Kinetics of enteric pathogen quantity during acute diarrhea in children in resource-limited settings

Pathogen quantity kinetics during childhood diarrhea have implications for etiology ascertainment. Using a multisite cohort, we modeled qPCR quantity by symptom duration. Rotavirus had the largest log reduction in quantity by day 7 (-1.98; 95% CI: -2.88, -1.08), followed by Shigella (-0.87; -1.46, -0.28) and heat stabile toxin-producing E. coli (-0.78; -1.57, 0.02). While peak quantity was robust to host factors, kinetics were not. For example, malnourished children had a minimal decline in Cryptosporidium quantity over the first 7 days of illness. Pathogen quantity, etiology attribution, and non-PCR test sensitivity all peaked early in illness. Diarrheal studies should collect samples early to reduce bias in etiology identification.