title: Next-Generation Sequencing for Infectious Disease Diagnosis and Management: A Report of the Association for Molecular Pathology.
abstract: Next-generation sequencing (NGS) technologies are increasingly being used for diagnosis and monitoring of infectious diseases. Herein, we review the application of NGS in clinical microbiology, focusing on genotypic resistance testing, direct detection of unknown disease-associated pathogens in clinical specimens, investigation of microbial population diversity in the human host, and strain typing. We have organized the review into three main sections: i) applications in clinical virology, ii) applications in clinical bacteriology, mycobacteriology, and mycology, and iii) validation, quality control, and maintenance of proficiency. Although NGS holds enormous promise for clinical infectious disease testing, many challenges remain, including automation, standardizing technical protocols and bioinformatics pipelines, improving reference databases, establishing proficiency testing and quality control measures, and reducing cost and turnaround time, all of which would be necessary for widespread adoption of NGS in clinical microbiology laboratories.
authors.affiliation: Association for Molecular Pathology Next-Generation Sequencing in Infectious Disease Work Group, Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California.
authors.forename: Martina I
authors.initials: MI
authors.lastname: Lefterova
authors.affiliation: Association for Molecular Pathology Next-Generation Sequencing in Infectious Disease Work Group, Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California.
authors.forename: Carlos J
authors.initials: CJ
authors.lastname: Suarez
authors.affiliation: Association for Molecular Pathology Next-Generation Sequencing in Infectious Disease Work Group, Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California.
authors.forename: Niaz
authors.initials: N
authors.lastname: Banaei
authors.affiliation: Association for Molecular Pathology Next-Generation Sequencing in Infectious Disease Work Group, Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California. Electronic address: bpinsky@stanford.edu.
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Pinsky
mesh_terms: D003141:Communicable Diseases / Q000175:diagnosis*; D019295:Computational Biology / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D059021:Laboratory Proficiency Testing / Q000379:methods; D057089:Pathology, Molecular / Q000379:methods