Comparison of microbiota in the upper versus lower respiratory tract in children during health and respiratory disease: protocol for a systematic review
Bibliographic record
Abstract
Abstract Background The upper respiratory tract of children is colonized by various microbial species during the healthy state, whereas the lungs are believed to be sterile. In children with respiratory infections, micro-organisms can be recovered from the upper respiratory sites, as well as the lungs. However, the correlation of microbial yield between the two sites is unclear. This systematic review is designed to explore the microbial composition of the respiratory system in healthy children, comparing the organisms identified in the upper airways versus the lungs. We will also compare the prevalence and pattern of upper respiratory micro-organisms in healthy children versus those with various respiratory diseases. We will additionally compare the organisms identified in the upper airway versus the lungs in children with respiratory disease. Methods We will search the following electronic databases: Epistemonikos and Cochrane Library for systematic reviews and MEDLINE (through PubMed), EMBASE, Cochrane CENTRAL, LIVIVO, Web of Science, Scopus, and CINAHL databases for primary studies. Reference lists of relevant studies will be examined for links to potential related articles. Two reviewers will independently determine eligibility for inclusion. The methodological quality and risk of bias of the included observational studies will be scored using the Newcastle–Ottawa Scale tool, and JBI Critical Appraisal Checklist for case series. We will present the data with descriptive statistics and provide pooled estimates of outcomes, wherever it is feasible to perform a meta-analysis. Heterogeneity in studies will be explored by using the Higgins and Thompson I 2 method. Sensitivity analysis will be done to explore the impact of study quality, and subgroup analysis will be done based on age, health condition, type of respiratory specimen, and method of identifying organisms. We will prepare a summary of findings’ table and assess the confidence in the evidence using the GRADE methodology. Results This is a protocol; hence, there are no results at this stage. Discussion The proposed systematic review will provide comparisons of the microbiota in the upper respiratory tract versus the lungs, in children, during health as well as respiratory disease. Similarly, the site-specific yield will be compared between healthy children and those with respiratory disease. This will provide clinicians, microbiologists, and respiratory therapists a better understanding of the respiratory system microbiota, suitability (or otherwise) of upper airway specimens in various respiratory diseases, and the potential role of upper airway colonization on specific respiratory diseases. We will disseminate the review through a peer-reviewed journal publication. Data that cannot be included in the published version will be made available on request. Systematic review registration PROSPERO CRD42020202115 .
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.007 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.008 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".