Gut microbiota in children receiving a strategy of short course vs standard treatment for community acquired pneumonia

Data are from a subset of 67 children, ages 6-71 months, enrolled in SCOUT-CAP. SCOUT-CAP was a multi-center, randomized, double-blind, placebo-controlled, superiority clinical trial that compared a 5-day beta-lactam (short) strategy to a 10-day (standard) beta-lactam strategy for the treatment of pediatric community-acquired pneumonia (Trial Registration Number: NCT02891915). The SCOUT-CAP trial provided a unique opportunity to examine relationships between the duration of antibiotic therapy, the selection of antibiotic resistance, and risk of antibiotic associated diarrhea. This substudy prospectively evaluated changes in the gut microbiota and antibiotic resistome in SCOUT-CAP participants who received short and standard durations of antibiotic therapy. Illumina-based shotgun metagenomic sequencing was used to compare the abundance of antibiotic resistance genes in stool samples from children receiving short vs. standard treatment strategies at the enrollment visit (study days 1-5) and outcome assessment visit two (study days 19-25). 16S rRNA gene sequencing was used to evaluate the gut microbiota at the enrollment visit (study days 1-5), outcome assessment visit one (study days 6-10), and outcome assessment visit two (day 24-30).