Respiratory Tract Pathogen Detection in Children: Clinical Practice and Considerations of mNGS and tNGS Technologies

Abstract Objective This study aims to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) technologies in detecting respiratory tract pathogens in hospitalized children. Methods We selected 1275 children hospitalized for respiratory tract infections from March to November 2024 as the study subjects. Based on clinical needs, mNGS/tNGS testing was conducted on these children, including 1225 oropharyngeal swab samples and 50 bronchoalveolar lavage fluid samples. Additionally, traditional microbial culture methods were used for testing in 574 children. Results The study revealed that children aged 3 to 6 were the primary population affected by respiratory tract infections, accounting for 37.65% of the cases, with 25.1% of them having lower respiratory tract infections. Bacterial and viral co-infections were the most common infection patterns in both oropharyngeal swab and bronchoalveolar lavage fluid samples, with positive rates of 55.02% and 46%, respectively. In bronchoalveolar lavage fluid samples, Mycoplasma pneumoniae had the highest infection rate at 41.67%, followed by Streptococcus pneumoniae and Haemophilus influenzae. The highest detection rate in bronchoalveolar lavage fluid samples was for human adenovirus at 28.3%, followed by rhinovirus and human parainfluenza virus type 3. In oropharyngeal swab samples, Streptococcus pneumoniae had the highest detection rate, followed by Staphylococcus aureus and Haemophilus influenzae. Rhinovirus had the highest detection rate in oropharyngeal swab samples at 25.07%, followed by cytomegalovirus (CMV) and human adenovirus. There was a high consistency between mNGS/tNGS and traditional culture methods in bacterial detection, with the top three being Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae. The serum IL-6 concentration in patients with single bacterial infections was higher than in those with single viral infections; the serum IL-6 in patients with bacterial and viral co-infections was higher than in those with single infections, with statistically significant differences. There were statistically significant differences in serum PCT concentration between patients with single bacterial infections and single viral infections, but no significant differences between patients with single bacterial infections and those with bacterial and viral co-infections. The most frequently detected resistance genes included CTX-M-108, NDM-6, OXA-163, tetM, KPC-2, and mecA. Conclusion mNGS/tNGS technology significantly improved the detection rate of respiratory tract pathogens in children, showing clear advantages over traditional bacterial culture methods in terms of timeliness, accuracy, and coverage of pathogen detection, providing strong technical support for early diagnosis and intervention of respiratory infections in children.