Enteropathogen Detection in Children with Diarrhea and/or Vomiting: A Cohort Study Comparing Rectal Flocked Swabs and Stool Specimens
Bibliographic record
Abstract
Abstract 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.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.004 |
| Meta-epidemiology (narrow) | 0.000 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".