Etiological and clinical characteristics of severe pediatric pneumonia: a large retrospective tNGS cohort study using bronchoalveolar lavage fluid in Shandong, China

Abstract Background Severe pneumonia is the leading infectious cause of death among children under five years of age. Targeted next-generation sequencing (tNGS), a rapid and cost-effective tool for comprehensive pathogen detection, is increasingly used in clinical settings. Methods A retrospective study was conducted among children admitted to Children’s Hospital Affiliated to Shandong University with diagnosis of severe pneumonia who underwent tNGS testing using bronchoalveolar lavage fluid (BALF) from January to December 2024. We analyzed clinical characteristics, pathogen spectrum, co-detection patterns, and macrolide resistance of Mycoplasma pneumoniae (MP) in this cohort. Results This retrospective study analyzed pathogen characteristics using tNGS of BALF from 1,552 hospitalized children with severe pneumonia. The cohort had a median age of 6.92 years (IQR: 5.32–8.10), and the overall cure and improvement rate reached 99.94%. Mycoplasma pneumoniae (MP) predominated, with a 96.07% detection rate and year-round circulation. Co-detection occurred in 47.23% of patients, most frequently MP-viral combinations (30.67%), particularly MP with rhinovirus (19.59%). Multivariable analysis confirmed that MP detection was independently associated with fever (aOR: 1.89), atelectasis (aOR: 3.71), and pleural effusion (aOR: 2.89), while rural residence was the strongest independent risk factor for respiratory failure (aOR: 3.51). Age-specific analysis revealed that viral and bacterial pathogens were more prevalent in younger children, while MP dominated in school-aged groups, peaking at 98.77% in children aged 5–7 years. Clinically, children with MP detection had higher atelectasis and pleural effusion rates compared with the non-MP group (both P < 0.001). Macrolide-resistant MP was strikingly high (89.94%, 1,341/1,491), predominantly the A2063G mutation, with two rare A2064G cases identified. Seasonally, MP persisted year-round, while other pathogens including rhinovirus, Streptococcus pneumoniae , and human parainfluenza virus exhibited distinct peaks. Conclusion This study demonstrates a diverse pathogen spectrum with high co-detection rates in severe pediatric pneumonia and highlights the clinical utility of tNGS in guiding resistance-adapted therapy and antimicrobial stewardship. Clinical trial number. Not applicable.