1. Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients
- Author
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Roman Rohrbach, Silvana Hengler, Alwin Krämer, Rogier Gaiser, Michael W. Müller, Felix J.F. Herth, Jochen Schneider, Dina Khalid, Nyssa Cullin, Theresa Hippchen, Christoph K. Stein-Thoeringer, Peter Hau, Stamatia M Papagiannarou, Matthias P. Ebert, Dirk Jäger, Yascha Khodamoradi, Andreas Teufel, Maria J G T Vehreschild, Ralf Bartenschlager, Bernd Salzberger, Daniel Duerschmied, Juliana de Castilhos, Andreas Hiergeist, Paul Schnitzler, André Gessner, Eran Elinav, Melanie Neubauer, Sabine Schmidt, Hendrik Poeck, Roland M. Schmid, Hanna Schumacher, Uta Merle, Tonia Müller-Esch, Bettina Beuthien-Baumann, Sabrina Kunz, Eli Zamir, and Johann F Eberhardt
- Subjects
Adult ,Microbiology (medical) ,medicine.medical_specialty ,medicine.drug_class ,Critical Illness ,medicine.medical_treatment ,Antibiotics ,Haemophilus ,microbiome ,medicine.disease_cause ,Internal medicine ,intensive medical care ,Major Article ,medicine ,Humans ,Microbiome ,Coronavirus ,Mechanical ventilation ,biology ,SARS-CoV-2 ,business.industry ,Microbiota ,COVID-19 ,dysbiosis ,medicine.disease ,biology.organism_classification ,Cross-Sectional Studies ,AcademicSubjects/MED00290 ,machine learning ,Infectious Diseases ,Respiratory virus ,Neisseria ,business ,Dysbiosis - 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.
- Published
- 2021