Additional file 1 of Limited effects of azithromycin on the oropharyngeal microbiome in children with CF and early pseudomonas infection
Creators: name: Wagner, Brandie D.
name: Zemanick, Edith T.
name: Sagel, Scott D.
name: Robertson, Charles E.
name: Stevens, Mark J.
name: Mayer-Hamblett, Nicole
name: Retsch-Bogart, George
name: Ramsey, Bonnie W.
name: Harris, J. Kirk
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Infectious Diseases
subject: FOS: Health sciences

description: Table E1. Changes in microbiome measures from baseline in the PA stratified cohort. Table E2. Describe low MH cohort. Table E3. Effect of AZ treatment on PEx outcomes stratified by changes in microbial composition. Figure E1. Compare bacterial communities between randomized groups at baseline. Heatmap with taxa presented in rows, samples in columns, the darker blue indicates higher RA. Figure E2. Initial eradication cohort. Large shifts in the communities between week 0 and 3 were observed. Morisita-Horn (A) values compare bacterial compositions between week 3 visit and baseline, MH values typically observed between replicates is indicated by the shaded area. Changes in the proportion of shared taxa between paired samples (B) averaged around 45%. Although these changes are significantly different across treatment groups the magnitude of difference is not clinically meaningful. Decreases were observed in both total bacterial load (C) and Shannon Diversity (D) after three weeks of treatment with either Placebo +TIS (n = 97) or azithromycin +TIS (n = 101). AZ=azithromycin; MH=Morisita-Horn beta diversity. Figure E3. Distributions of differences between week 3 and baseline. Boxplots of the differences in RA for select taxa by treatment group are displayed. AZ=azithromycin. Figure E4. Bacterial communities over time. Heatmap with taxa presented in rows, samples in columns, the darker blue indicates higher RA. Figure E5. Distribution of MH by PA stratified cohorts comparing communities at each study visit to baseline. Figure E6. Distribution of change in TBL and SDI over time by PA stratified cohorts. TBL=total bacterial load; SDI = Shannon Diversity Index. Figure E7. Change from baseline for microbial measures by PA stratified cohorts. Figure E8. PEx outcomes (any PEx (top) 0=no, 1=yes; number of PEx (bottom)) plotted versus MH0-13 stratified by treatment. Figure E9. Time to PEx based on initial eradication treatment group stratified by community stability (MH &lt; 0.2). bacterial community profiles for 22 individuals with large shifts in community composition between baseline and week 13 had differential response to treatment. Figure E10. Microbial community composition for 22 subjects with low MH0-13. Each subject is displayed in a separate panels showings amples from each study visit. Labels on top of panels represent the randomized treatment group, age, de-identified id, number and days to 1st PEx (or censoring time if 0 PEx). Figure E11. PCoA showing whether the 22 subjects with low MH0-13 are converging to a similar community (top), subjects with higher MH0-13 are plotted for comparison (bottom).