ABSTRACT
Background
The COVID-19 pandemic has intensified interest in how the infection affects the lung microbiome of critically ill patients and how it contributes to acute respiratory distress syndrome (ARDS). We aimed to characterize the lower respiratory tract mycobiome of critically ill patients with COVID-19 in comparison to patients without COVID-19.
Methods
We performed an internal transcribed spacer 2 (ITS2) profiling with the Illumina MiSeq platform on 26 respiratory specimens from patients with COVID-19 as well as from 26 patients with non–COVID-19 pneumonia.
Results
Patients with COVID-19 were more likely to be colonized with Candida spp. ARDS was associated with lung dysbiosis characterized by a shift to Candida species colonization and a decrease of fungal diversity. We also observed higher bacterial phylogenetic distance among taxa in colonized patients with COVID-19. In patients with COVID-19 not colonized with Candida spp., ITS2 amplicon sequencing revealed an increase of Ascomycota unassigned spp. and 1 Aspergillus spp.–positive specimen. In addition, we found that corticosteroid therapy was frequently associated with positive Galactomannan cell wall component of Aspergillus spp. among patients with COVID-19.
Conclusion
Our study underpins that ARDS in patients with COVID-19 is associated with lung dysbiosis and that an increased density of Ascomycota unassigned spp. is present in patients not colonized with Candida spp.
【저자키워드】 COVID-19, ARDS, NGS, Next-generation sequencing, acute respiratory disease syndrome, Dysbiosis, Mycobiome, 【초록키워드】 Pneumonia, COVID-19 pandemic, Infection, lung, Patient, Microbiome, Aspergillus, platform, fungal, Bacterial, acute respiratory distress, Amplicon sequencing, Lower respiratory tract, Candida, Phylogenetic, Critically ill patient, galactomannan, Illumina Miseq, specimen, syndrome, positive, corticosteroid therapy, Affect, Cell, decrease, spacer, Result, respiratory specimen, performed, addition, characterized, contribute, transcribed, Ascomycota, patients with COVID-19, patients without COVID-19, with COVID-19, 【제목키워드】 lung, Patient, fungal, Candida, microbial, Critically ill patient, reduced, with COVID-19,