PT  - JOURNAL ARTICLE
AU  - Graf, Erin
TI  - The Emergence of Pathogen Genomics in Diagnostic Laboratories
AID  - 10.29074/ascls.2019001776
DP  - 2019 Apr 01
TA  - American Society for Clinical Laboratory Science
PG  - 67--69
VI  - 32
IP  - 2
4099  - http://hwmaint.clsjournal.ascls.org/content/32/2/67.short
4100  - http://hwmaint.clsjournal.ascls.org/content/32/2/67.full
SO  - Clin Lab Sci2019 Apr 01; 32
AB  - 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 cost-effective 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. These include workforce skills required for high-complexity wet-bench protocols and data analysis, as well as validation approaches for interpretation given the lack of US Food and Drug Administration–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.