Integrating DNA and RNA sequencing for enhanced pathogen detection in respiratory infections.

Summary

A tailored targeted NGS panel that captures both DNA and RNA pathogens achieved 97.73% sensitivity and 75.41% specificity versus a composite standard within 16 hours, with LOD of 100–200 CFU/mL. It simultaneously subtyped 61.4% of target viruses and detected AMR markers with 80.56% concordance to susceptibility testing.

Key Findings

• Turnaround time ~16 hours with 5M reads and LOD of 100–200 CFU/mL.
• Sensitivity 97.73% and specificity 75.41% versus composite reference, outperforming culture/CMT.
• 61.40% of target viruses were subtype-resolved with validated cutoffs; subtyping fully concordant with PCR.
• Concurrent detection of AMR markers with 80.56% concordance to phenotypic susceptibility testing.

Clinical Implications

Clinicians could obtain same-day comprehensive results (pathogen ID, viral subtype, AMR markers) to rationalize empiric therapy, streamline isolation/cohorting decisions, and target antivirals or narrow-spectrum antibiotics sooner.

Limitations

• Retrospective design may introduce selection bias and limits prospective clinical utility assessment.
• Specificity (75.41%) indicates potential detection of colonizers or low-level contaminants without clinical correlation.

Future Directions

Prospective trials incorporating antimicrobial stewardship endpoints (time-to-targeted therapy, clinical outcomes) and cost-effectiveness analyses across diverse care settings.