Insights of how lung microbiome can contribute to COVID-19 severity in intensive care unit patients

Abstract

Objectives: Secondary bacterial and fungal infections are associated with respiratory viral infections and invasive mechanical ventilation. Microbiome influence on COVID-19 severity in patients admitted to intensive care units (ICU) remains poorly understood. This work described the lung microbiota of Brazilian COVID-19 patients and explored how microbial pathogens can contribute to Coronavirus disease 2019 clinical outcome. Methods: Total DNA of bronchoalveolar lavage fluids from 21 Brazilian COVID-19 patients was extracted. All patients were positive RT-PCR and admitted to intensive care units in two Brazilian centers. For metagenomic analyses, sequenced reads were submitted to bioinformatic tools for taxonomic and functional inferences. Results: We identified respiratory, nosocomial, and opportunistic pathogens as prevalent bacteria in the lung, suggesting a dysbiosis process (microbial imbalance) in ICU COVID-19 patients. Microbial functional analyses showed metabolic pathways associated with virulence repertoire, such as biofilm production, secreted toxins, capsular polysaccharides, and iron acquisition. Microbial pathogens and their virulence mechanisms were associated with host immunological responses, and a cellular model suggesting how bacterial species could participate in COVID-19 worsening was presented. Conclusion: We explore how microbial species present in the lung could potentially modulate and aggravate the immunological processes of patients admitted to intensive care units, contributing to COVID-19 severity.