A68-19 Evaluation of Targeted Next-Generation Sequencing Versus Standard Culture for Microbial Detection in Pleural Effusions

Abstract Introduction Pleural effusions (500 cc) are prevalent in patients admitted to the ICU and contribute to atelectasis, persistent hypoxemia, impaired resolution of pneumonia, and prolonged mechanical ventilation. Thoracentesis, with pleural fluid culture and chemistry analysis, helps determine whether the effusion can be managed conservatively or requires aggressive interventions, such as chest tube thoracostomy and prolonged antibiotics. However, the decision for any of these aggressive interventions can depend on culture results, which have a low diagnostic yield (20%), limiting their utility. Methods A single-center retrospective evaluation was performed to compare standard fluid culture with targeted next-generation sequencing (NGS) testing for pleural effusions with minimum 500 cc submitted for matched testing from 01/2020 to 02/2025. NGS testing was ordered through a commercial test provider (MicroGenDX, Lubbock, TX), consisting of a limited quantitative PCR panel, 16s rRNA, and ITS gene sequencing. Pleural effusions were classified as transudates or exudates using Light’s criteria. We calculated the sensitivity, specificity, and overall accuracy with 95% confidence intervals for each diagnostic method comparing pleural exudates. Results Of the 145 samples, 92% were exudates. Standard pleural fluid culture sensitivity was 12.8% (95% CI: 8.1-19.5%) to exudates, while NGS was significantly more sensitive at 39.8% (95% CI: 31.9-48.3%, p 0.001, Table 1). Specificity for both diagnostics was 100%, indicating no false positives for pleural transudates. Notably, 74% (39/53) of culture-negative exudates observed additional information through NGS. Extended antibiotic use (7 days) before sampling was associated with larger discrepancies in test positivity, with NGS positive in 59% (33/56) of exudates versus 13% (7/56) for culture (p 0.001). NGS matched 84% (16/19) of possible organisms for culture-positive exudates. Accuracy for NGS was significantly better compared to standard culture (45% vs 20%, p 0.001). NGS detected 89 species unique from culture, including a range of notable pathogenic and fastidious organisms such as Mycoplasma (n = 6), Campylobacter (n = 5), Stenotrophomonas (n = 2), Granulicatella (n = 2), Citrobacter (n = 1), and various Streptococci (S. pneumoniae, n = 3; S. constellatus, n = 2). Conclusions Next-generation sequencing (NGS) demonstrated superior sensitivity (39.8% vs. 12.8%) and accuracy (45% vs. 20%) over standard culture in detecting pathogens from large pleural effusions. It was particularly beneficial for patients with extended antibiotic use and enabled rapid identification of fastidious organisms (anaerobes & Mycoplasma). These findings support routine NGS use to improve diagnosis and guide management of exudative effusions. This abstract is funded by: None