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The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia
  1. Tetyana Zakharkina1,
  2. Ignacio Martin-Loeches2,
  3. Sébastien Matamoros1,
  4. Pedro Povoa3,
  5. Antoni Torres4,
  6. Janine B Kastelijn1,
  7. Jorrit J Hofstra5,
  8. B de Wever5,
  9. Menno de Jong6,
  10. Marcus J Schultz1,
  11. Peter J Sterk8,
  12. Antonio Artigas7,
  13. Lieuwe D J Bos1,8
  1. 1Intensive Care, Academic Medical Center, Amsterdam, Netherlands
  2. 2Intensive Care, St James Hospital, Dublin, Ireland
  3. 3Intensive Care, Centro Hospitalar de Lisboa Central, Lisbon, Portugal
  4. 4Department of Pneumology, Hospital Clinic i Provincial, Barcelona, Spain
  5. 5Clinical Microbiology, Academic Medical Center, Amsterdam, Netherlands
  6. 6Department of Microbiology, Academic Medical Center, Amsterdam, Netherlands
  7. 7Critical Care Centre, Corporació Sanitària I Universitaria Parc Taulí—Hospital De Sabadell-Ciber Enfermedades Respiratorias, Sabadell, Spain
  8. 8Department of Respiratory Medicine, Academic Medical Center, Amsterdam, Netherlands
  1. Correspondence to Dr Lieuwe DJ Bos, University of Amsterdam, Meibergdreef 9, room M0-127, Amsterdam 1105AZ, The Netherlands; L.d.bos{at}amc.uva.nl

Abstract

Rationale Ventilator-associated pneumonia (VAP) is the most common nosocomial infections in patients admitted to the ICU. The adapted island model predicts several changes in the respiratory microbiome during intubation and mechanical ventilation.

Objectives We hypothesised that mechanical ventilation and antibiotic administration decrease the diversity of the respiratory microbiome and that these changes are more profound in patients who develop VAP.

Methods Intubated and mechanically ventilated ICU-patients were included. Tracheal aspirates were obtained three times a week. 16S rRNA gene sequencing with the Roche 454 platform was used to measure the composition of the respiratory microbiome. Associations were tested with linear mixed model analysis and principal coordinate analysis.

Measurements and main results 111 tracheal aspirates were obtained from 35 patients; 11 had VAP, 18 did not have VAP. Six additional patients developed pneumonia within the first 48 hours after intubation. Duration of mechanical ventilation was associated with a decrease in α diversity (Shannon index; fixed-effect regression coefficient (β): −0.03 (95% CI −0.05 to −0.005)), but the administration of antibiotic therapy was not (fixed-effect β: 0.06; 95% CI −0.17 to 0.30). There was a significant difference in change of β diversity between patients who developed VAP and control patients for Bray-Curtis distances (p=0.03) and for Manhattan distances (p=0.04). Burkholderia, Bacillales and, to a lesser extent, Pseudomonadales positively correlated with the change in β diversity.

Conclusion Mechanical ventilation, but not antibiotic administration, was associated with changes in the respiratory microbiome. Dysbiosis of microbial communities in the respiratory tract was most profound in patients who developed VAP.

  • Pneumonia
  • Bacterial Infection

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Footnotes

  • Contributors TZ: Literature search, data collection, data analysis, data interpretation and writing. IM-L: Study design, data collection, data interpretation and writing. SM: Data collection, data analysis, data interpretation and writing. PP: Study design, data collection, data interpretation and writing. AT: Study design, data collection, data interpretation and writing. JBK: Data collection, data interpretation and writing. JJH: Data collection, data analysis, data interpretation and writing. BdW: Data collection, data interpretation and writing. MdJ: Data collection, data interpretation and writing. MJS: Study design, data interpretation and writing. PJS: Study design, data interpretation and writing. AA: Study design, data collection, data interpretation and writing. LDJB: Study design, literature search, data collection, data analysis, data interpretation and writing.

  • Funding Grant by the Instituto de Salud Carlos III (ISCIII) (ISCIII/FIS-PI 12/01815) Spanish Government and Institut Merieux Research grant.

  • Competing interests None declared.

  • Patient consent Obtained.

  • Ethics approval Parc Tauli, Sabadell, Spain (IRB: 2008/524).

  • Provenance and peer review Not commissioned; externally peer reviewed.

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