Applications of Next-Generation Sequencing (NGS) in Infection Management
Next-generation sequencing (NGS) is transforming clinical microbiology and public health laboratories by providing comprehensive approaches that complement or replace many conventional laboratory tests for infection diagnosis, pathogen identification, antimicrobial resistance detection, and outbreak investigation.
Key Applications of NGS in Infection Management
Pathogen Identification and Diagnosis
- Metagenomic NGS (mNGS): Enables identification of all pathogens directly from clinical samples based on sequence homology 1
- Whole-genome sequencing (WGS): Used for complete characterization of bacterial, viral, and fungal pathogens
- Targeted NGS (tNGS): Focuses on specific pathogens through multiplex PCR amplification or probe capture with excellent sensitivity (70.8-95.0%) 2
- Detection advantages: NGS shows significantly higher detection rates (95.0%) compared to traditional culture methods (60.0%) for bacterial and fungal infections 3
Antimicrobial Resistance Detection
- Identifies resistance genes and mechanisms, particularly valuable for:
- Mycobacterium tuberculosis drug resistance detection 2
- Predicting antimicrobial susceptibility profiles
- Guiding appropriate antibiotic selection
Outbreak Investigation and Surveillance
- Tracks transmission patterns of hospital-acquired infections
- Supports public health surveillance through the CDC's Advanced Molecular Detection (AMD) Initiative 1
- Informs infection control practices by better understanding hospital outbreaks 1
Microbiome Analysis
- Characterizes microbial population diversity within the human host
- Identifies polymicrobial infections that may be missed by conventional methods
Clinical Implementation Considerations
Quality Assurance Requirements
- Validation of NGS assays requires establishing:
- Analytical performance specifications
- Quality control procedures
- Proficiency testing 1
- The Clinical Laboratory Improvement Amendments (CLIA) regulations apply to NGS testing 1
Limitations of Current NGS Applications
- Interpretation challenges: NGS often identifies more bacteria than conventional cultures, raising questions about clinical significance 1
- Cost and accessibility: High costs and limited availability restrict widespread clinical adoption 1
- Turnaround time: Current mNGS techniques do not yet lead to shorter pathogen identification times 1
- Distinction limitations: Unable to distinguish dead from living bacterial cells 1
Recommended Use in Clinical Practice
- For bacterial/fungal infections: Conventional culture remains first-line for pathogen identification 1
- For suspected bone/joint infections: Strong recommendation to use conventional rather than molecular techniques for first-line pathogen identification 1
- For fracture-related infections: NGS shows promise but is not yet standard practice; conventional culture remains the gold standard 1
Future Directions
- Development of standardized bioinformatics pipelines and reference databases 1
- Integration of NGS with clinical decision support systems
- Reduction in cost and turnaround time to enable wider adoption
- Establishment of proficiency testing and quality control measures 4
- Refinement of targeted NGS approaches to improve accessibility and cost-effectiveness 2
Conclusion
While NGS technologies show tremendous promise for transforming infection diagnosis and management, conventional microbiological methods remain the current standard of care. As NGS technologies mature and become more accessible, they will likely play an increasingly important role in clinical microbiology, particularly for complex, culture-negative, or polymicrobial infections.