Additional file 1 of Oropharyngeal and intestinal concentrations of opportunistic pathogens are independently associated with death of SARS-CoV-2 critically ill adults

Additional file 1: Table S1. Result of the initial 16S rDNA sequencing in rectal samples. Table S2. Per pathogen rectal and oropharyngeal culture positivity, time to first positivity and abundance at first positivity. Table S3. Adjusted impact of abundance of Enterococcus spp., S. aureus and Candida spp. in oropharynx and rectum on day 90 mortality. (one adjusted model for each). Table S4. Univariate analysis of day 90 mortality* comparing survivors versus descedents. Fig S1. Quantitative culturing on agar plates. CFU: colony-forming unit. Fig S2. Pie chart of the distribution of Enterococcus spp. and Candida spp. species obtained by culture of all the rectal swabs (A) and oropharyngeal (B) swabs. Fig S3. Dot plots of the intestinal Enterococcus spp. and Candida spp. with regards to intestinal richness (genus level), Shannon and inverse Simpson indices. The Pearson correlation test was used (with the intestinal concentrations being considered as continuous variables)