Targeted next-generation sequencing-based pathogens detection in children with severe pneumonia in the pediatric intensive care unit

Background Severe pneumonia is predominantly caused by multiple pathogenic microorganisms. Conventional microbiological tests (CMTs) often have limited sensitivity or a narrow detection spectrum of pathogens, potentially leading to delayed diagnosis. Based on multiplex PCR and high-throughput sequencing, targeted next-generation sequencing (tNGS) overcomes previous limitations. However, research on the use of tNGS in severe pediatric pneumonia remains quite scarce. This study focused on comparing the effectiveness of tNGS with that of CMTs among children with severe pneumonia in the pediatric intensive care unit (PICU). Methods This study enrolled 344 patients with severe pneumonia, admitted to PICU at the Maternal and Child Health Hospital in Guangxi Province, China, between June 2021 and December 2024. Both tNGS and CMTs were performed to detect pathogenic microorganisms in all patients. Results Pathogens were identified in 343 out of 344 patients, with the detection rate by tNGS significantly higher than that of CMTs (99.71% vs. 49.71%, p < 0.05). Among these cases, 290 (84.30%) involved multiple pathogen infections. Bacterial-viral co-infection was the predominant type (31.20%, 107/343). 86 pathogens were identified, among which the four most prevalent were respiratory syncytial virus (39.24%), cytomegalovirus (28.20%), rhinovirus (24.13%), and Mycoplasma pneumoniae (22.67%). Notably, tNGS detected antimicrobial resistance genes in 10.17% (35/344) of cases, including the A2063G macrolide-resistance mutation in 29.49% (23/78) of Mp and 7.69% (1/13) of Bordetella pertussis isolates. Additionally, 20% (4/20) of Staphylococcus aureus carried the mecA gene, while two bla_CTX-M and five bla_NDM resistance genes were identified among Enterobacteriaceae and non-fermenting Gram-negative bacilli. One patient died during hospitalization. In 35 patients, treatment was withdrawn per family request, and 14 of them died shortly after discharge. The length of hospital stay was 15 days. Conclusions This study demonstrates that tNGS substantially enhances etiologic diagnosis in children in the PICU with severe pneumonia. It revealed a high burden of viral and mixed infections and identified resistance genes with potential implications for antimicrobial therapy.