Longitudinal dynamics of respiratory microbiome composition in infants after tracheostomy placement

Abnormal respiratory microbiomes are reported in children with artificial airways, yet the timing and persistence of these disruptions have not been defined in infants following new tracheostomy placement. We conducted a prospective longitudinal study to characterize airway microbiome dynamics following new tracheostomy placement during early life, a critical period for microbiome development. Fifteen hospitalized infants <=12 months contributed 84 tracheal aspirate samples collected from day 1 through 3 to 4 months post-procedure. 16S rRNA sequencing revealed immediate and sustained community shifts. <i>Staphylococcus</i> abundance increased after tracheostomy, peaking at 40 days (mean 27%) before declining, with a more pronounced bloom in infants without home mechanical ventilation (HMV). Alpha diversity decreased significantly in the first 30 days (p<0.05) and returned to baseline by 61 to 90 days. Beta diversity analysis demonstrated marked compositional changes immediately post-tracheostomy and ongoing divergence through 3 to 4 months. Time since tracheostomy and clinical factors (gestational age, HMV, neurologic impairment) were significantly associated with microbiome structure (p=0.001). These findings provide novel evidence that tracheostomy induces rapid and prolonged airway microbiome disruption in infants, highlighting a previously uncharacterized window of vulnerability with implications for respiratory health and individualized care.