Lung microbiota but not mycobiota predicts day 28 mortality in critically ill influenza patients: a feasibility study

The aim of this study is to assess the prognostic value of lung microbiota in critically ill influenza patients. Every PCR-proven influenza patient admitted to intensive care unit of two hospitals for respiratory failure during 2019-2020 pandemics were included (NCT04131296). Sputum or tracheal aspirates were sampled and DNA extraction was performed by QIAamp® PowerFecal® Pro DNA kit (QIAgen®). V3-V4 regions of 16SRNA coding gene was amplified to analyse the bacterial kingdom of lung microbiota (bacteriobiota) and ITS2 to analyse the fungal kingdom (mycobiota). Sequencing (2x250bp paired-end reads) was performed on MiSeq sequencer (Illumina®) and DADA2 pipeline on R software was used for bioinformatics analyses.