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A method of processing nasopharyngeal swabs to enable multiple testing.

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  • 1Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.

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This study presents a new method for analyzing single nasopharyngeal swabs, enabling multiple tests for bacteria, viruses, and genetic material in children. This approach enhances diagnostic capabilities for pediatric respiratory infections.

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Area of Science:

  • Pediatric infectious diseases
  • Microbiology
  • Molecular biology

Background:

  • Nasopharyngeal (NP) swabs are crucial for diagnosing respiratory infections in children.
  • Current methods often require multiple swabs or limit the scope of analysis.
  • Developing a single-swab protocol can streamline diagnostics and research.

Purpose of the Study:

  • To develop and validate a method for performing multiple diagnostic and research tests on a single nasopharyngeal swab.
  • To assess the feasibility of analyzing bacterial and viral pathogens, cytokine expression, and genetic material from one swab.
  • To evaluate the impact of sample processing on data quality.

Main Methods:

  • Collected NP swabs from children aged 2-12 with acute sinusitis.
  • Processed swabs for bacterial culture, viral detection, cytokine expression, 16S ribosomal RNA gene sequencing, and RNA sequencing.
  • Modified sample processing by cutting the swab tip to include RNA analysis.

Main Results:

  • High rates of bacterial (72.4%) and viral (69.5%) detection were observed.
  • Successful cytokine measurement and robust yields from 16S ribosomal RNA gene sequencing (2646 OTUs) and RNA sequencing were achieved.
  • Cutting the swab tip did not compromise the recovery of bacteria, viruses, or microbiome diversity.

Conclusions:

  • A minimally invasive protocol using a single NP swab allows for comprehensive diagnostic and research investigations in children.
  • This method supports multiplex testing, improving efficiency in pediatric respiratory illness assessment.
  • The validated protocol facilitates deeper insights into the pathogenesis of childhood sinusitis.