Pathogen landscape and synergistic interactions in pediatric ARIs: implications for broad-spectrum surveillance via targeted NGS

Acute respiratory infections (ARIs) in children present complex interactions between respiratory pathogens and host, contributing to high morbidity, hospitalization, and mortality. In this cross-sectional study, 2,044 pediatric in-patient samples were tested for 198 pathogens using targeted next-generation sequencing (tNGS). Pathogen spectrum and co-infection pattern were analyzed alongside blood-test results and clinical data. Pediatric ARIs presented staggered viral epidemics and age-specific infection patterns from 2022 to 2023. Viral infections were predominant in children under 3 years (67.5%). Specific viral-bacterial co-infections were associated with disease severity, including human metapneumovirus (HMPV)-<i>Streptococcus pneumoniae</i> (OR = 3.172, 95% CI: 1.257-8.009), human parainfluenza virus (HPIV)-<i>Fusobacterium nucleatum</i> (3.016, 1.051-8.653), and HPIV-<i>S. pneumoniae</i> (2.825, 1.007-7.927). Subnormal levels of prealbumin and creatinine served as biomarkers for homeostasis disruption in viral-bacterial co-infections. From June to December 2023, <i>Mycoplasma pneumoniae</i> (MP) became the dominant pathogen in preschool (31.3%) and school-age (45.3%) children. High MP loads were correlated with elevated eosinophil, IL-4, and IL-6 and decreased IgG and IL-2, linking to airway hyperreactivity and inflammation. At low MP loads, patients co-detected with human herpesvirus (HHV) (50.0%), or <i>Haemophilus influenzae</i> (40.0%) had a high proportion of severe cases. This study delineated the complex pathogen landscape of pediatric ARIs and highlighted the major role of viral-bacterial and MP-bacterial co-infections. Monitoring these pathogens through tNGS can aid in precise diagnosis and targeted treatment to improve clinical outcomes in children.IMPORTANCEMoving beyond the outdated "one germ, one disease" model, this study characterizes the etiological and epidemiological landscape and highlights co-infection patterns of virus-bacterium or MP-bacterium in 2044 pediatric respiratory in-patient children across three epidemic phases. Specific pathogen combinations are associated with clinical severity, as well as host immune and metabolic profiles. Our findings underscore the necessity of detecting pathogen-pathogen and host-pathogen dynamics, rather than individual pathogens, thereby informing precision diagnostics and targeted intervention strategies.