Duration of post-diarrheal enteric pathogen carriage in young children in low-resource settings

Document Type



Paediatrics and Child Health; Women and Child Health


Background: Prolonged enteropathogen shedding after diarrhea complicates the identification of etiology in subsequent episodes and is an important driver of pathogen transmission. A standardized approach has not been applied to estimate the duration of shedding for a wide range of pathogens.
Methods: We used a multi-site birth cohort of children 0-24 months of age from whom diarrheal and monthly non-diarrheal stools were previously tested by qPCR for 29 enteropathogens. We modeled the probability of detection of the etiologic pathogen before and after diarrhea using a log-normal accelerated failure time survival model and estimated the median duration of pathogen carriage as well as differences in sub-clinical pathogen carriage 60 days after diarrhea onset in comparison to a pre-diarrhea baseline.
Results: We analyzed 3247 etiologic episodes of diarrhea for the nine pathogens with the highest attributable burdens of diarrhea. The median duration of post-diarrheal carriage varied widely by pathogen, from about one week for rotavirus (median 8.1 days; 95% confidence interval: 6.2, 9.6) to more than one month for Cryptosporidium (39.5 days; 95% CI: 30.6, 49.0). The largest increases in sub-clinical pathogen carriage before and after diarrhea were seen for Cryptosporidium (prevalence difference between 30 days prior and 60 days after diarrhea onset of 0.30; 95% confidence interval: 0.23, 0.39) and Shigella (prevalence difference 0.21; 95% CI: 0.16, 0.27).
Conclusions: Post-diarrheal shedding was widely variable between pathogens, with strikingly prolonged shedding seen for Cryptosporidium and Shigella. Targeted antimicrobial therapy and vaccination for these pathogens may have a relatively large impact on transmission.


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Clinical Infectious Diseases