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Finding and Following Bugs

Genomic tools are helping researchers and clinicians detect pathogens, the Journal of the American Medical Association reports.

For instance, JAMA recounts, next-generation sequencing of a blood sample from a Kansas man with a mysterious and eventually lethal infection uncovered a novel virus, now dubbed the Bourbon virus for the county in which he lived. Similarly, genomic tools have enable researchers and clinicians to track a Klebsiella pneumonia outbreak at the NIH Clinical Center.

As such tools are becoming faster and cheaper, JAMA says they may become more common in tertiary medical centers, but that everyday clinical care will likely rely on rapid PCR-based molecular diagnostic tests that are based on what such sequencing endeavors uncover.

"We don't need to do genome sequencing for a patient who comes in with an E. coli urinary tract infection, but we do need it in the context of an ICU that cares for, say, a critically ill patient who has had a bone marrow transplant, to find out what [microbes] that person was colonized with," Julie Segre from the National Human Genome Research Institute tells JAMA.

Others caution that issues like sample contamination underscore the need to test the validity of genomic approaches.