16S sequencing on pediatric blood detects DNA signatures of commensals and pathogenic microbes that correlate with clinical features

The presence of bacterial DNA in the blood of pediatric patients is largely unstudied frontier. We performed 16S rRNA sequencing on 147 apparently healthy 1- and 2-year-old children to explore potential microbial communities in the blood. Interestingly, 16S data detected some common pediatric pathogens in 6 out of 147 children. These were Staphylococcus, Streptococcus, Haemophilus and Deinococcus. Four of these 6 children also had a recorded history of some kind of infection, supporting the 16S data. More than 20K sequencing reads supported these pathogen signatures, which is similar to the counts observed in active infections. Beside these, the assay also picked up DNA signatures of several commensals such as Firmicutes, Bacteroides and Proteobacteria. Although the read count supporting these OTUs were hundreds of folds lower than their typical abundance in gut or stool samples, 16S data stratified samples into four major clusters differing in microbial composition. Cluster 1 was dominated by Proteobacteria. Cluster 2 was present in almost 50% of the samples, comprised of 60-70% Firmicutes. Cluster 3 was mix in composition and present in 18% of the samples. Cluster 4 was dominated by Actinobacteria and represented by 4% of the samples. Interestingly, Cluster 1 was found significantly (p=0.002) associated with higher BMI in children. To investigate the potential source of blood microbial signatures we studied microbiota in stool, skin and blood of germ-free and conventional mice. So, while more work remains to be done to establish if an active microbial community exist in pediatric blood, the our data suggest that 16S sequencing assay can rapidly detect microbial DNA signatures of commensals and pathogens in blood to assist with infectious disease diagnosis.