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E. faecium micrograph courtesy of Nathan Shankar, University of Oklahoma Health Sciences Center (OUHSC).

The pace of microbial genome analysis is accelerating at a dizzying rate. The genome of Enterococcus faecium—a hospital-acquired pathogen of increasing importance because of its broad and still-widening resistance to available antibiotics, including vancomycin—was sequenced in one day’s concentrated effort by a team of researchers from the Department of Energy (DOE) Joint Genome Institute (JGI) in Walnut Creek, Calif., and the University of Texas Houston Medical School (UTHMS) and Baylor College of Medicine, both in Houston.

The E. faecium genome contains 2.8 million base pairs encoding some 3,000 genes, according to Barbara Murray and George Weinstock of the UTHMS Center for the Study of Emerging and Re-Emerging Pathogens. "This research paves the way for preventive vaccines, in addition to better diagnostic tests and treatments," Weinstock says. Researchers at UTHMS and at Baylor continue to compile and further analyze the sequencing data, a task that will likely take many months. The pathogen can cause serious infections of the blood, heart, urinary tract, central nervous system, and wounds.

Meanwhile, the sequencing team at JGI has set high standards for themselves and others whose focus is on ever-faster, cheaper, but still accurate DNA sequencing pyrotechnics. "We leapt at the chance to both demonstrate the capability and provide a useful service to the medical community," says JGI Director Elbert Branscomb, describing the institute’s part in the E. faecium project. "I believe this kind of fast response capability could prove to be very useful to researchers in medical, national security, and agricultural contexts."

DOE established JGI early in 1997, combining genome programs from three national laboratories in its system that had genomic programs of their own. JGI staff members moved into a new facility in January 1999, where they have focused on improving genomic throughput rates. Branscomb says the overall productivity rate increased 20-fold in little more than one year, and now amounts to about 25 million raw bases of DNA sequence per day.

Jeffrey L. Fox