Combined oropharyngeal nasal (ON) swabs for the molecular detection of respiratory pathogens including <i>M. pneumoniae</i> in symptomatic children

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 <i>Mycoplasma pneumoniae</i> 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 <i>M. pneumoniae</i>, paired ON and NP swabs were collected and tested on the RP 2.1 in a quality improvement initiative. All <i>M. pneumoniae</i>-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 <i>M. pneumoniae</i> (sensitivity of 94%, confidence interval [CI] [86, 98] ON vs 64% [61-75] NP, <i>P</i> = 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], <i>P</i> < 0.0001). ON swab performance was similar to NP swabs for the detection of respiratory viruses and showed improved diagnostic yield of <i>M. pneumoniae</i>. Given their higher acceptability ratings, ON swabs should be considered as a less-invasive diagnostic option for children.IMPORTANCEThe 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 <i>Mycoplasma pneumoniae</i>, 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 <i>M. pneumoniae</i>, ON swabs are a patient-centered alternative to NP swabs and should be considered as a preferred diagnostic option for children.