- Lower respiratory tract infections (LRTIs) remain a leading cause of morbidity and mortality worldwide, and accurate pathogen identification is critical to guide appropriate therapy.
- Standard culture methods are limited by slow turnaround and inability to recover fastidious or difficult-to-culture organisms.
- Metagenomic next genertion sequencing (mNGS) offers a culture-independent, broad-spectrum approach that can improve detection, particularly for co-infections and rare pathogens, providing a more complete microbial profile than conventional diagnostics.
Key Findings: Yi et al. (2025) assessed diagnostic performance of mNGS, Sanger sequencing, and conventional culture methods across 506 clinical respiratory specimens (184 bronchoalveolar lavage fluid (BALF) and 322 sputum samples) collected from patients with LRTI symptoms. Sanger sequencing served as reference for evaluating concordance.1
- Higher agreement with Sanger sequencing: mNGS matched Sanger results in 88.2% of sputum and 91.3% of BALF samples, indicating high consistency between molecular methods.
- Culture shows limited concordance: mNGS matched culture in only ~53% of sputum and ~55% of BALF samples, reflecting culture’s restricted sensitivity.
- Expanded pathogen detection: mNGS identified organisms in cases where culture failed, particularly for pathogens known to be non-culturable or difficult to grow (e.g., Pneumocystis jirovecii, Legionella pneumophila, human adenovirus).
- Improved co-infection detection: Among BALF specimens, mNGS detected 66 samples with co-infections, compared with 22 by culture, demonstrating enhanced detection of multiple concurrent pathogens.
- Common pathogen performance: For 18 typical respiratory pathogens, mNGS and Sanger sequencing showed strong sensitivity and specificity (>96%) with high agreement rates (Kappa >0.75), whereas culture missed many of these organisms, especially fastidious ones.
Bigger Picture: This comparative study validates mNGS as a powerful adjunct to conventional diagnostics in lower respiratory tract infections. While standard culture remains effective for many common bacterial pathogens, it significantly under-detects co-infections and organisms that are slow-growing or difficult to cultivate. mNGS — supported by Sanger sequencing concordance — enhances pathogen detection and characterization, enabling clinicians to make more informed treatment decisions, particularly in complex or culture-negative cases. However, considerations such as cost, turnaround time, and data interpretation frameworks remain important for integration of mNGS into routine clinical workflows.
(Image Credit: iStock/ FabrikaCr)
References:
- Yi et al. (2025). Comparative Analysis of Metagenomic Next-Generation Sequencing, Sanger Sequencing, and Conventional Culture for Detecting Common Pathogens Causing Lower Respiratory Tract Infections in Clinical Samples. Microorganisms.
