The Emergence of Pathogen Genomics in Diagnostic Laboratories

Abstract

Next generation sequencing (NGS) technologies enable one to obtain genomic information about pathogens directly from clinical samples or isolates on a scale never before possible with polymerase chain reaction or Sanger sequencing. Clinical microbiology laboratories are rapidly finding the low-hanging fruit-type applications for this disruptive technology as it becomes affordable with reasonable turn-around times. This includes the use of metagenomic NGS for pathogen detection in primary clinical samples. It also includes the use of NGS for detection of antimicrobial resistance genes in bacteria that are difficult and/or slow to grow in culture. Finally, NGS offers improvement in resolution of viral and bacterial outbreaks and streamlines workflows for a one-size-fits-all protocol. There are still significant barriers to implementation that must be considered. This includes workforce skills required for high complexity wet bench protocols and data analysis as well as validation approaches for interpretation given the lack of FDA approved systems. Regardless, NGS will continue to be a game-changer in clinical microbiology and laboratories must be prepared to face the challenges associated with adoption of this technology.