de Castilhos, Juliana ORCID: 0000-0001-9966-8657, Zamir, Eli, Hippchen, Theresa, Rohrbach, Roman ORCID: 0000-0003-3458-6620, Schmidt, Sabine, Hengler, Silvana, Schumacher, Hanna ORCID: 0000-0003-2665-9236, Neubauer, Melanie, Kunz, Sabrina, Mueller-Esch, Tonia, Hiergeist, Andreas, Gessner, Andre, Khalid, Dina, Gaiser, Rogier, Cullin, Nyssa, Papagiannarou, Stamatia M., Beuthien-Baumann, Bettina, Kraemer, Alwin, Bartenschlager, Ralf, Jaeger, Dirk, Mueller, Michael, Herth, Felix, Duerschmied, Daniel, Schneider, Jochen, Schmid, Roland M., Eberhardt, Johann F., Khodamoradi, Yascha ORCID: 0000-0001-5972-0967, Vehreschild, Maria J. G. T., Teufel, Andreas, Ebert, Matthias P., Hau, Peter, Salzberger, Bernd, Schnitzler, Paul, Poeck, Hendrik, Elinav, Eran, Merle, Uta and Stein-Thoeringer, Christoph K. (2022). Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients. Clin. Infect. Dis., 75 (1). S. E1063 - 9. CARY: OXFORD UNIV PRESS INC. ISSN 1537-6591

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Abstract

Background At the entry site of respiratory virus infections, the oropharyngeal microbiome has been proposed as a major hub integrating viral and host immune signals. Early studies suggested that infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are associated with changes of the upper and lower airway microbiome, and that specific microbial signatures may predict coronavirus disease 2019 (COVID-19) illness. However, the results are not conclusive, as critical illness can drastically alter a patient's microbiome through multiple confounders. Methods To study oropharyngeal microbiome profiles in SARS-CoV-2 infection, clinical confounders, and prediction models in COVID-19, we performed a multicenter, cross-sectional clinical study analyzing oropharyngeal microbial metagenomes in healthy adults, patients with non-SARS-CoV-2 infections, or with mild, moderate, and severe COVID-19 (n = 322 participants). Results In contrast to mild infections, patients admitted to a hospital with moderate or severe COVID-19 showed dysbiotic microbial configurations, which were significantly pronounced in patients treated with broad-spectrum antibiotics, receiving invasive mechanical ventilation, or when sampling was performed during prolonged hospitalization. In contrast, specimens collected early after admission allowed us to segregate microbiome features predictive of hospital COVID-19 mortality utilizing machine learning models. Taxonomic signatures were found to perform better than models utilizing clinical variables with Neisseria and Haemophilus species abundances as most important features. Conclusions In addition to the infection per se, several factors shape the oropharyngeal microbiome of severely affected COVID-19 patients and deserve consideration in the interpretation of the role of the microbiome in severe COVID-19. Nevertheless, we were able to extract microbial features that can help to predict clinical outcomes. Coronavirus disease 2019 (COVID-19) infections can affect the architecture of the oropharyngeal microbiome in severe cases. Neisseriaor Haemophilusspp. can predict poor outcomes in hospitalized patients, but antibiotic treatments, ventilation, or sampling timepoints are major confounders when considering microbiome features as biomarkers.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
de Castilhos, JulianaUNSPECIFIEDorcid.org/0000-0001-9966-8657UNSPECIFIED
Zamir, EliUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hippchen, TheresaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rohrbach, RomanUNSPECIFIEDorcid.org/0000-0003-3458-6620UNSPECIFIED
Schmidt, SabineUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hengler, SilvanaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schumacher, HannaUNSPECIFIEDorcid.org/0000-0003-2665-9236UNSPECIFIED
Neubauer, MelanieUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kunz, SabrinaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mueller-Esch, ToniaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hiergeist, AndreasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gessner, AndreUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Khalid, DinaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gaiser, RogierUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Cullin, NyssaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Papagiannarou, Stamatia M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Beuthien-Baumann, BettinaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kraemer, AlwinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Bartenschlager, RalfUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jaeger, DirkUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mueller, MichaelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Herth, FelixUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Duerschmied, DanielUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schneider, JochenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schmid, Roland M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Eberhardt, Johann F.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Khodamoradi, YaschaUNSPECIFIEDorcid.org/0000-0001-5972-0967UNSPECIFIED
Vehreschild, Maria J. G. T.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Teufel, AndreasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ebert, Matthias P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hau, PeterUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Salzberger, BerndUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schnitzler, PaulUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Poeck, HendrikUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Elinav, EranUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Merle, UtaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Stein-Thoeringer, Christoph K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-692583
DOI: 10.1093/cid/ciab902
Journal or Publication Title: Clin. Infect. Dis.
Volume: 75
Number: 1
Page Range: S. E1063 - 9
Date: 2022
Publisher: OXFORD UNIV PRESS INC
Place of Publication: CARY
ISSN: 1537-6591
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
Immunology; Infectious Diseases; MicrobiologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/69258

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