Genetic sequences of drug-resistant bacteria have helped scientists better understand how these dastardly infections evolve and elude treatment. Preventive measures such as increasing health care worker hand washing and isolating infected patients have reduced the spread of many health care–acquired infections. Yet these preventable infections still kill some 100,000 patients in the U.S. every year.

Researchers might soon be able to track outbreaks in real time, thanks to advances in sequencing technology. Genomics has the capacity to “revolutionize current practice in clinical microbiology,” wrote Mark Walker and Scott Beatson of the School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Center at the University of Queensland in Australia, in an essay published online last November in Science. Until now clinical microbiology has relied primarily on culturing pathogens in the laboratory 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 health care workers allowed epidemiologists to track the outbreak to a single patient and to trace its spread. Moving closer to real-time tracking, researchers sequenced and analyzed strains from a 2011 outbreak of methicillin-resistant Staphylococcus aureus (MRSA) in a hospital in Cambridge, England, while the outbreak was still occurring. The tests helped doctors and researchers identify a clear infection cluster in the neonatal intensive care unit, differentiating the bacteria from strains present in other clinics and hospital areas. Microbiologists were then able to trace potential means of spread and reduce the risk of further infections.

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 wrote. Such sequencing and analysis are still too expensive and labor-intensive for most health care institutions. Yet as technologies improve, putting the tools within reach, clinical microbiologists might be soon able to stop these superbug outbreaks before they start.