Diagnostic performance, acceptability, and implementation of caregiver-collected oropharyngeal nasal (ON) swabs for molecular detection of respiratory pathogens in symptomatic children

Objective: Evaluate the diagnostic yield and acceptability of parent/caregiver-collected oropharyngeal nasal (ON) swab samples compared to healthcare worker (HCW)-collected nasopharyngeal (NP) swabs for detection of respiratory viruses and Mycoplasma pneumoniae in children. Methods: Symptomatic children presenting to the BC Children’s Hospital Emergency Department provided HCW-collected NP and parent/caregiver-collected ON swabs. Acceptability was assessed using a 5-point Likert scale. Both samples were tested using the SARS-CoV-2/Influenza A+B/RSV GeneXpert® assay and a subset were tested on the BioFire® Respiratory Panel (RP) 2.1 during the initial research phase. In a subsequent implementation phase during a period of increased M. pneumoniae incidence, paired ON and NP swabs were collected and tested on the RP 2.1 as part of a quality improvement initiative. All M. pneumoniae positive samples underwent additional testing for cycle threshold (Ct) values. Results: A total of 139 matched swab pairs were analyzed during the research phase and 219 during the implementation phase. Detection rates for SARS-CoV-2, influenza A/B, and respiratory syncytial virus were comparable between ON and NP swabs. Among 273 paired samples tested using the RP2.1, ON swabs demonstrated significantly higher detection of M. pneumoniae (sensitivity 94% [86, 98] ON vs 64% [61-75] NP, p = 0.0020) while maintaining comparable detection for other respiratory pathogens. ON swabs produced moderately higher Ct values than NP swabs for viral targets, but this did not translate into clinically meaningful differences in clinical sensitivity. Caregivers rated ON swab collection as significantly more acceptable than NP swabs (median 4.5 [4–5] ON vs. 2 [IQR 1–3] NP, p < 0.0001). Conclusion: Parent/caregiver-collected ON swab demonstrated viral detection comparable to HCW-collected NP swabs and significantly improved detection of M. pneumoniae, a clinically relevant treatable cause of paediatric community-acquired pneumonia. Higher caregiver rated acceptability and comparable sensitivity for viral targets support the use of ON swabs as a less-invasive sampling approach for paediatric respiratory pathogen testing. These findings informed implementation of ON swabs as an alternative respiratory sample collection method at BC Children’s Hospital.