A2018163)
    • Principle Award Recipient: Zhi-jian Yu
  • Specialized Research Fund for the Doctoral Program of Higher Education of China (CN) (Award No. 2019032, NO.2019001, NO.2019004, NO.2019005, NO.2019027, NO2018064)
    • Principle Award Recipient: Zhi-jian Yu
  • Shenzhen Key Medical Discipline Construction Fund (Award No.SZXK06162)
    • Principle Award Recipient: Zhi-jian Yu
  • the Science, Technology and Innovation Commission of Shenzhen Municipality (Award No. JCYJ20170412143551332)
    • Principle Award Recipient: Zhi-jian Yu
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.001259
2020-11-24
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/jmm/70/1/jmm001259.html?itemId=/content/journal/jmm/10.1099/jmm.0.001259&mimeType=html&fmt=ahah

References

  1. Lozano R, Naghavi M, Foreman K, Lim S, Shibuya K et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the global burden of disease study 2010. Lancet 2012; 380:2095–2128 [View Article][PubMed]
     [Google Scholar]
  2. Magill SS, Edwards JR, Bamberg W, Beldavs ZG, Dumyati G et al. Multistate point-prevalence survey of health care-associated infections. N Engl J Med 2014; 370:1198–1208 [View Article][PubMed]
     [Google Scholar]
  3. Lim WS, Baudouin SV, George RC, Hill AT, Jamieson C et al. Bts guidelines for the management of community acquired pneumonia in adults: update 2009. Thorax 2009; 64:iii1–iii55 [View Article][PubMed]
     [Google Scholar]
  4. Søgaard M, Nørgaard M, Dethlefsen C, Schønheyder HC. Temporal changes in the incidence and 30-day mortality associated with bacteremia in hospitalized patients from 1992 through 2006: a population-based cohort study. Clin Infect Dis 2011; 52:61–69 [View Article][PubMed]
     [Google Scholar]
  5. Lee JH, Kim YH. Predictive factors of true bacteremia and the clinical utility of blood cultures as a prognostic tool in patients with community-onset pneumonia. Medicine 2016; 95:e5058 [View Article][PubMed]
     [Google Scholar]
  6. Jain S, Self WH, Wunderink RG, Fakhran S, Balk R et al. Community-Acquired pneumonia requiring hospitalization among U.S. adults. N Engl J Med 2015; 373:415–427 [View Article][PubMed]
     [Google Scholar]
  7. Ramanujam P, Rathlev NK. Blood cultures do not change management in hospitalized patients with community-acquired pneumonia. AcadEmerg Med 2006; 13:740–745 [View Article]
     [Google Scholar]
  8. Forbes JD, Knox NC, Ronholm J, Pagotto F, Reimer A et al. Metagenomics: the next culture-independent game changer. Front Microbiol 2017; 8:1069 [View Article][PubMed]
     [Google Scholar]
  9. Goldberg B, Sichtig H, Geyer C, Ledeboer N, Weinstock GM et al. Making the leap from research laboratory to clinic: challenges and opportunities for next-generation sequencing in infectious disease diagnostics. mBio 2015; 6:e01888–15 [View Article][PubMed]
     [Google Scholar]
  10. Thorburn F, Bennett S, Modha S et al. The use of next generation sequencing in the diagnosis and typing of respiratory infections. J Clin Virol 2015
     [Google Scholar]
  11. Horiba K, Kawada J-I, Okuno Y, Tetsuka N, Suzuki T et al. Comprehensive detection of pathogens in immunocompromised children with bloodstream infections by next-generation sequencing. Sci Rep 2018; 8:3784 [View Article][PubMed]
     [Google Scholar]
  12. Parize P, Muth E, Richaud C, Gratigny M, Pilmis B et al. Untargeted next-generation sequencing-based first-line diagnosis of infection in immunocompromised adults: a multicentre, blinded, prospective study. Clin Microbiol Infect 2017; 23:574.e1–57574 [View Article][PubMed]
     [Google Scholar]
  13. van Beek J, de Graaf M, Smits S, Schapendonk CME, Verjans GMGM et al. Whole-Genome next-generation sequencing to study within-host evolution of norovirus (nov) among immunocompromised patients with chronic nov infection. J Infect Dis 2017; 216:1513–1524 [View Article][PubMed]
     [Google Scholar]
  14. Mandell LA, Wunderink RG, Anzueto A, Bartlett JG, Campbell GD et al. Infectious diseases society of America/American thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults. Clin Infect Dis 2007; 44 Suppl 2:S27–S72 [View Article][PubMed]
     [Google Scholar]
  15. de Grooth HJ, Geenen IL, Girbes AR, Vincent J-L, Parienti J-J et al. SOFA and mortality endpoints in randomized controlled trials: a systematic review and meta-regression analysis. Crit Care 2017; 21:38 [View Article][PubMed]
     [Google Scholar]
  16. Selvaraju SB, Selvarangan R, Rangaraj S. Evaluation of three influenza A and B real-time reverse transcription-PCR assays and a new 2009 H1N1 assay for detection of influenza viruses. J Clin Microbiol 2010; 48:3870–3875 [View Article][PubMed]
     [Google Scholar]
  17. Bai B, Wang H, Li M, Ma X, Zheng J et al. Two cases of influenza B virus-related fatal fulminant pneumonia complicated with Staphylococcus aureus infection in China diagnosed using next-generation sequencing (2018). Front Public Health 2020; 8: [View Article]
     [Google Scholar]
  18. Chen N, Jin K, Xu J, Zhang J, Weng Y. Human African trypanosomiasis caused by Trypanosoma brucei gambiense: the first case report in China. Int J Infect Dis 2019; 79:34–36 [View Article][PubMed]
     [Google Scholar]
  19. Zhou X, Wu H, Ruan Q, Jiang N, Chen X et al. Clinical evaluation of diagnosis efficacy of active Mycobacterium tuberculosis complex infection via metagenomic next-generation sequencing of direct clinical samples. Front Cell Infect Microbiol 2019; 9:351 [View Article][PubMed]
     [Google Scholar]
  20. Vincent J, Rello J, Marshall J, Silva E, Anzueto A et al. International study of the prevalence and outcomes of infection in intensive care units. JAMA 2009; 302:2323–2329 [View Article][PubMed]
     [Google Scholar]
  21. Brooks D, Smith A, Young D, Fulton R, Booth MG et al. Mortality in intensive care: the impact of bacteremia and the utility of systemic inflammatory response syndrome. Am J Infect Control 2016; 44:1291–1295 [View Article][PubMed]
     [Google Scholar]
  22. Klein EY, Monteforte B, Gupta A, Jiang W, May L et al. The frequency of influenza and bacterial coinfection: a systematic review and meta-analysis. Influenza Other Respir Viruses 2016; 10:394–403 [View Article][PubMed]
     [Google Scholar]
  23. Rozencwajg S, Bréchot N, Schmidt M, Hékimian G, Lebreton G et al. Co-Infection with influenza-associated acute respiratory distress syndrome requiring extracorporeal membrane oxygenation. Int J Antimicrob Agents 2018; 51:427–433 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.001259
Loading
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. 70, 001259 (2021); https://doi.org/10.1099/jmm.0.001259
/content/journal/jmm/10.1099/jmm.0.001259
/content/journal/jmm/10.1099/jmm.0.001259
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error