Additional file 1 of Bridging gut microbiota composition with extended-spectrum beta-lactamase Enterobacteriales faecal carriage in critically ill patients (microbe cohort study)
Creators: name: Prevel, Renaud
name: Enaud, Raphaël
name: Orieux, Arthur
name: Camino, Adrian
name: Sioniac, Pierre
name: M’Zali, Fatima
name: Dubois, Véronique
name: Berger, Patrick
name: Boyer, Alexandre
name: Delhaes, Laurence
name: Gruson, Didier
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Non metric Bray-curtis analysis of β-diversity of the V3-V4 sequencing run. XXA, B, and C samples: gut bacteriobiota samples. GXX: lung bacteriobiota samples. BlancV3-V4: negative control. Mock: mock community. Figure S2. Non metric Bray-curtis analysis of β-diversity of ITS2 sequencing run. XXA, B, and C samples: gut mycobiota samples. GXX: lung mycobiota samples. Blanc1 and blanc2: negative controls. Mock: mock community. Figure S3. Comparison of gut bacteriobiota and mycobiota between critically ill ESBL-producing Enterobacteriales fecal carriers and non-carriers. A. Boxplot of estimated α-diversity for gut bacteriobiota by Shannon index. B. Boxplot of estimated α-diversity for gut bacteriobiota by Simpson index. C. Metric Bray-curtis analysis of β-diversity for gut bacteriobiota. Threshold for statistical significance: p=0.05. D. Boxplot of estimated α-diversity for gut mycobiota by Shannon index. E. Boxplot of estimated α-diversity for gut mycobiota by Simpson index. F. Metric Bray-curtis analysis of β-diversity for gut mycobiota. Threshold for statistical significance: p=0.05. ATB: prior antimicrobial therapy within the 3 previous months. no-ATB: no prior antimicrobial therapy within the 3 previous months. Figure S4. Comparison of gut mycobiota between critically ill ESBL-producing Escherichia coli and Klebsiella pneumoniae faecal carriers. A. Boxplot of estimated α-diversity by Shannon index. B. Boxplot of estimated α-diversity by Simpson index. C. Boxplot of estimated α-diversity by evenness. D. Metric Bray-curtis analysis of β-diversity. red: E. coli, green: K. pneumoniae. Threshold for statistical significance: p=0.05. Figure S5. Comparison of gut bacteriobiota between critically ill ESBL-producing Escherichia coli (in red) and matched non ESBL-E (in blue) faecal carriers. A. Boxplot of estimated α-diversity by Shannon index. B. Boxplot of estimated α-diversity by Simpson index. C. Boxplot of estimated α-diversity by evenness. D. Metric Bray-curtis analysis of β-diversity. Threshold for statistical significance: p=0.05. Figure S6. Comparison of gut mycobiota between critically ill ESBL-producing Escherichia coli faecal carriers (in red) and matched non ESBL-E faecal carriers (in blue). A. Boxplot of estimated α-diversity by Shannon index. B. Boxplot of estimated α-diversity by Simpson index. C. Boxplot of estimated α-diversity by evenness. D. Metric Bray-curtis analysis of β-diversity. Threshold for statistical significance: p=0.05. Figure S7. Comparison of gut mycobiota between critically ill ESBL-producing Klebsiella pneumoniae faecal carriers (in red) and matched non ESBL-E faecal carriers (in blue). A. Boxplot of estimated α-diversity by Shannon index. B. Boxplot of estimated α-diversity by Simpson index. C. Boxplot of estimated α-diversity by evenness. D. Metric Bray-curtis analysis of β-diversity. Threshold for statistical significance: p=0.05.