What is the role of molecular diagnostics, such as Polymerase Chain Reaction (PCR) and Next-Generation Sequencing (NGS), in clinical decision making for infectious diseases?

Role of Molecular Diagnostics in Clinical Decision Making in Infectious Diseases

Molecular diagnostics should be adopted in critically ill patients with suspected infections as they significantly improve the timing of appropriate therapy initiation and potentially improve patient outcomes.1

Key Applications of Molecular Diagnostics

Rapid Pathogen Identification

• Molecular techniques like PCR and NGS provide faster identification of pathogens compared to conventional culture methods (hours vs. days/weeks)1
• Particularly valuable for critically ill patients where timely treatment is crucial for survival1
• Enables detection of fastidious organisms and pathogens affected by prior antimicrobial exposure that might be missed by culture1
• Allows for pathogen-agnostic testing when the causative agent is unknown1

Antimicrobial Resistance Detection

• Rapid detection of resistance genes (e.g., mecA, blaKPC, blaNDM) guides appropriate antibiotic selection1
• A study showed that blaKPC PCR testing on positive blood cultures decreased time to appropriate therapy and reduced mortality for CRE bacteremia1
• Enables detection of mixed infections and subpopulations of resistant strains1

Clinical Impact

• Reduces time to appropriate antimicrobial therapy in critically ill patients1
• Supports antimicrobial stewardship by enabling targeted therapy and avoiding unnecessary broad-spectrum antibiotics1
• Facilitates detection of pathogens from culture-negative samples in prosthetic joint infections, chronic wound infections, and endocarditis1

Implementation Considerations

Laboratory Workflow Integration

• Molecular tests must be carefully integrated into laboratory workflow schemes to maximize their impact1
• 24-hour availability is recommended for critically ill patients requiring continuous monitoring1
• Rapid communication of results to clinicians is essential for immediate adjustment of antibiotic treatment1

Quality Assurance

• Clinical laboratories must validate NGS-based tests in-house in the absence of FDA-approved assays1
• Quality control measures include:
  • Use of internal, positive, and negative controls (recommended for all metagenomic studies)1
  • Standardized bioinformatics pipelines2
  • Proficiency testing1

Contamination Management

• Meticulous laboratory practice is required to minimize contamination risks1
• Bioinformatic approaches should be used to exclude contamination and confirm true infections1

Specific Applications and Recommendations

For Critically Ill Patients

• Rapid molecular identification from blood cultures and detection of resistance mechanisms should be implemented1
• Strong recommendation for adoption of rapid diagnostic tests (RDTs) in critically ill patients1

For Diagnostic Stewardship

• Clinical consultation may be required for complex molecular tests like metagenomic NGS1
• Laboratory-driven consultation processes should be developed through consensus with key stakeholders1

For Surveillance and Outbreak Investigation

• NGS supports infection control by tracking transmission patterns of hospital-acquired infections2
• Enables better understanding of hospital outbreaks2

Limitations and Challenges

Technical Challenges

• Human DNA contamination (median 91% of sequence reads) necessitates improved depletion methods1
• High per-read error rates in some platforms (e.g., Oxford Nanopore) can be problematic with low coverage depth1
• Need for optimized bioinformatic approaches to handle large, complex metagenomic datasets1

Clinical Interpretation Challenges

• Distinguishing true pathogens from contaminants or colonizers1
• Understanding clinical significance of organisms detected by molecular methods but not by culture2
• Inability to distinguish dead from living bacterial cells2

Cost and Resource Considerations

• Average consumable cost per sample ranges from $130 (multiplexed) to $685 (single sample)1
• High costs and limited availability restrict widespread clinical adoption2

Future Directions

• Development of standardized bioinformatics pipelines and reference databases2
• Integration with clinical decision support systems2
• Reduction in cost and turnaround time to enable wider adoption2
• Establishment of proficiency testing and quality control measures2

Despite these challenges, molecular diagnostics represent a transformative approach to infectious disease diagnosis, enabling faster, more accurate identification of pathogens and resistance mechanisms, ultimately improving patient outcomes through timely and appropriate antimicrobial therapy.