Next Generation Sequencing for Outbreak Investigation in the Clinical Microbiology Laboratory

Abstract

With the advent of next generation sequencing (NGS) technologies, genomic investigations of pathogen outbreaks are now possible at unprecedented resolution. Prior methods, requiring highly pathogen-specific protocols, can now be replaced with a single universal protocol for whole genome sequencing. Clinical applications have shown improvement in our understanding of pathogen transmission dynamics from the hospital to global level. However, there are several barriers to routine implementation in clinical microbiology laboratories. These include financial support for a non-billable test, workforce training needs, particularly for highly complex data analysis methods, and lack of FDA approved methods requiring extensive laboratory validation.