• Stéphane Emonet, Vladimir Lazarevic, Corinne Leemann Refondini, Nadia Gaïa, Stefano Leo, Myriam Girard, Nocquet Boyer Valérie V Division of Intensive Care, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland., Hannah Wozniak, Lena Després, Gesuele Renzi, Khaled Mostaguir, Elise Dupuis Lozeron, Jacques Schrenzel, and Jérôme Pugin.
• Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, University of Geneva, 4 Rue Gabrielle-Perret-Gentil, 1211, Geneva, Switzerland. stephane.emonet@hcuge.ch.
• Intensive Care Med. 2019 Aug 1; 45 (8): 1082-1092.

PurposeTo compare bacteria recovered by standard cultures and metataxonomics, particularly with regard to ventilator-associated pneumonia (VAP) pathogens, and to determine if the presence of particular bacteria or microbiota in tracheal and oropharyngeal secretions during the course of intubation was associated with the development of VAP.MethodsIn this case-control study, oropharyngeal secretions and endotracheal aspirate were collected daily in mechanically ventilated patients. Culture and metataxonomics (16S rRNA gene-based taxonomic profiling of bacterial communities) were performed on serial upper respiratory samples from patients with late-onset definite VAP and their respective controls.ResultsMetataxonomic analyses showed that a low relative abundance of Bacilli at the time of intubation in the oropharyngeal secretions was strongly associated with the subsequent development of VAP. On the day of VAP, the quantity of human and bacterial DNA in both tracheal and oropharyngeal secretions was significantly higher in patients with VAP than in matched controls with similar ventilation times. Molecular techniques identified the pathogen(s) of VAP found by culture, but also many more bacteria, classically difficult to culture, such as Mycoplasma spp. and anaerobes.ConclusionsMolecular analyses of respiratory specimens identified markers associated with the development of VAP, as well as important differences in the taxa abundance between VAP and controls. Further prospective trials are needed to test the predictive value of these markers, as well as the relevance of uncultured bacteria in the pathogenesis of VAP.

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