Patterns in the longitudinal oropharyngeal microbiome evolution related to ventilator-associated pneumonia.

Sommerstein, Rami; Merz, Tobias M.; Berger, Sabine; Krämer, Julia G.; Marschall, Jonas; Hilty, Markus (2019). Patterns in the longitudinal oropharyngeal microbiome evolution related to ventilator-associated pneumonia. Antimicrobial Resistance and Infection Control, 8, p. 81. BioMed Central 10.1186/s13756-019-0530-6

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The aim of the study was to evaluate the composition and the temporal evolution of the oropharyngeal microbiome in antibiotic-naïve patients requiring mechanical ventilation and to gain new insights into the pathogenesis of ventilator-associated pneumonia (VAP).


Prospective, observational single-center nested case-control study. Patients with acute critical illness and anticipated duration of mechanical ventilation > 4 days were eligible. We took oropharyngeal swabs (and if available, tracheal secretions) daily, starting at the day of intubation. The microbiota was characterized by 16S rRNA high-throughput sequencing and compared between patients developing VAP versus controls.


Five patients developed VAP. In three patient the causative pathogens were Enterobacteriaceae and in two . Locally weighted polynomial regression suggested that the within diversity (=alpha) was lower in Enterobacteriaceae VAP patients between days two to five of mechanical ventilation when compared to controls. Detection of Enterobacteriaceae in the oropharynx occurred on day two of follow-up and consisted of a single operational taxonomic unit in 2/3 patients with enterobacterial VAP.


In acutely-ill patients who developed enterobacterial VAP the causative pathogen gained access to the oropharynx early after starting mechanical ventilation and outgrew the commensal members of the microbiome. Whether a specific pattern of the oropharyngeal microbiome between days three to five of mechanical ventilation may predict VAP enterobacterial VAP has to be evaluated in further studies.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Department of Intensive Care, Emergency Medicine and Anaesthesiology (DINA) > Clinic of Intensive Care
04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Clinic of Infectiology
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases

UniBE Contributor:

Sommerstein, Rami, Merz, Tobias, Krämer, Julia Gabriele, Marschall, Jonas, Hilty, Markus


500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health




BioMed Central




Annelies Luginbühl

Date Deposited:

13 Aug 2019 11:45

Last Modified:

05 Dec 2022 15:28

Publisher DOI:


PubMed ID:


Uncontrolled Keywords:

Infection prevention Intensive care Nosocomial pneumonia Oropharyngeal and tracheal microbiome Ventilator-associated pneumonia




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