Why This Matters:
- Culture-negative infection cases present a significant diagnostic challenge in clinical microbiology, often delaying effective treatment and contributing to inappropriate antibiotic use.
- Traditional culture methods commonly fail to detect organisms — particularly anaerobes and fastidious bacteria — leading to empirical therapy and increased healthcare costs.
- E.g., culture-negative test outcomes occur in ~ 40% of infective endocarditis and sepsis cases.
- Metagenomic NGS (Next-Generation Sequencing) is a culture-independent molecular method that sequences genetic material (DNA or RNA) directly from a clinical or environmental sample to identify microorganisms without prior cultivation or targeted primers.
- Culture-independent approach to pathogen detection can indentify presence of organisms missed by conventional methods.
Key Findings:
Rimoldi et al. (2024) evaluated the utility of 16S-based metagenomic NGS on 105 culture-negative surgical samples (tissue/biopsy, abscess, and lymph nodes) obtained from patients receiving empiric antibiotic therapy in orthopedics, neurosurgery, cardiac surgery, general surgery, or other clinical settings at a hospital in Italy.1
- High NGS positivity rate: 74.3% (78/105) of culture-negative samples tested positive for one or more bacterial taxa via 16S NGS, indicating substantial additional diagnostic yield.
- Strong monomicrobial detection: A single pathogen was detected in 68.6% (72/105) of samples; polymicrobial infections were identified in 5.7% (6/105) of samples.
- Diverse bacterial species identified: Across all samples, 32 distinct bacterial taxa were detected, with Cutibacterium acnes (11%), Staphylococcus epidermidis (10.4%), Staphylococcus aureus (9.5%), Actinomyces spp. (3.8%), Streptococcus gallolyticus (3.8%), and Finegoldia magna (3.8%) being the most frequent.
- Anatomic site variation: NGS detected bacteria in 100% of lung, head and neck, and eye specimens, with variable detection by other clinical contexts; the highest absence of both culture and NGS positivity was seen for CNS (62.5% positive) and heart (63.6% positive) samples.
- Unidentifiable isolates resolved: Among 13 isolates that could not be identified by traditional methods, NGS revealed nine additional bacterial species, including Acinetobacter lwoffii and Peptostreptococcus spp.
Bigger Picture:This study demonstrates that 16S-based metagenomic NGS substantially improves pathogen detection in clinical samples where traditional culture fails, offering a powerful complement to standard diagnostics. By capturing a broader range of bacteria — including fastidious, anaerobic, or slow-growing organisms — NGS can inform more accurate, evidence-based antimicrobial therapy and may help reduce unnecessary empirical treatments and associated healthcare costs. Integrating metagenomic approaches into routine workflows could advance clinical microbiology beyond culture dependency, though challenges such as data interpretation, clinical correlation, and guideline development remain critical for broader adoption.
(Image Credit: iStock/JuSun)
References:
- Rimoldi et al. (2024). Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections. Pathogens.
