Genomic Applications in the Clinical Management of Infectious Diseases

Abstract

Next-generation sequencing (NGS) approaches to infectious disease diagnosis and monitoring demonstrate significant sensitivity and throughput advantages over conventional sequencing strategies. As NGS technologies become increasingly accessible and affordable, they are likely to become an important component of clinical microbiology testing. Here, we discuss recent studies that have used NGS platforms to address questions with relevance to diagnostic virology, bacteriology, and mycology. We focus on the advances made in the areas of viral drug resistance testing, detection of unknown disease-associated pathogens in clinical specimens, and investigation of microbial population diversity within the human host. We review different sequencing strategies, distinguishing between targeted amplicon sequencing versus whole-genome sequencing (WGS) approaches, and consider the technical and bioinformatics challenges that have emerged. Although NGS holds enormous promise for clinical microbiology, much remains to be accomplished, particularly in regard to standardizing technical protocols and bioinformatics tools, which would be prerequisites for the adoption of NGS methods in diagnostic testing.