title: How next-generation sequencing and multiscale data analysis will transform infectious disease management.
abstract: Recent reviews have examined the extent to which routine next-generation sequencing (NGS) on clinical specimens will improve the capabilities of clinical microbiology laboratories in the short term, but do not explore integrating NGS with clinical data from electronic medical records (EMRs), immune profiling data, and other rich datasets to create multiscale predictive models. This review introduces a range of "omics" and patient data sources relevant to managing infections and proposes 3 potentially disruptive applications for these data in the clinical workflow. The combined threats of healthcare-associated infections and multidrug-resistant organisms may be addressed by multiscale analysis of NGS and EMR data that is ideally updated and refined over time within each healthcare organization. Such data and analysis should form the cornerstone of future learning health systems for infectious disease.
authors.affiliation: Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
authors.forename: Theodore R
authors.initials: TR
authors.lastname: Pak
authors.affiliation: Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
authors.forename: Andrew
authors.initials: A
authors.lastname: Kasarskis
mesh_terms: D003141:Communicable Diseases / Q000175:diagnosis / Q000382:microbiology / Q000628:therapy; D019295:Computational Biology / Q000379:methods; D019468:Disease Management; D057286:Electronic Health Records; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015201:Meta-Analysis as Topic; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
keywords: electronic medical records; healthcare-associated infections; hospital-acquired infections; multiscale analysis; whole genome sequencing