ARDS may induce dysbiosis of the respiratory tract microbiota and lead to long-term pulmonary sequelae. In COVID-19-related ARDS, it is to date unclear if the presence of a disrupted microbiota is associated with long-term pulmonary function impairment. We investigated the association between oropharyngeal microbiota and outcomes in lung function after severe COVID-19 comparing subjects who suffered from COVID-19-related ARDS to those who did not develop ARDS.

16S rRNA amplicon sequencing was performed on oropharyngeal swabs at 3 to 12 months after hospitalisation from 83 subjects (n=174 samples) previously admitted to the ICU with severe COVID-19 (Swiss COVID lung study, NCT04581135). Subjects underwent 1-3 follow-up visits during which lung function testing was performed to investigate correlation with microbiota composition.

Fifty-three subjects (64%) suffered from ARDS and had altered microbiota composition compared to non-ARDS subjects at all time-points. This was independent of antibiotics administration during hospitalisation. TLC was negatively correlated with bacterial richness 12 months post-hospitalisation (p=0.05 in both groups). Among subjects with COVID-19-related ARDS, ongoing respiratory impairment (TLC <80%) was associated with a higher abundance in Leptotrichia compared to subjects with TLC ≥80%. In contrast, patients without ARDS had a higher abundance in Leptotrichia when TLC ≥80%, in comparison to TLC impairment (p=0.017).

Up to 12 months post-hospitalisation, patients recovering from severe COVID-19 have a distinct oropharyngeal microbiota from those with impaired total lung capacity, relative to ARDS status. Analyses on bacterial species are ongoing.