Abstract
BACKGROUND: Pleural effusion is a common symptom in children with respiratory diseases, with infections being the leading cause. Currently, the use of metagenomic next-generation sequencing (mNGS) for pleural effusion has not been fully evaluated in pediatric lung disease patients. METHODS: Patients who had undergone mNGS for pleural effusion were included in the study. Patients were categorized into a clinically useful group and a not clinically useful group on the basis of their clinical data, laboratory results, and mNGS results. RESULTS: A total of 48 children were included in this study. The number of positive mNGS results was 32/48 (66.7%), which was greater than that of conventional tests (22/48 [45.8%]). The diagnostic concordance of mNGS for detecting bacterial infections was 62.5% (20/32) higher than that of conventional detection methods, which was 15.6% (5/32). However, the diagnostic concordance of mNGS in detecting mycoplasma infections (4/9 vs. 7/9) and tuberculosis infections (0/5 vs. 5/5) was lower than that of conventional detection methods. Compared with the not clinically useful group, the clinically useful group had a lower mean age (50.50 [IQR, 32.25, 102.50] vs. 98.00 [IQR, 60.00, 118.50] months, P = 0.019), a greater incidence of wheezing (n = 5/23 vs. n = 0/23, P = 0.018), a greater incidence of pulmonary consolidation (n = 15/23 vs. n = 8/23, P = 0.039), and a greater incidence of loculated pleural effusion (n = 5/23 vs. n = 0/23, P = 0.018). Additionally, the clinically useful group had a longer hospital stay (17.0 [IQR, 10.75, 25.0] vs. 12.0 [IQR, 6.75, 15.00] days, P = 0.011). Nevertheless, the rate of improvement after treatment was greater in the clinically useful group than in the not clinically useful group (100% vs. 73.9%, P = 0.009). CONCLUSION: mNGS has distinct diagnostic advantages, with more accurate bacterial identification in pediatric pleural effusion. Negative results may prompt exploration of non-infectious causes. However, pathogen-specific limitations should be considered. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12890-026-04117-1.