Critically ill patients with COVID-19 show lung fungal dysbiosis with reduced microbial diversity in Candida spp colonized patients

Objectives: The COVID-19 pandemic has intensified interest in how the infection impacts the lung microbiome of critically ill patients and contributes to acute respiratory distress syndrome (ARDS). We aimed to characterize the lower respiratory tract mycobiome of COVID-19 critically ill patients in comparison to COVID-19-negative patients. Methods: We performed an Internal transcribed spacer 2 (ITS2) profiling, with the Illumina MiSeq platform, on 26 respiratory specimens from COVID-19 positive patients as well as from 26 patients with non-COVID-19 pneumonia. Results: COVID-19+ patients were more likely to be colonized with Candida spp. and ARDS was associated with lung dysbiosis characterised by a shift to Candida species colonisation and a decrease of fungal diversity. We also observed higher bacterial phylogenetic distance among taxa in COVID-19+ colonized patients. In COVID-19+ patients non-colonized with Candida spp, ITS2 amplicon sequencing revealed an increase of Ascomycota unassigned spp. and one Aspergillus spp positive specimen. Then, we found that corticosteroid therapy was frequently associated with positive Galactomannan cell wall component of Aspergillus spp among COVID-19+ patients. Conclusions: Our study underpins that ARDS in COVID-19+ patients is associated with lung dysbiosis and that an increased density of Ascomycota unassigned spp. is present in patients not colonized with Candida spp.