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

Data are from a subset of 171 children enrolled in the double-blind, placebo-controlled SCOUT-CAP trial (NCT02891915). The goal of the SCOUT-CAP trial was to compare clinical outcomes among children 6 months to < 6 years of age with community-acquired pneumonia (CAP) randomized to a short (5-day) vs. standard (10-day) Beta-lactam treatment strategy. The state-of-the-art SCOUT-CAP study provides an unprecedented opportunity to address critical questions regarding relationships between duration of antibiotic therapy and selection of antibiotic resistance. This substudy prospectively evaluated changes in the microbiota and antibiotic resistome in SCOUT-CAP participants. We used Illumina-based shotgun metagenomic sequencing to compare the abundance of antibiotic resistance genes in throat 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), which occurred at the end of the study. 16S rRNA gene sequencing and statistical models were used to compare microbial communities in throat samples at the enrollment visit (study days 1-5), outcome assessment visit one (study days 6-10), and outcome assessment visit two (day 24-30).