Hospitalisation dynamics.

Simulations of the hospitalisation evolution (solid lines) are compared to data from Fig 1 (diamonds). Simulations were performed with the new hospitalisation simulations from Fig 5F as input, and with hospital parameters extracted from the clinical data in Fig 6). The simulations after February 2021 show the hospitalisation progression in a scenario where the social restrictions from January 2021 would have persisted throughout 2021 without the impact of new viral strains and vaccinations. (A-D) Evolution of patients hospitalised (A), in ICU (B), deceased in ICU (C), and recovered patients that were released from hospitals (D). The simulated recovered are the sum of patients released from hospital compartments j = 3 and j = 5. (E) Age group dependent Infection Fatality Ratio (IFR) computed by dividing the cumulated deceased from (C) with the cumulated new infections from Fig 5A. The dashed lines indicate the analytic values 0.0005%, 0.019%, 0.24%, 0.81%, and 2.62% computed with the probabilities for asymptomatic to become symptomatic, for symptomatic to become hospitalised, to be transferred to ICU, and to die in ICU. For the mean IFR we find 0.2%.</p

Checkpoint events where we changed the social contact matrix.

Events that had a confining effect are marked with bold font, deconfining events with italic font. The simulation period starts at 01/01/2020.</p

Conditional probabilities of symptoms to highlight the major differences among clusters.

<p>Cluster 1: the young symptomatic. Cluster 2: the old obese. Cluster 3: the multi-disease (MD) old obese. Cluster 4: the young snorers. Cluster 5: the drowsy obese. Cluster 6: the MD obese symptomatic</p

Conditional probabilities of BMI, age and risk factors to highlight the major differences among clusters.

<p>Cluster 1: the young symptomatic. Cluster 2: the old obese. Cluster 3: the multi-disease (MD) old obese. Cluster 4: the young snorers. Cluster 5: the drowsy obese. Cluster 6: the MD obese symptomatic</p

Patients characteristics of the entire cohort and by clusters: Co-morbidities.

<p>Values in Numbers (%).</p

Conditional probabilities of co-morbidities to highlight the major differences among clusters.

<p>Cluster 4 was not represented in this figure because the probability to have cardiovascular and metabolic co-morbidities was near 0. Cluster 1: the young symptomatic. Cluster 2: the old obese. Cluster 3: the multi-disease (MD) old obese. Cluster 5: the drowsy obese. Cluster 6: the MD obese symptomatic</p

Patients characteristics of the entire cohort and by clusters: Anthropometric and demographic characteristics.

<p>Values in Numbers (%) or median [IQR]. Body Mass Index (BMI). Cluster 1: the young symptomatic. Cluster 2: the old obese. Cluster 3: the multi-disease (MD) old obese. Cluster 4: the young snorers. Cluster 5: the drowsy obese. Cluster 6: the MD obese symptomatic.</p

Representation of six clusters after ascending hierarchical clustering analysis.

<p>Axes correspond to individual coordinates for the two main dimensions of the multiple correspondence analysis. Cluster 1: the young symptomatic. Cluster 2: the old obese. Cluster 3: the multi-disease (MD) old obese. Cluster 4: the young snorers. Cluster 5: the drowsy obese. Cluster 6: the MD obese symptomatic.</p

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)

Characteristics of study population at the ICU admission.

<p>Characteristics of study population at the ICU admission.</p