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Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia

Nature Medicine volume 29, pages 2793–2804 (2023)Cite this article

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Abstract

Respiratory microbial dysbiosis is associated with acute respiratory distress syndrome (ARDS) and hospital-acquired pneumonia (HAP) in critically ill patients. However, we lack reproducible respiratory microbiome signatures that can increase our understanding of these conditions and potential treatments. Here, we analyze 16S rRNA sequencing data from 2,177 respiratory samples collected from 1,029 critically ill patients (21.7% with ARDS and 26.3% with HAP) and 327 healthy controls, sourced from 17 published studies. After data harmonization and pooling of individual patient data, we identified microbiota signatures associated with ARDS, HAP and prolonged mechanical ventilation. Microbiota signatures for HAP and prolonged mechanical ventilation were characterized by depletion of a core group of microbes typical of healthy respiratory samples, and the ARDS microbiota signature was distinguished by enrichment of potentially pathogenic respiratory microbes, including Pseudomonas and Staphylococcus. Using machine learning models, we identified clinically informative, three- and four-factor signatures that predicted ARDS, HAP and prolonged mechanical ventilation with relatively high accuracy (area under the curve of 0.751, 0.72 and 0.727, respectively). We validated the signatures in an independent prospective cohort of 136 patients on mechanical ventillation and found that patients with microbiome signatures associated with ARDS, HAP or prolonged mechanical ventilation had longer times to successful extubation than patients lacking these signatures (hazard ratios of 1.56 (95% confidence interval (CI) 1.07–2.27), 1.51 (95% CI 1.02–2.23) and 1.50 (95% CI 1.03–2.18), respectively). Thus, we defined and validated robust respiratory microbiome signatures associated with ARDS and HAP that may help to identify promising targets for microbiome therapeutic modulation in critically ill patients.

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Fig. 1: Respiratory microbiome alterations along the airways of critically ill patients.
Fig. 2: Respiratory microbiome signatures of ARDS in ETAs.
Fig. 3: Respiratory microbiome signatures of HAP in ETAs.
Fig. 4: Respiratory microbiome signatures of successful extubation in ETAs.
Fig. 5: External validation of respiratory microbiome signatures in an independent prospective cohort.

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Data availability

Correspondence and requests should be addressed to A.R. The 16S rRNA sequence dataset of the validation cohort has been deposited in a secure file by CHU Nantes (HAP2 data hub) and in the BioProject repository (PRJNA1020542). The data from the studies included in the meta-analysis can be found at figshare at https://figshare.com/s/46c402c6465c8a289c18, https://doi.org/10.6084/m9.figshare.3496412, https://doi.org/10.6084/m9.figshare.3496538, https://doi.org/10.6084/m9.figshare.3485201 and in the BioProject repository: PRJEB26875, PRJEB13056, PRJEB20913, PRJNA267584, SRP062137, PRJEB20665, PRJNA678854, PRJNA595346, SRP112361, PRJNA553560, PRJNA553560, SRP076183, PRJNA339755. The accession for each study is reported in Supplementary Tables 1–3.

Code availability

All analyses were performed using publicly available software and published code as described in the Methods. All custom codes generated for data analyses in this study are reported in the Methods.

References

  1. He, Q. et al. The epidemiology and clinical outcomes of ventilator-associated events among 20,769 mechanically ventilated patients at intensive care units: an observational study. Crit. Care 25, 44 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  2. Bellani, G. et al. Epidemiology, patterns of care, and mortality for patients with acute respiratory distress syndrome in intensive care units in 50 countries. JAMA 315, 788–800 (2016).

    Article  CAS  PubMed  Google Scholar 

  3. Roquilly, A. et al. Implementation of French recommendations for the prevention and the treatment of hospital-acquired pneumonia: a cluster-randomized trial. Clin. Infect. Dis. 73, e1601–e1610 (2020).

    Article  Google Scholar 

  4. Magill, S. S. et al. Changes in prevalence of health care–associated infections in U.S. hospitals. N. Engl. J. Med. 379, 1732–1744 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Roquilly, A. et al. Interferon gamma-1b for the prevention of hospital-acquired pneumonia in critically ill patients: a phase 2, placebo-controlled randomized clinical trial. Intensive Care Med. 49, 530–544 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Luyt, C.-E. et al. Pulmonary infections complicating ARDS. Intensive Care Med. 46, 2168–2183 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Morris, A. & Flores, S. C. Study of the lung microbiome. Have we reached the end of the beginning?. Am. J. Resp. Crit. Care Med. 195, 15–16 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  8. Charlson, E. S. et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am. J. Resp. Crit. Care Med. 184, 957–963 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Man, W. H., Piters, W. A. A., de, S. & Bogaert, D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat. Rev. Microbiol. 15, 259–270 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Dickson, R. P. et al. Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography. Ann. Am. Thorac. Soc. 12, 821–830 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Dickson, R. P., Erb-Downward, J. R. & Huffnagle, G. B. Homeostasis and its disruption in the lung microbiome. Am. J. Physiol. Lung Cell. Mol. Physiol. 309, L1047–L1055 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Dickson, R. P. et al. The lung microbiota of healthy mice are highly variable, cluster by environment, and reflect variation in baseline lung innate immunity. Am. J. Resp. Crit. Care Med. 198, 497–508 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Dickson, R. P. et al. Lung microbiota predict clinical outcomes in critically ill patients. Am. J. Resp. Crit. Care Med. 201, 555–563 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Dickson, R. P. et al. Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome. Nat. Microbiol. 1, nmicrobiol2016113 (2016).

    Article  Google Scholar 

  15. Kelly, B. J. et al. Composition and dynamics of the respiratory tract microbiome in intubated patients. Microbiome 4, 7 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Kitsios, G. D. et al. Respiratory tract dysbiosis is associated with worse outcomes in mechanically ventilated patients. Am. J. Resp. Crit. Care Med. 202, 1666–1677 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Panzer, A. R. et al. Lung microbiota is related to smoking status and to development of acute respiratory distress syndrome in critically ill trauma patients. Am. J. Resp. Crit. Care Med. 197, 621–631 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Emonet, S. et al. Identification of respiratory microbiota markers in ventilator-associated pneumonia. Intensive Care Med. 45, 1082–1092 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Sommerstein, R. et al. Patterns in the longitudinal oropharyngeal microbiome evolution related to ventilator-associated pneumonia. Antimicrob. Resist. Infect. Control 8, 81 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  20. Qi, X. et al. Lower respiratory tract microbial composition was diversified in Pseudomonas aeruginosa ventilator-associated pneumonia patients. Respir. Res. 19, 139 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  21. Fromentin, M., Ricard, J.-D. & Roux, D. Respiratory microbiome in mechanically ventilated patients: a narrative review. Intensive Care Med. 47, 292–306 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Force, A. D. T. et al. Acute respiratory distress syndrome: the Berlin definition. JAMA 307, 2526–2533 (2012).

    Google Scholar 

  23. Torres, A. et al. International ERS/ESICM/ESCMID/ALAT guidelines for the management of hospital-acquired pneumonia and ventilator-associated pneumonia. Eur. Respir. J. 50, 1700582 (2017).

    Article  PubMed  Google Scholar 

  24. Kalil, A. C. et al. Management of adults with hospital-acquired and ventilator-associated pneumonia: 2016 clinical practice guidelines by the Infectious Diseases Society of America and the American Thoracic Society. Clin. Infect. Dis. 63, e61–e111 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  25. Dickson, R. P. et al. Bacterial topography of the healthy human lower respiratory tract. mBio 8, e02287–16 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Morris, A. et al. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am. J. Resp. Crit. Care Med. 187, 1067–1075 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  27. Bassis, C. M. et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. mBio 6, e00037–15 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  28. Chotirmall, S. H. et al. Therapeutic targeting of the respiratory microbiome. Am. J. Resp. Crit. Care Med. 206, 535–544 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  29. François, B. et al. Efficacy and safety of suvratoxumab for prevention of Staphylococcus aureus ventilator-associated pneumonia (SAATELLITE): a multicentre, randomised, double-blind, placebo-controlled, parallel-group, phase 2 pilot trial. Lancet Infect. Dis. 21, 1313–1323 (2021).

    Article  PubMed  Google Scholar 

  30. Johnstone, J. et al. Effect of probiotics on incident ventilator-associated pneumonia in critically ill patients. JAMA 326, 1024–1033 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Litton, E. et al. Early and sustained Lactobacillus plantarum probiotic therapy in critical illness: the randomised, placebo-controlled, restoration of gut microflora in critical illness trial (ROCIT). Intensive Care Med. 47, 307–315 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Cheng, A. G. et al. Design, construction, and in vivo augmentation of a complex gut microbiome. Cell 185, e19 (2022).

    Article  Google Scholar 

  33. Rangan, K. J. et al. A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens. Science 353, 1434–1437 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Mitsi, E. et al. Nasal pneumococcal density is associated with microaspiration and heightened human alveolar macrophage responsiveness to bacterial pathogens. Am. J. Resp. Crit. Care Med. 201, 335–347 (2019).

    Article  Google Scholar 

  35. Stewart, C. J. et al. Associations of nasopharyngeal metabolome and microbiome with severity among infants with bronchiolitis. A multiomic analysis. Am. J. Resp. Crit. Care Med. 196, 882–891 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Fatahi-Bafghi, M. Characterization of the Rothia spp. and their role in human clinical infections. Infect. Genet. Evol. 93, 104877 (2021).

    Article  CAS  PubMed  Google Scholar 

  37. Crémet, L. et al. Evaluation of the FilmArray® Pneumonia Plus panel for rapid diagnosis of hospital-acquired pneumonia in intensive care unit patients. Front. Microbiol. 11, 2080 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  38. Pendleton, K. M. et al. Rapid pathogen identification in bacterial pneumonia using real-time metagenomics. Am. J. Resp. Crit. Care Med. 196, 1610–1612 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Guillotin, F. et al. Potential impact of rapid multiplex PCR on antimicrobial therapy guidance for ventilated hospital-acquired pneumonia in critically ill patients, a prospective observational clinical and economic study. Front. Cell. Infect. Microbiol. 12, 804611 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Moy, A.-C. et al. Performance evaluation of a PCR panel (FilmArray® Pneumonia Plus) for detection of respiratory bacterial pathogens in respiratory specimens: a systematic review and meta-analysis. Anaesth. Crit. Care Pain Med. 42, 101300 (2023).

    Article  PubMed  Google Scholar 

  41. Wirbel, J. et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat. Med. 25, 679–689 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Lee, K. A. et al. Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nat. Med. 28, 535–544 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Chanderraj, R. et al. In critically ill patients, anti-anaerobic antibiotics increase risk of adverse clinical outcomes. Eur. Respir. J. 61, 2200910 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Kitsios, G. D. et al. The upper and lower respiratory tract microbiome in severe aspiration pneumonia. iScience 26, 106832 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Amir, A. et al. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2, e00191–16 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  46. Kyo, M. et al. Unique patterns of lower respiratory tract microbiota are associated with inflammation and hospital mortality in acute respiratory distress syndrome. Respir. Res. 20, 246 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  47. Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. McDonald, D. et al. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience 1, 7 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  49. DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Hafenbrädl, S., Waeger, D., Marewski, J. N. & Gigerenzer, G. Applied decision making with fast-and-frugal heuristics. J. Appl. Res. Mem. Cogn. 5, 215–231 (2016).

    Article  Google Scholar 

  51. Raab, M. & Gigerenzer, G. The power of simplicity: a fast-and-frugal heuristics approach to performance science. Front. Psychol. 6, 1672 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  52. Phillips, N. D., Neth, H., Woike, J. K. & Gaissmaier, W. FFTrees: a toolbox to create, visualize, and evaluate fast-and-frugal decision trees. Judgm. Decis. Mak. 12, 344–368 (2017).

    Article  Google Scholar 

  53. Hothorn, T., Hornik, K., van de Wiel, M. A. & Zeileis, A. Implementing a class of permutation tests: the coin package. J. Stat. Softw. 28, 1–23 (2008).

    Article  Google Scholar 

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Acknowledgements

We thank the Genomics and Bioinformatics Core Facility of Nantes (GenoBiRD, Biogenouest) for its technical support and the Biological Resource Center for Biobanking of CHU Nantes (Centre de Ressources Biologiques, Nantes, France; BRIF no. BB-0033-00040). We thank D. Flattres Duchaussoy (CHU Nantes) for administrative assistance. The study was funded by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 847782 (HAP2 project). A.R. and R.D. received grants from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 847782. A.R. received funding from the Agence National de la Recherche (ANR) PROGRAM project and the MSD Avenir grant (Phenomenon project). R.D. was funded by the NIH (grants R01HL144599 and K24HL159247). S.V.L. was funded by the NIH (grants RO1 HL143998, P01 AI148104 and P01 AI128482). G.D.K. received funding from the NIH (grants K23 HL139987 and R03 HL162655) and Karius. B.J.K. received funding from the NIH (grant K23 AI121485). R.P.D. received funding from the NIH (grants R01 HL144599 and K24 HL159247) and Horizon H2020 (grant no. 847782). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Author information

Authors and Affiliations

  1. Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes Université, Inserm, CHU Nantes, Nantes, France

    Emmanuel Montassier & Antoine Roquilly

  2. Service des Urgences, Nantes Université, CHU Nantes, Nantes, France

    Emmanuel Montassier & Quentin Le Bastard

  3. Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA

    Georgios D. Kitsios & Josiah E. Radder

  4. Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA

    Georgios D. Kitsios & Josiah E. Radder

  5. Department of Medicine, Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA, USA

    Brendan J. Kelly

  6. Department of Medicine, Division of Gastroenterology, University of California, San Francisco, CA, USA

    Ariane Panzer & Susan V. Lynch

  7. Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA

    Carolyn S. Calfee

  8. Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Health System, Ann Arbor, MI, USA

    Robert P. Dickson

  9. Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA

    Robert P. Dickson

  10. Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI, USA

    Robert P. Dickson

  11. Service d’Anesthesie Réanimation, Nantes Université, CHU Nantes, Nantes, France

    Antoine Roquilly

  12. Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia

    Antoine Roquilly

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Contributions

E.M., G.D.K., R.P.D. and A.R. selected studies, performed data analyses, interpreted results and drafted the manuscript. J.E.R., Q.L.B., B.J.K., A.P., S.L. and C.S.C. interpreted results and revised the manuscript. All authors have approved the final manuscript for publication.

Corresponding authors

Correspondence to Emmanuel Montassier or Antoine Roquilly.

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Competing interests

A.R. has received grants from MSD and bioMerieux, and consulting fees from MSD. G.D.K. has received funding from Karius. S.V.L. is a co-founder and board member of Siolta Therapeutics and has received consulting fees from Sanofi. All other authors have no competing interests.

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Nature Medicine thanks Leo Celi, Willem Joost Wiersinga and the other, anonymous, reviewer for their contribution to the peer review of this work. Primary Handling Editor: Alison Farrell, in collaboration with the Nature Medicine team.

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Montassier, E., Kitsios, G.D., Radder, J.E. et al. Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia. Nat Med 29, 2793–2804 (2023). https://doi.org/10.1038/s41591-023-02617-9

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