Genetic sequences of drug-resistant bacteria have helped scientists better understand how these dastardly infections evolve—and elude treatment. But these superbugs are still claiming lives of many who acquire them in hospitals, clinics and nursing homes. And recent outbreaks of these hard-to-treat infections can spread easily in healthcare settings.

Researchers might soon be able to track outbreaks in real time, thanks to advances in sequencing technology. So say Mark Walker and Scott Beaston, both of the School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Center at the University of Queensland in Australia, in an essay published online November 29 in Science. "Genomic sequencing can provide information that gives facilities a head start in implementing preventive measures," they wrote.

Current preventive measures, such as increasing healthcare worker hand washing and isolating infected patients, have helped to reduce the spread of many healthcare-acquired infections. But these preventable infections still kill some 100,000 patients in the U.S. each year.

Walker and Beatson think genomics has the capacity to "revolutionize current practice in clinical microbiology," which currently relies primarily on culturing pathogens in the lab to study strain differences—a time-consuming process. Some promising examples have already emerged.

A 2011 outbreak of Klebsiella pneumoniae (KPC), which is resistant to most known antibiotics, at the National Institutes of Health's Clinical Center killed 11 patients and infected many others. Genetic sequencing of samples from patients and from healthcare workers allowed epidemiologists to track the outbreak to a single patient and to trace its spread.

The KPC analysis even pinpointed a transmission event in which a contaminated ventilator was used on a new patient. This level of detail points to the ability of "genome sequencing-based epidemiology to influence hospital management practices," the researchers noted.

These discoveries, however, were made after the outbreak was underway. "In a real-time clinical situation, this information would enable further targeted testing of other patients or healthcare professionals to identify intermediate carriers," Walker and Beatson wrote.

Moving closer to real-time tracking, researchers sequenced and analyzed strains from a 2011 outbreak of methicillin-resistant Staphylococcus aureus (MRSA) in a neonatal intensive care unit in Cambridge, in the U.K., while the outbreak was still occurring. A local clinical microbiologist wondered whether infants who had contracted the superbug had strains related to those currently circulating in other clinics and hospital areas. A team sequenced samples and found that not all of the strains were related, but that there was indeed a clear outbreak cluster in the neonatal unit. The microbiologists were then able to trace potential means of spread and thereby reduce the risk of further spread. The genetic sequencing, completed on a bench-top sequencer, also provided information about the strain's virulence and nature of its antibiotic resistance.

These instances "point to a future in which direct sequencing of clinical samples allows same-day diagnosis, antibiotic resistance gene profiling and virulence gene detection," Walker and Beatson noted. Such sequencing and analysis is still too expensive and labor-intensive for most health care institutions. But as technologies improve, putting the tools within reach, clinical microbiologists might be soon able to stop these superbug outbreaks before they start.