Performance of broad-spectrum targeted next-generation sequencing in lower respiratory tract infections in ICU patients: a prospective observational study

Abstract

Purpose: Targeted next-generation sequencing (tNGS) has emerged as an advanced diagnostic technique. While tNGS is increasingly recognized as a valuable tool for detecting infections, its most relevant clinical indications remain underdefined. This study aimed to evaluate the clinical utility of tNGS for lower respiratory tract infections (LRTIs).

Methods: We conducted a prospective, observational study to evaluate the clinical diagnostic value of broad-spectrum targeted Next-Generation Sequencing (bstNGS) covering 1872 microorganisms in critically ill patients with LRTIs. We compared the microbial detection performance of bstNGS, mNGS, and traditional culture methods in bronchoalveolar lavage fluid (BALF). Additionally, we used the odds ratio (OR) from multiple logistic regression to assess the impact of relevant clinical variables on the detection of pathogens by bstNGS. We also examined the correlation between bstNGS pathogen detection results and clinical outcomes.

Results: Between August 23, 2023, and April 24, 2024, samples from 150 patients were analyzed. bstNGS detected 96.33% and 91.15% of the microorganisms discovered by mNGS and culture respectively, and was capable of identifying microorganisms with even lower loads. According to the diagnostic criteria, bstNGS, mNGS, and culture methods detected pathogens in 87.33%, 82.00%, and 46.00% of the samples respectively. Moreover, the NGS methods demonstrated a stronger pathogen detection ability compared to culture (p < 0.05). Further comparing the diagnostic performance of the three methods, bstNGS exhibited higher diagnostic accuracy than both mNGS (90.67% vs 86.00%, p < 0.05) and culture (90.67% vs 49.33%, p < 0.0001). Multivariate analysis revealed that immunocompromise was associated with a lower efficiency of pathogen detection by bstNGS (p = 0.04), while other included clinical features had no significant correlation with bstNGS detection. Additionally, compared with patients in whom no pathogen was detected, patients in whom a pathogen was detected by bstNGS were associated with better outcomes of antibiotic treatment (89.68% vs. 62.50%; OR 7.53, 95% CI 1.41-45.30; p = 0.02).

Conclusion: This study shows the effectiveness of bstNGS in detecting pathogens of LRTIs, as well as its value as a potential auxiliary diagnostic method in the ICU.

Keywords: Capture probe enrichment; Lower respiratory tract infections; Pathogen; mNGS; tNGS.