Trajectories of richness, Shannon variety and Simpsons evenness before treatment (T0), in T1, in T2, and by the end from the observation period (T3) are shown on phylum rank (A) and types rank (B) for both antibiotic treatments. diversity and evenness trajectories. A heatmap with microbiome diversity trajectories at phylum level is displayed in (A), at species level in (B), of microbiome evenness at phylum level in (C), and at species level in (D). Microbiome diversity was calculated using the Shannon index, and evenness using the reciprocal of Simpsons dominance (see patients and methods). Diversity and evenness values are printed in all boxes for each study participant (Patient ID, on y-axis) and Salbutamol sulfate (Albuterol) day of stool collection (T0 – T3, on x-axis). Treatment period was from T1 to T3. T0 is the sample before antibiotic exposures. Orange heatmaps include patients from the ciprofloxacin cohort, blue heatmaps patients from the cotrimoxazole cohort. The bottom row of the heatmaps presents the mean value of each column, here the sample collection time point. The intensity of the color bar reflects the diversity and evenness values, with a deeper color for higher values. (PDF 1281 kb) 12915_2019_692_MOESM6_ESM.pdf (1.2M) GUID:?21034A5F-DD81-49A6-B8A6-D0C4DCE69162 Additional file 7: Figure S3. Trajectories of richness, diversity and evenness of both cohorts over the entire observation period. Trajectories of richness, Shannon diversity and Simpsons evenness before treatment (T0), at T1, at T2, and at the end of the observation period (T3) are shown on phylum rank (A) and species rank (B) for both antibiotic treatments. Blue data points are measurements at T0, yellow data points at T1, green data points at T2, and dark orange data points at T3. Boxplots indicate the distribution of data. The connecting magenta line shows the means at each time point and their development under treatment. Under ciprofloxacin treatment, richness and Shannon diversity decrease significantly while Simpsons evenness remains stable. NCR1 In contrast, under cotrimoxazole, loss of richness and diversity is less pronounced. (PDF 2405 kb) 12915_2019_692_MOESM7_ESM.pdf (2.3M) GUID:?1A549C95-D287-4AB5-B3B4-BBBA8FD2A86D Additional file 8: Figure S4. Comparison of length corrected relative abundances from antimicrobial resistance gene classes before treatment and at the Salbutamol sulfate (Albuterol) end of observation. Trajectories of antimicrobial resistance genes quantification by LCRA before treatment (T0) and at the end of the observation period (T3) are shown for both antibiotic treatments. Pink data points are measurements at T0, purple data points at T3. Boxplots indicate the distribution of data. The connecting magenta line shows the means at each time point and their development under treatment (paired valuewhite blood cells Stool samples were collected before treatment (T0, from now on called baseline), day 1 (T1), day 3 (T2) after initiation of antibiotic treatment, and at the end of the observation period (T3), which was after a median of 6?days on antibiotic treatment. Shotgun metagenomics was performed at each time point, with a median sequencing depth of 83,345,082 raw sequence reads per sample and 82,616,415 sequence reads per sample after Salbutamol sulfate (Albuterol) filtration (about 12.39?Gb output). Microbiome, resistome, and plasmidome parameters at baseline did not differ between both treatment cohorts (Table?1). The mean time period between hospital admission and collection of the baseline stool sample (with a subsequent start of antibiotic treatment) was 1.95?days in the ciprofloxacin cohort (range 0C6?days) and 1.47?days in the cotrimoxazole cohort (range 0C7?days) (Additional?file?2: Table S1). We did not detect a statistical difference between both cohorts regarding time to baseline stool sample (value is displayed at the top of each box and indicates statistical significant differences between T0 and T3 within each treatment cohort (paired and value is displayed at the top of each box and indicates statistical significant differences between T0 and T3 within each treatment cohort (paired value (likelihood ratio test)antibiotic resistance gene, plasmid-mediated cefotaximases, macrolide-lincosamide-streptogramin Normalized coefficients are based on the mean baseline ARG length-corrected relative abundance (LCRA) and demonstrate a relative change in ARG LCRA per defined daily dose (DDD) of the antibiotic Particularly interesting was the comparison of antimicrobial selection pressure from all ARG classes between both antibiotic Salbutamol sulfate (Albuterol) treatments using the likelihood ratio test (LR). This revealed significant differences in antimicrobial selection.