Dynamics of the respiratory infectome in children with community-acquired pneumonia: insights from large and short time-scale analyses

Community-acquired pneumonia (CAP) remains a leading threat to children's health globally, with shifting pathogen dynamics post-COVID-19 posing new challenges. This study reveals how pandemic control measures and their relaxation influenced the respiratory "infectome"-the full spectrum of pathogens-in children with CAP. By integrating multi-sequencing technologies, we uncovered critical trends: a resurgence of virulent pathogens like <i>Mycoplasma pneumoniae</i> and respiratory syncytial virus after restrictions eased, frequent viral-bacterial co-infections linked to prolonged pneumonia, and distinct infection patterns during hospitalization that predict recovery or complications. These findings highlight the need for dynamic, multi-pathogen surveillance to guide clinical decisions, particularly in managing co-infections and preventing secondary infections. Our work provides actionable insights for pediatricians and public health experts to anticipate post-pandemic pathogen behavior, tailor treatments, and mitigate risks during future outbreaks, ultimately improving care for vulnerable young patients.