| Summary: | Febrile episodes are common in children and the most frequent reason for attending emergency services. Although most infections have a benign and self-limiting course, severe and sometimes life-threatening infections occur. This prospective study describes a cohort of children presenting to a single-centre pediatric emergency department (ED) with suspected invasive bacterial infection, and explores the relationships between nasopharyngeal microbes and outcomes. All children attending the ED who had a blood culture taken were offered to participate over a two-year period. In addition to conventional medical care, a nasopharyngeal swab was obtained., which was analysed for respiratory viruses and three bacterial species using a quantitative PCR. Fisher’s exact test, Wilcoxon rank sum, and multivariable models were used for statistical analyses of the 196 children (75% younger than four years) who were enrolled and had sufficient data for analysis; 92 had severe infections according to the study protocol, while five had bloodstream infections. Radiologically confirmed pneumonia was the most common severe infection found in 44/92 patients. The presence of respiratory viruses and the carriage of <i>Streptococcus pneumoniae</i> and <i>Haemophilus influenzae</i> were associated with a higher risk of pneumonia. Higher density colonisation with these bacteria were independent risk factors for pneumonia, whereas <i>Moraxella catarrhalis</i> carriage was associated with lower risk. Our data support the hypothesis that higher nasopharyngeal density of pneumococci and <i>H. influenzae</i> could play a role in the development of bacterial pneumonia in children. A preceding viral infection of the respiratory tract may be a trigger and play a role in the progression to severe lower respiratory tract infection.
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