Microscopic Review of Nasopharyngeal Swabs as a Means of Benchside Quality Assurance.

OBJECTIVE

Nasopharyngeal swabs (NPS) are the collection modality of choice for reverse-transcription polymerase chain reaction (RT-PCR) multiplex array for respiratory viruses. NPS gather both extracellular material and human respiratory epithelial cells and, when used with RT-PCR, have reliable sensitivity for detection of viral infection.

GOALS: At our institution, we identified a 1.7% re-order rate within 7-days for NPS destined for RT-PCR respiratory pathogen multiplex, which we hypothesize may be due in part to low confidence in adequate collection. We sought an inexpensive and accessible strategy for benchside quality assurance of NPS adequacy by observing microscopic content of viral transport media.

PROCEDURE: For eight-hundred one NPS samples collected during routine clinical practice in November 2019, aliquots of viral transport media were air-dried and safranin-stained on glass slides under a fume hood. We then counted morphologically distinct ciliated columnar epithelial cells (CCEs), which are prevalent in the nasopharynx.

RESULTS

Twenty percent of samples negative for respiratory pathogens by RT-PCR (BioFire FilmArray RP2, Cepheid GeneXpert) had no CCEs, while just seven percent of positive samples had no CCEs. Pearson's Chi-squared test was used to compare presence of CCEs between samples that were positive and negative for respiratory pathogens by RT-PCR (p=1.6×10-36).

CONCLUSION

We posit that samples without identifiable CCEs have a greater likelihood of inadequate collection. The basic, benchside protocol that we describe here demonstrates potential to reduce unnecessary re-testing when deployed to confirm negative tests despite high clinical suspicion: a strategy which may help conserve NPS reagents.