Metagenomic sequencing analysis of respiratory pathogens in the Jiangsu region of China: a multicenter epidemiological study (2025)

Abstract Background Acute respiratory infection (ARI) ranks as the leading cause of morbidity and mortality among children worldwide. Targeted metagenomic next-generation sequencing (tNGS) allows unbiased and comprehensive pathogen detection. This study aimed to investigate the epidemiological characteristics of respiratory pathogen infections in Jiangsu Province, China, using the tNGS platform. Methods A total of 28 736 clinical specimens were collected from patients with respiratory tract infections across 13 regions of Jiangsu Province between January and December 2025 and subjected to tNGS detection. All detected pathogens were classified into four categories: bacteria, viruses, atypical pathogens, and other pathogens. Stratified analyses were performed according to age, geographical region, season, and infection pattern (single infection versus mixed infection). The Chi-square test was applied for statistical analysis, with a two-tailed P value < 0.05 considered statistically significant. Results At least one respiratory pathogen was detected in 28,736 of 28,736 included specimens (100%); however, this reflects the high analytical sensitivity of tNGS and does not necessarily indicate clinically significant infection in every case. Bacteria exhibited the highest detection rate of 72.4%, followed by viruses (66.6%), atypical pathogens (6.3%), and other pathogens (3.2%). Mixed infections accounted for 68.7% of all cases, with the highest prevalence in children aged 1–4 years (73.5%) and the lowest in those aged ≥ 60 years (46.2%). The top five predominant pathogens were Haemophilus influenzae (26.4%), Streptococcus pneumoniae (23.0%), Moraxella catarrhalis (21.1%), Staphylococcus aureus (18.4%), and Acinetobacter baumannii (13.1%). Statistically significant differences were observed in pathogen distribution across age (χ² = 412.7, P < 0.001), geographical region (χ² = 189.3, P < 0.001), and season (χ² = 48.2, P < 0.001). The most prevalent mixed infection combination was Haemophilus influenzae combined with Streptococcus pneumoniae. Conclusion This large-scale tNGS study reveals a complex pathogen spectrum of acute respiratory infections in East China, characterized by a high prevalence of mixed infections and significant disparities in age, regional, and seasonal distributions. The findings provide epidemiological evidence for precise clinical diagnosis and treatment as well as public health intervention strategies.