Exploratory pilot study on transcriptome analysis in blood and urine for identifying potential miRNA biomarker candidates to dustinguish of bacterial vs. viral infections in children with fever

There is a lack of fast, reliable and non-invasive methods for distinguishing between bacterial and viral infections in modern clinical practice. It negatively impacts the effectiveness of treatment and increases the risk of unnecessary antibiotic administration and thus antibiotic resistance spread. Using microRNA biomarkers in urine may become the solution to the problems listed. miRNAs in urine are relatively stable and can provide an indirect yet specific insight into systemic infections, thus offering a promising diagnostic tool. Combining urine microRNA analysis with blood transcriptomics allows to explore systemic changes that are not limited to a single biological fluid, improving reliability by cross-verifying findings. In this pilot study, the analysis of urine microRNA and blood full transcriptome sequencing data was carried out in children with bacterial (n = 7), viral infections (n = 7) and controls (n = 8) with the goal of determining microRNA diagnostic signatures that distinguish between the said infections, and connecting differentially expressed urine microRNA with differentially expressed transcripts in blood. Using LASSO regularised regression and ANOVA statistical analysis, microRNA biomarker candidates were prioritised and miRNA:mRNA high-likelihood interactions were analysed using correlation analysis and target prediction to further explore systemic changes in response to infection. The differential expression analysis revealed unique features and common patterns in microRNA expression in infections with bacterial or viral etiology. The resultant five microRNAs chosen by both feature selection methods have shown the ability to cluster bacterial infections patients, viral infections and controls. Subsequent correlation analysis and target prediction revealed the role of microRNA regulation in various immune processes such as the interaction of cytokine and cytokine receptors, as well as the regulation of T-cell activation. Our study suggests that prioritised urine microRNA biomarkers have a strong potential for implementation in clinical diagnostics. This could enable a targeted and timely treatment, potentially reducing the risk of spread of antibiotic resistance. Non-coding RNA-seq profiling of urine samples from children with confirmed bacterial or viral infections as well as age-matched controls with no signs of infection.