RT Journal Article
SR Electronic
T1 The Emergence of Pathogen Genomics in Diagnostic Laboratories
JF American Society for Clinical Laboratory Science
JO Clin Lab Sci
FD American Society of Chemistry and Laboratory Science
SP 67
OP 69
DO 10.29074/ascls.2019001776
VO 32
IS 2
A1 Graf, Erin
YR 2019
UL http://hwmaint.clsjournal.ascls.org/content/32/2/67.abstract
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.