Abstract
Objective
To develop a method to perform multiple tests on a single nasopharyngeal (NP) swab.
Methods
We collected a NP swab on children aged 2–12 years with acute sinusitis and processed it for bacterial culture, viruses, cytokine expression, and 16S ribosomal RNA gene sequencing analysis. During the course of the study, we expand the scope of evaluation to include RNA-sequencing, which we accomplished by cutting the tip of the swab.
Results
Of the 174 children enrolled, 126 (72.4%) had a positive bacterial culture and 121 (69.5%) tested positive for a virus. Cytokine measurement, as judged by adequate levels of a housekeeping enzyme (glyceraldehyde 3-phosphate dehydrogenase), appeared successful. From the samples used for 16S ribosomal sequencing we recovered, on average, 16,000 sequences per sample, accounting for a total of 2646 operational taxonomic units across all samples sequenced. Samples used for RNA-sequencing had a mean RNA integrity number of 6.0. Cutting the tip of the swab did not affect the recovery yield for viruses or bacteria, nor did it affect species richness in microbiome analysis.
Conclusion
We describe a minimally invasive sample collection protocol that allows for multiple diagnostic and research investigations in young children.
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Acknowledgements
We thank the Microbiology Department at UPMC Children’s Hospital of Pittsburgh. This work was supported by Grant Numbers U01AI118506, 5 UL1 TR001857. Its contents are solely the responsibility of the authors and do not necessarily represent the official view of NCATS, NIAID, or NIH.
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S.M.C.L., J.M.M., N.S., J.V.W., M.J. and M.K.-L. contributed to conception, design, acquisition of data, analysis and interpretation of data, drafted the article and revised it critically for important intellectual content, and gave final approval of the version to be published. All authors revised it critically for important intellectual content and gave final approval of the version to be published.
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Lopez, S.M.C., Martin, J.M., Johnson, M. et al. A method of processing nasopharyngeal swabs to enable multiple testing. Pediatr Res 86, 651–654 (2019). https://doi.org/10.1038/s41390-019-0498-1
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DOI: https://doi.org/10.1038/s41390-019-0498-1
