Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients.
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de Castilhos Juliana, Zamir Eli, Hippchen Theresa, Rohrbach Roman, Schmidt Sabine, Hengler Silvana, Schumacher Hanna, Neubauer Melanie, Kunz Sabrina, Müller-Esch Tonia, Hiergeist Andreas, Gessner André, Khalid Dina, Gaiser Rogier, Cullin Nyssa, Papagiannarou Stamatia M, Beuthien-Baumann Bettina, Krämer Alwin, Bartenschlager Ralf, Jäger Dirk, Müller Michael, Herth Felix, Duerschmied Daniel, Schneider Jochen, Schmid Roland M, Eberhardt Johann F, Khodamoradi Yascha, Vehreschild Maria J G T, Teufel Andreas, Ebert Matthias P, Hau Peter, Salzberger Bernd, Schnitzler Paul, Poeck Hendrik, Elinav Eran, Merle Uta, Stein-Thoeringer Christoph K
Аннотация
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.