PRJNA433896
The Novel Identification of the Pediatric Urinary Microbiome
Background: The urinary tract was once thought to be sterile. The composition of the urinary microbiome in health and disease is only just starting to be explored in the adult population. How the urinary microbiome develops in childhood is unknown.Aims: To examine the urinary microbiome of children less than 48 months and to investigate if microbiome metrics change across demographic and clinical factors.Methods: Children under 48 months of age having a urinary catheterization for clinical purposes in the Pediatric Emergency Room were recruited and urine samples collected. Detailed demographic and clinical information was recorded. Urine samples underwent DNA extraction and 16s ribosomal RNA gene sequencing on the Illumina MiSeq platform; standard urinalysis and urine culture were also performed. A urinary tract infection (UTI) was defined as growth of >50,000 cfu/ml by culture. Alpha diversity, beta diversity and the relative abundance of taxa were compared across demographic and clinical factors.Results: 85 children were included; 69% female (N=59) and 31% male (N=26). A urinary microbiome was identified in every child, even in those under 30 days of age. 9 children had Escherichia coli UTIs identified. Those with UTIs had a significantly decreased alpha diversity (t-test, p<0.001) compared to those without UTIs; the composition of the microbiome also clustered separately compared to those without UTIs and there was a large increase in the relative abundance of the genus Escherichia. 28 children had taken antibiotics within 3 months prior to the urine sample collection. There was decreased alpha diversity in those who had taken antibiotics within 2 weeks before the urine sample compared to those without antibiotic use (t-test, p=0.017); no differences were detected if antibiotics were taken greater than 2 weeks prior to sample collection. Some differences in microbiome metrics were seen between genders, but not between in delivery mode, maternal ethnicity or probiotic use.Conclusions: A urinary microbiome was observed in all children, even neonates. Changes in microbiome diversity and composition were observed in patients with a standard culture positive UTI. Further longitudinal exploration of when these microbiome changes occur in relationship to the development of a UTI is warranted. The urinary microbiome has just begun to be explored, especially in the pediatric population, and the implications it has on long term disease processes deserve further investigation.