Concordance of Pathogenic Bacteria in the Upper and Lower Airway in Children With Severe Viral Lower Respiratory Tract Infections

Background: Viral lower respiratory tract infections (LRTIs) are a leading cause of mortality among children. Bacterial coinfections in viral LRTI are associated with severe clinical outcomes. Identifying lower airway bacterial involvement in viral LRTI is challenging. Our objective was to define the concordance of bacterial detection between paired upper nasopharyngeal (NP) swabs and lower endotracheal airway samples (ETAs) in children with severe viral LRTI. Methods: Convenience sample of children <5 years intubated with LRTI. Children were enrolled within 48 hours of ICU admission, and NP/ETAs were obtained for the detection of Moraxella catarrhalis , Streptococcus pneumoniae , Haemophilus influenzae and Staphylococcus aureus. Concordance was assessed via intraclass correlation coefficient (ICC), according to the respiratory virus and age. Clinical outcomes were also assessed. Results: From 2017 to 2021, we enrolled 76 children [median age: 2.1 (1.2–4.3) months]. The most common respiratory virus was respiratory syncytial virus (RSV) (73.7%). Overall concordance for bacterial detection was high for M. catarrhalis , H. influenzae , and S. pneumoniae (ICC ≥0.75) but low for S. aureus (ICC 0.36). Detection rates varied by viral pathogen, with M. catarrhalis and S. pneumoniae showing the highest agreement in children with RSV. Agreement was higher in infants <6 months. Prolonged intubation was observed in children with RSV and NP codetection of S. pneumoniae or H. influenzae . Conclusions: Concordance was high for M. catarrhalis , H. influenzae , and S. pneumoniae, but not for S. aureus, and was influenced by the viral etiology and age. These findings suggest the applicability of NP swabs as surrogates for lower airway cultures for specific bacterial-virus combinations in children with severe LRTI.