Combined oropharyngeal nasal (ON) swabs for the molecular detection of respiratory pathogens including <i>M. pneumoniae</i> in symptomatic children
Bibliographic record
Abstract
ABSTRACT This study aimed to evaluate the diagnostic yield and acceptability of parent-/caregiver-collected oropharyngeal nasal (ON) swabs compared with healthcare worker (HCW)-collected nasopharyngeal (NP) swabs for detecting respiratory viruses and Mycoplasma pneumoniae in children. Symptomatic children (0–4 years) presenting to the BC Children’s Hospital Emergency Department provided HCW-collected NP and caregiver-collected ON swabs. Acceptability was assessed using a 5-point Likert scale. Samples were tested using the SARS-CoV-2/Influenza A + B/RSV GeneXpert assay, and a subset was tested on the BioFire respiratory panel (RP) 2.1 during the initial research phase. In a subsequent implementation phase during a high incidence of M. pneumoniae , paired ON and NP swabs were collected and tested on the RP 2.1 in a quality improvement initiative. All M. pneumoniae -positive samples underwent testing for cycle threshold values. We analyzed 139 pairs from the research phase and 219 from the implementation phase. Detection rates for SARS-CoV-2, influenza A/B, and RSV were similar across swab types. Of 273 pairs tested on BioFire, ON swabs demonstrated significantly higher detection of M. pneumoniae (sensitivity of 94%, confidence interval [CI] [86, 98] ON vs 64% [61–75] NP, P = 0.0020) and comparable detection for other pathogens. Caregivers rated ON swab collection as more acceptable than NP swabs (median 4.5 [4–5] vs 2 [IQR 1–3], P < 0.0001). ON swab performance was similar to NP swabs for the detection of respiratory viruses and showed improved diagnostic yield of M. pneumoniae . Given their higher acceptability ratings, ON swabs should be considered as a less-invasive diagnostic option for children. IMPORTANCE The current clinical standard for diagnosing respiratory infections in children typically requires a nasopharyngeal (NP) swab, which may be uncomfortable for the patient and must be collected by a healthcare worker. This study presents a less-invasive option, an oropharyngeal nasal (ON) swab collected by a parent or caregiver, that has comparable detection for common respiratory viruses and improved detection for Mycoplasma pneumoniae , a common but treatable cause of childhood pneumonia. Additionally, parents/caregivers rated ON swabs as significantly more acceptable than NP swabs on a scale of 1 to 5. Given the increased acceptability and superior detection of treatable M. pneumoniae , ON swabs are a patient-centered alternative to NP swabs and should be considered as a preferred diagnostic option for children.
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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 | 0.002 | 0.007 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".