gut microbiota and ESBL-E fecal carriage. Microbe

The aim of this study is to assess the link between gut microbiota composition and ESBL-E fecal carriage in critically ill influenza patients. Every patient with ESBL-E fecal carriage and 2 sex- and age-matched critically ill patients admitted to intensive care unit from October 2019 to March 2020 were included (Microbe study, NCT04131569,). Rectal swabs 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.