The novel coronavirus SARS-CoV-2, responsible for the COVID-19 pandemic, may result in long- term pulmonary sequelae in patients having suffered from severe disease. Increasing evidence shows that abnormal pulmonary function, especially diffusing capacity for carbon monoxide (DLCO), total lung capacity (TLC) and desaturation during the 6-minute walk test (6-MWT) are correlated with severe disease, even after 12 months. It has been reported that SARS-CoV-2 is associated with disturbed respiratory microbiota during the acute phase of infection, which may contribute to further inflammation and tissue destruction, thus affecting lung function. However, it is not clear whether the disrupted microbiota is associated with long-term pulmonary damage. The objective of our study was to determine whether oropharyngeal microbiota alteration following severe SARS-CoV-2- infection is associated with long-term pulmonary function abnormalities. To our knowledge, this is the first follow-up study to analyse the link between respiratory microbiota and lung function in severe COVID-19 patients 3, 6 and 12 months after hospitalisation.
We conducted 16S rRNA sequencing on oropharyngeal swabs collected 3 to 12 months after hospitalisation from 31 patients with severe COVID-19. Patients underwent 1 to 3 follow-up visits during which lung function tests (DLCO, TLC) and a 6-MWT were performed. We analysed the composition and structure of the bacterial communities and, employing dedicated bioinformatics tools in RStudio sought for associations with DLCO, TLC and desaturation values.
We observed an association between oropharyngeal microbiota richness and both DLCO and desaturation during the 6-MWT. In addition, the oropharyngeal microbiota in recovered COVID-19 patients with normal pulmonary function differed from the profile observed in patients with ongoing respiratory impairment that was associated with a decrease in phylum heterogeneity and a high relative abundance of Bacteroidetes. In contrast, Firmicutes dominated the oropharyngeal microbiota in recovered patients with normal pulmonary function.
Our results provide evidence of an altered respiratory microbiota in patients with impaired pulmonary function 3 to 12 months following severe COVID-19. Therefore, this data constitutes a basis for further studies, aiming to specify the role of the microbiota in long-term pulmonary sequelae. In addition, this would promote the implementation and development of therapeutic strategies and prevention of severe COVID-19 pulmonary sequelae.