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Bronchoalveolar Lavage BAL for Research; Obtaining Adequate Sample Yield
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Optimizing a Metatranscriptomic Next-Generation Sequencing Protocol for Bronchoalveolar Lavage Diagnostics.

Weihua Huang1, Changhong Yin1, Guiqing Wang2

  • 1Department of Pathology, New York Medical College, Valhalla, New York.

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|November 4, 2018
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Summary
This summary is machine-generated.

Next-generation sequencing (NGS) offers a novel diagnostic approach for detecting infectious pathogens. This RNA-based metatranscriptomic NGS (mtNGS) protocol provides rapid, culture-independent pathogen identification from clinical samples.

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Area of Science:

  • Microbiology
  • Genomics
  • Infectious Disease Diagnostics

Background:

  • Conventional diagnostic methods for infectious pathogens have limitations.
  • Next-generation sequencing (NGS) offers a culture-independent approach for microbial detection.
  • RNA-based metatranscriptomic sequencing (mtNGS) is an emerging diagnostic strategy.

Purpose of the Study:

  • To describe an optimized RNA-based metatranscriptomic NGS (mtNGS) protocol for pathogen detection.
  • To establish a simplified bioinformatics pipeline for sequence data processing.
  • To evaluate mtNGS for clinical diagnostic applications.

Main Methods:

  • Development of an RNA-based metatranscriptomic NGS (mtNGS) workflow.
  • Utilized clinical bronchoalveolar lavage specimens for testing.
  • Incorporated a spike-in RNA mix as an internal control for data accuracy.

Main Results:

  • The mtNGS protocol detects a wide range of bacteria, viruses, and fungi within 24-36 hours.
  • The internal RNA control mitigates false-positive and false-negative results.
  • The method identified antibiotic resistance genes and virulence factors.

Conclusions:

  • RNA-based mtNGS is a promising alternative for diagnosing emerging infectious pathogens.
  • The protocol provides valuable information for clinical treatment decisions.
  • Further optimization is required to enhance sensitivity and accuracy.