Etiology of Lower Respiratory Tract Infections in Children Requiring Mechanical Ventilation: A Multicenter Prospective Surveillance Study Incorporating Airway Metagenomics

Background: Lower respiratory tract infections (LRTI) are a leading cause of mortality in children with critical illness. Despite this, the pathogenic microbes in this vulnerable demographic frequently remain unknown. Metagenomic next generation sequencing (mNGS) can complement traditional diagnostics in epidemiologic surveillance studies by providing broad-range pathogen detection. Methods: We conducted a prospective, multicenter cohort study of critically ill children ages 31 days to 17 years with respiratory failure requiring prolonged mechanical ventilation. Using a combination of clinically-ordered testing and tracheal aspirate mNGS we determined the prevalence, seasonal variation, and genetic relatedness of respiratory pathogens in children with clinically adjudicated LRTI (n=276) or no LRTI (n=121). Findings: A presumptive microbiologic etiology was identified in 92% of children, with RSV (46%), Haemophilus influenzae (25%) and Moraxella catarrhalis (24%) being most common. mNGS identified uncommon pathogens including Ureaplasma parvum (<1%) and Bocavirus (3%). Co-detection of viral and bacterial pathogens occurred in 52% of cases. Incidental carriage of potentially pathogenic microbes was observed in 68% of children without LRTI, with rhinovirus (25%) most prevalent. RSV, H. influenzae and M. catarrhalis were statistically more prevalent in children under five. Both viral and bacterial LRTI occurred predominantly during winter months, and RSV infection was characterized by seasonal and geographic clusters of related strains. Interpretation: The combination of clinical diagnostics and mNGS enabled comprehensive pathogen surveillance in critically ill children with LRTI. RSV, H. influenzae , and M. catarrhalis were disproportionately represented. Carriage of potentially pathogenic microbes was common in children without LRTI. Funding Statement: NIH, Chan Zuckerberg Biohub Declaration of Interests: All authors declare no competing interests. Ethics Approval Statement: The study was approved by a central IRB at the University of Utah.