title: Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients.
abstract: The spread of microorganisms in hospitals is an important public health threat, and yet few studies have assessed how human microbial communities (microbiota) evolve in the hospital setting. Studies conducted so far have mainly focused on a limited number of bacterial species, mostly pathogenic ones and primarily during outbreaks. We explored the bacterial community diversity of the microbiota from oral and respiratory samples of intubated patients hospitalized in the intensive care unit and we discuss the technical challenges that may arise while using culture-independent approaches to study these types of samples.
authors.affiliation: Genomic Research Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Lazarevic
authors.affiliation: Genomic Research Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland.
authors.forename: Nadia
authors.initials: N
authors.lastname: Gaïa
authors.affiliation: Clinical Microbiology Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland ; Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals Geneva, Switzerland.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Emonet
authors.affiliation: Genomic Research Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland.
authors.forename: Myriam
authors.initials: M
authors.lastname: Girard
authors.affiliation: Clinical Microbiology Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland.
authors.forename: Gesuele
authors.initials: G
authors.lastname: Renzi
authors.affiliation: Clinical Microbiology Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland.
authors.forename: Lena
authors.initials: L
authors.lastname: Despres
authors.affiliation: Clinical Microbiology Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland.
authors.forename: Hannah
authors.initials: H
authors.lastname: Wozniak
authors.affiliation: Medical Diagnostic Discovery Department, BioMérieux Grenoble, France.
authors.forename: Javier
authors.initials: J
authors.lastname: Yugueros Marcos
authors.affiliation: Data and Knowledge Laboratory, BioMérieux Marcy l'Etoile, France.
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Veyrieras
authors.affiliation: Research and Development Microbiology, BioMérieux La Balme-les-Grottes, France.
authors.forename: Sonia
authors.initials: S
authors.lastname: Chatellier
authors.affiliation: Research and Development Microbiology, BioMérieux La Balme-les-Grottes, France.
authors.forename: Alex
authors.initials: A
authors.lastname: van Belkum
authors.affiliation: Laboratory of Intensive Care, Department of Anaesthesiology, Pharmacology and Intensive Care, Geneva University Hospitals Geneva, Switzerland.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Pugin
authors.affiliation: Genomic Research Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland ; Clinical Microbiology Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland.
authors.forename: Jacques
authors.initials: J
authors.lastname: Schrenzel
mesh_terms: D058448:Biota; D006801:Humans; D007362:Intensive Care Units; D007442:Intubation, Intratracheal; D008828:Microbiological Techniques / Q000379:methods; D064307:Microbiota; D008967:Molecular Biology / Q000379:methods; D009055:Mouth / Q000382:microbiology*; D010865:Pilot Projects; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012137:Respiratory System / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 16S rDNA profiling; bacterial communities; endotracheal aspirate; microbiota; supraglottic secretions