title: Characterisation of Candida within the Mycobiome/Microbiome of the Lower Respiratory Tract of ICU Patients.
abstract: Whether the presence of Candida spp. in lower respiratory tract (LRT) secretions is a marker of underlying disease, intensive care unit (ICU) treatment and antibiotic therapy or contributes to poor clinical outcome is unclear. We investigated healthy controls, patients with proposed risk factors for Candida growth in LRT (antibiotic therapy, ICU treatment with and without antibiotic therapy), ICU patients with pneumonia and antibiotic therapy and candidemic patients (for comparison of truly invasive and colonizing Candida spp.). Fungal patterns were determined by conventional culture based microbiology combined with molecular approaches (next generation sequencing, multilocus sequence typing) for description of fungal and concommitant bacterial microbiota in LRT, and host and fungal biomarkes were investigated. Admission to and treatment on ICUs shifted LRT fungal microbiota to Candida spp. dominated fungal profiles but antibiotic therapy did not. Compared to controls, Candida was part of fungal microbiota in LRT of ICU patients without pneumonia with and without antibiotic therapy (63% and 50% of total fungal genera) and of ICU patients with pneumonia with antibiotic therapy (73%) (p<0.05). No case of invasive candidiasis originating from Candida in the LRT was detected. There was no common bacterial microbiota profile associated or dissociated with Candida spp. in LRT. Colonizing and invasive Candida strains (from candidemic patients) did not match to certain clades withdrawing the presence of a particular pathogenic and invasive clade. The presence of Candida spp. in the LRT rather reflected rapidly occurring LRT dysbiosis driven by ICU related factors than was associated with invasive candidiasis.
authors.affiliation: Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
authors.forename: Robert
authors.initials: R
authors.lastname: Krause
authors.affiliation: Bioinformatics, Institute for Knowledge Discovery, University of Technology, Graz, Austria and OMICS Center Graz, Graz, Austria.|BioTechMed-Graz, Graz, Austria.|Institute of Pathology, Medical University of Graz, Graz, Austria.
authors.forename: Bettina
authors.initials: B
authors.lastname: Halwachs
authors.affiliation: Institute of Molecular Biotechnology, University of Technology, Graz, Austria.
authors.forename: Gerhard G
authors.initials: GG
authors.lastname: Thallinger
authors.affiliation: Center for Medical Research, Medical University of Graz, Graz, Austria.
authors.forename: Ingeborg
authors.initials: I
authors.lastname: Klymiuk
authors.affiliation: Institute of Pathology, Medical University of Graz, Graz, Austria.
authors.forename: Gregor
authors.initials: G
authors.lastname: Gorkiewicz
authors.affiliation: Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
authors.forename: Martin
authors.initials: M
authors.lastname: Hoenigl
authors.affiliation: Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Prattes
authors.affiliation: Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Valentin
authors.affiliation: Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.|Department of Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Heidrich
authors.affiliation: Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
authors.forename: Walter
authors.initials: W
authors.lastname: Buzina
authors.affiliation: Division of Clinical Infectious Diseases, Research Center Borstel, Leibnitz Center for Medicine and Biosciences, Borstel, Germany.
authors.forename: Helmut J F
authors.initials: HJ
authors.lastname: Salzer
authors.affiliation: Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria.
authors.forename: Jasmin
authors.initials: J
authors.lastname: Rabensteiner
authors.affiliation: Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria.
authors.forename: Florian
authors.initials: F
authors.lastname: Prüller
authors.affiliation: Division of Angiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
authors.forename: Reinhard B
authors.initials: RB
authors.lastname: Raggam
authors.affiliation: Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria.
authors.forename: Andreas
authors.initials: A
authors.lastname: Meinitzer
authors.affiliation: Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
authors.forename: Christine
authors.initials: C
authors.lastname: Moissl-Eichinger
authors.affiliation: Theodor Escherich Laboratory for Microbiome Research, Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
authors.forename: Christoph
authors.initials: C
authors.lastname: Högenauer
authors.affiliation: Institute for Medical Informatics, Statistics, and Documentation, Medical University of Graz, Graz, Austria.
authors.forename: Franz
authors.initials: F
authors.lastname: Quehenberger
authors.affiliation: Institute of Pathology, Medical University of Graz, Graz, Austria.
authors.forename: Karl
authors.initials: K
authors.lastname: Kashofer
authors.affiliation: Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
authors.forename: Ines
authors.initials: I
authors.lastname: Zollner-Schwetz
mesh_terms: D000368:Aged; D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D002175:Candida / Q000145:classification / Q000187:drug effects / Q000235:genetics / Q000472:pathogenicity*; D002177:Candidiasis / Q000175:diagnosis / Q000188:drug therapy; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007362:Intensive Care Units / Q000706:statistics & numerical data*; D008297:Male; D064307:Microbiota / Q000502:physiology*; D008875:Middle Aged; D009055:Mouth / Q000382:microbiology; D000072761:Mycobiome / Q000502:physiology*; D010802:Phylogeny; D011014:Pneumonia / Q000188:drug therapy / Q000382:microbiology; D012137:Respiratory System / Q000382:microbiology*; D012307:Risk Factors
chemical_list: D000900:Anti-Bacterial Agents