Aptamer based proteomic pilot study reveals a urine signature indicative of pediatric urinary tract infections

Liang Dong, Joshua Watson, Sha Cao, Samuel Arregui, Vijay Saxena, John Ketz, Abduselam K. Awol, Daniel M. Cohen, Jeffrey M. Caterino, David S. Hains, Andrew L. Schwaderer

Research output: Contribution to journalArticle

Abstract

Objective Current urinary tract infection (UTI) diagnostic strategies that rely on leukocyte esterase have limited accuracy. We performed an aptamer-based proteomics pilot study to identify urine protein levels that could differentiate a culture proven UTI from culture negative samples, regardless of pyuria status. Methods We analyzed urine from 16 children with UTIs, 8 children with culture negative pyuria and 8 children with negative urine culture and no pyuria. The urine levels of 1,310 proteins were quantified using the Somascan™ platform and normalized to urine creatinine. Machine learning with support vector machine (SVM)-based feature selection was performed to determine the combination of urine biomarkers that optimized diagnostic accuracy. Results Eight candidate urine protein biomarkers met filtering criteria. B-cell lymphoma protein, C-XC motif chemokine 6, C-X-C motif chemokine 13, cathepsin S, heat shock 70kDA protein 1A, mitogen activated protein kinase, protein E7 HPV18 and transgelin. AUCs ranged from 0.91 to 0.95. The best prediction was achieved by the SVMs with radial basis function kernel. Conclusions Biomarkers panel can be identified by the emerging technologies of aptamer-based proteomics and machine learning that offer the potential to increase UTI diagnostic accuracy, thereby limiting unneeded antibiotics.

Original languageEnglish (US)
Article numbere0235328
JournalPloS one
Volume15
Issue number7 July
DOIs
StatePublished - Jul 2020

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Dong, L., Watson, J., Cao, S., Arregui, S., Saxena, V., Ketz, J., Awol, A. K., Cohen, D. M., Caterino, J. M., Hains, D. S., & Schwaderer, A. L. (2020). Aptamer based proteomic pilot study reveals a urine signature indicative of pediatric urinary tract infections. PloS one, 15(7 July), [e0235328]. https://doi.org/10.1371/journal.pone.0235328