Transcriptome analysis reveals increased abundance and diversity of opportunistic fungal pathogens in nasopharyngeal tract of COVID-19 patients

Abstract

We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species. Likewise, Recovered humans NT samples were predominated by Aspergillus penicillioides (36.64%), A. keveii (23.36%), A. oryzae (10.05%) and A. pseudoglaucus (4.42%). Conversely, Nannochloropsis oceanica (47.93%), Saccharomyces pastorianus (34.42%), and S. cerevisiae (2.80%) were the top abundant fungal species in Healthy controls nasal swabs. Importantly, 16% commensal fungal species found in the Healthy controls were not detected in either COVID-19 patients or when they were cured from COVID-19 (Recovered). We also detected several altered metabolic pathways correlated with the dysbiosis of fungal mycobiota in COVID-19 patients. Our results suggest that SARS-CoV-2 infection causes significant dysbiosis of mycobiome and related metabolic functions possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. These findings might be helpful for developing mycobiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.

Metagenomic insights into fungal community composition of the nasopharyngeal region of COVID‐19 associated mucormycosis patients from India

“…It was also seen that opportunistic pathogens like Candida sp. increased in abundance 26 . In our analysis, we found that the alpha diversity was lower ( p < 0.05) between the healthy cohort and the SCT2 cohort.…”

“…increased in abundance. 26 In our analysis, we found that the alpha diversity was lower (p < 0.05) between the healthy cohort and the SCT2 cohort. These were the group of patients who had received systemic corticosteroids, antibiotics, and antivirals.…”

Longitudinal study across SARS-CoV-2 variants identifies transcriptionally active microbes (TAMs) associated with Delta severity

“…To overcome this problem, we analyzed Kraken2 output with Bracken2 (Bayesian Re-estimation of Abundance after classification with KrakEN), which uses the taxonomy assigned by Kraken2 to estimate the number of reads per sample that come from different species, using the Kraken report output file. 13 , 14 , 15 , 16 , 17 The Kraken2 database was utilized to construct a Bracken-compatible database using the Bracken build function. An in-house Python program was written to combine the output from the bracken report file and add lineage information and convert it into a biom file using Kraken-biome to import into R for further analysis.…”

“… 13 Many studies have demonstrated the superiority of commensal microbial composition over opportunistic pathogens in the early recovery of COVID-19 patients. 14 , 15 , 16 These findings suggest the importance of understanding the dynamics of TAMs in longitudinal studies with respect to the COVID-19 patients who were exposed to the virus during several waves, and if so, how this could be coupled to the severity of the disease and the patients' clinical outcomes.…”

Brief Overview of Clinical Evidence for Homeopathic Interventions in the Management of COVID-19 Patients

“…6,7 In addition to its recognized use in treating chronic diseases, individualized homeopathy may also be effective in resolving or managing acute cases, including epidemic diseases. 8,9 However, it is important to emphasize that the use of customized homeopathy requires precise diagnosis and treatment to ensure its efficacy and safety. In epidemic diseases, which often present similar symptomatology in affected individuals, the individualized homeopathic medicine should be selected based on the signs and symptoms that the patient presents at different stages or phases of the outbreak.…”