SARS-CoV-2 infection can alter the microbial composition of the upper respiratory tract, favoring the growth of opportunistic fungi. In this context, understanding microbiome structure, with emphasis on the fungal community, is essential to evaluate possible clinical implications. Therefore, this study aimed to characterize the fungal diversity of the upper respiratory tract in individuals with COVID-19, comparing those with and without associated comorbidities. Nasopharyngeal samples from COVID-19 patients underwent shotgun metagenomic sequencing on the Illumina NextSeq500 platform. Taxonomic classification was performed with Kraken2 using the PlusPFP-16 database, and abundances were aggregated at the family level. Diversity metrics (Shannon and Simpson indices) and richness (number of detected families) were estimated, comparing groups with and without comorbidities using the Wilcoxon test. Analyses and visualizations were conducted in R v. 4.5.1. A total of 226 samples were analyzed, of which 50 contained fungal reads, including 34 fungal families, with emphasis on Saccharomycetaceae, Aspergillaceae, Debaryomycetaceae, Cryptococcaceae, and Malasseziaceae. Total fungal abundance was significantly higher in patients with comorbidities (p = 0.039), including immunodeficiency, chronic heart disease, chronic lung disease, chronic kidney disease, and diabetes mellitus. Fungal richness was slightly higher in this group (p = 0.26), while Shannon (p = 0.29) and Simpson (p = 0.29) diversity indices showed no significant differences. The most abundant families varied between groups, with predominance of Aspergillaceae and Saccharomycetaceae in patients with comorbidities. Metagenomic analysis revealed substantial fungal diversity in the upper respiratory tract of individuals with COVID-19, with higher total fungal burden in patients with clinical comorbidities. Despite the absence of significant differences in diversity indices, the higher abundance of opportunistic fungi in individuals with chronic conditions suggests an associated mycological imbalance. These findings highlight the relevance of monitoring the respiratory mycobiome in viral infection contexts, especially given the possibility of secondary fungal infections that may worsen the clinical course and negatively impact outcomes.
Cruz et al. (Sun,) studied this question.