Enteropathogen Detection in Children with Diarrhea and/or Vomiting: A Cohort Study Comparing Rectal Flocked Swabs and Stool Specimens

BACKGROUND: Diarrheal stool samples are currently preferred for enteropathogen detection, but they are inconvenient to collect if they are not immediately available, leading to suboptimal return rates and delayed or missed diagnostic opportunities. We sought to compare the enteropathogen yields of rectal swabs and stool specimens in an outpatient cohort of children with diarrhea and/or vomiting. METHODS: Eligible children were < 18 years of age, with ≥3 episodes of vomiting or diarrhea in 24 hours and <7 days of symptoms. After excluding those enrolled within the prior fortnight, unable to follow-up, having psychiatric illness, neutropenia, or requiring emergent care, we attempted to collect rectal swabs and stool from all participants. Specimens were subjected to testing with the Luminex xTAG Gastrointestinal Pathogen Panel, an in-house 5-virus panel and bacterial culture. Primary outcomes were comparative (submitted paired specimens only) and overall (all specimens, unsubmitted specimens analyzed as negative) yields. We used McNemar’s test to conduct pathogen-specific analyses, and generalized estimating equations to perform global (i.e., any) pathogen analyses with adjustments made for the presence of diarrhea, location, and their interactions with specimen type. RESULTS: Of the 1,519 subjects enrolled, 1,147 (75·5%) and 1,514 (99·7%) provided stool and swab specimens, respectively. The proportions of specimens positive for any pathogen were 75.9% (871/1,147) and 67.6% (1,024/1,514); P < 0.0001. Comparative yield adjusted OR in stool relative to swabs were 1.24 (95% CI: 1.11, 1.38) and 1.76 (95% CI: 1.47, 2.11) in children with and without diarrhea at presentation, respectively. Overall concordance analysis yielded a kappa of 0.76 (95% CI: 0.71, 0.80). Paired positive viral specimens had lower median cycle threshold values (i.e., higher viral loads; P < 0·0001) in SSs compared with swabs for all viruses. In overall yield analysis, the proportions positive for a pathogen were 57.3% and 67.4 for stool and rectal swabs, respectively; unadjusted OR: 0.65 (95% CI: 0.59, 0.72) for stool relative to swab. CONCLUSION: Rectal swabs should be performed when enteropathogen identification, and/or rapid detection, is needed, molecular diagnostic technology available, and stool not immediately available. DISCLOSURES: All authors: No reported disclosures.