Dysbiosis: an indicator of COVID-19 severity in critically ill patients

Abstract Background: Research into the association between the microbiome and SARS-CoV-2 infection and acute respiratory distress syndrome remains unclear. Here we examined the dynamics of the gut and respiratory microbiomes in severe COVID-19 cases in need of mechanical ventilation in the intensive care unit (ICU).Methods: We recruited 76 critically ill patients (48 with COVID-19 and 32 without COVID-19) and 17 healthy controls (HCs) and monitored them for up to 4 weeks. We analyzed the bacterial and fungal taxonomic profiles and loads of 232 gut and respiratory samples and we measured blood levels of Interleukin 6, IgG, and IgM in COVID-19 patients.Results: At ICU admission, bacterial composition and load in the gut and respiratory samples were altered in critically ill patients compared to HCs. Six bacterial species could discriminate ICU-COV(+) from ICU-COV(-) cases. During their time in the ICU, all patients experienced increased bacterial and fungal loads, decreased bacterial richness, and progressive changes in bacterial and fungal taxonomic profiles. In ICU-COV(+) patients, Pseudomonas was found positively and Streptococcus negatively correlated with the length of ICU stay. Respiratory bacterial signatures, associated with disease severity and inflammation markers, were predictive of death and a fecal dysbiosis score, associated negatively with PaO2/FiO2 ratio, could be used as an additional indicator for ICU admission.Conclusion: We propose using a high-throughput sequencing approach as an alternative to traditional isolation techniques to monitor the ICU-COV(+) patient infection.