Navigating the outbreak: a comprehensive analysis of pediatric pneumonia via targeted next-generation sequencing in Wuhan, 2022-2023.

This study aims to delineate the epidemiological characteristics and impacts of the (MP) outbreak, utilizing targeted next-generation sequencing (tNGS) to assess pathogen prevalence and co-infections in pediatric pneumonia cases. Pediatric patients admitted to Wuhan Children's Hospital with pneumonia from 1 October 2022 to 31 October 2023 were included. tNGS was used for comprehensive pathogen detection, including MP and other respiratory pathogens, with additional sequencing of the 23S rRNA gene V region to identify macrolide resistance mutations. This study enrolled 10,223 patients with pneumonia with a positivity rate of 98.4% by targeted next-generation sequencing. Fever (86.4%) and cough (79.3%) were the most common symptoms of pneumonia (MPP). Lung consolidation (25.8%) was a common imaging feature, and corticosteroid use was noted in 22.5% of MPP patients. MP proved to be the primary pathogen, particularly evident during the MP pandemic, which began in March 2023 and peaked in October with a detection rate of 63.2%. Of the 4,397 MPP cases, 34.5% were sole infections, while 65.6% were co-infections, mostly with viruses. The main causative agents of co-infections were and . The macrolide resistance rate was 79.03%. The A2063G mutation in the 23S rRNA V region is the dominant mutation. High-sensitivity C-reactive protein and serum amyloid A were significantly elevated in MPP, while the absolute counts of CD3T, CD4T, CD8T, CD19B, and NK cells were significantly reduced. This study demonstrates the utility of tNGS in identifying MP co-infections and macrolide resistance and highlights the role of inflammatory markers and lymphocyte subpopulations in differentiating MPP from non- pneumonia for clinical management.IMPORTANCEOur study is of great scientific value as it provides practical solutions to clinical challenges and supports both clinical decision-making and public health policy. First, it presents new and important insights into the application of targeted next-generation sequencing (tNGS) technology, which enables rapid and accurate pathogen detection and overcomes the limitations of conventional diagnostic methods. Second, the large sample size, focusing specifically on children during a epidemic, provides valuable epidemiologic data specifically for the Wuhan region. Finally, by integrating rapid tNGS detection with inflammatory markers and lymphocyte subsets, our study demonstrates direct clinical applications that have the potential to improve patient outcomes. This approach highlights the practical utility of our research in enhancing clinical decision-making and contributes important knowledge to the field.