Julie Segre, Tara Palmore and the Team

During a nerve-racking 12-month period in 2011 and 2012, a rare, deadly strain of antibiotic-resistant bacteria was spreading through the nation’s premier research hospital.

Every effort to halt the outbreak was failing until a team of biomedical detectives led by Drs. Julie Segre and Tara Palmore at the National Institutes of Health (NIH) used a revolutionary new technology to track and contain the infection.

In the end, 18 seriously ill patients acquired the bacteria and seven died from the infection—a tragedy for the patients, their families and the NIH. But the frightening episode prompted the NIH for the first time to sequence the bacteria’s DNA to decipher how the pathogen spread from patient to patient, which then allowed the doctors to detect the origins of the infections, trace the transmission path and implement robust measures to put an end to the outbreak.

This use of genomics could radically transform the way hospital-acquired infections are identified and halted, leading to quicker response times and saving tens of thousands of lives. There are nearly 100,000 deaths a year in the U.S. attributed to these infections.

“It is a groundbreaking advance in one hospital that will now have an impact across the world and will become the standard,” said Dr. Francis Collins, director of the NIH. “It is a fantastic example of taking a challenging medical problem and applying technologies in a new way to come up with a remarkable result. We now have a new weapon in the battle to stop the spread of drug-resistant organisms.”

Dr. John Gallin, director of the NIH’s Clinical Center, said the breakthrough by the NIH team is “a magnificent demonstration of how a hospital can contain these infections when they occur.”

“With this new genomic approach, we can now with exquisite precision track the evolution of an infection in a hospital and from one hospital to another, one city to another and one country to another,” he said.

When the cluster of infections began at the elite 243-bed research hospital, Palmore, along with Dr. David Henderson, led the infection-control team. Segre, who has been involved in the Human Genome Project for 20 years, and colleague Evan Snitkin worked on the bacterial sequencing.

The deadly multidrug-resistant bacteria strain known as Klebsiella pneumoniae first entered the NIH’s Clinical Center in June 2011 from a patient who had been transferred from a health care facility in New York. The NIH hospital thought it had taken steps to prevent patient-to-patient transmission, but another patient soon acquired the bacteria, followed quickly by multiple other cases.

After the second case, Palmore said she and her team “took rigorous outbreak control measures in escalating fashion” to stop the infection from spreading. Despite their best efforts, there still was no clear explanation of how the bacteria were spreading or where it all started. That’s when Segre stepped in.

By sequencing the DNA from bacteria from each of the infected patients, Segre was able to definitively trace the strain to a single source, the New York patient.

When combined with traditional epidemiology tracking data, the genome sequence results showed the New York patient’s bacteria were transmitted to other patients on three separate occasions. The sequencing allowed Segre and her colleagues to track the exact route of the infections as the microbes hopscotched around the hospital in ways that were somewhat unexpected.

Using the sequencing results, Palmore undertook intense infection control measures and vigilant hospital-wide surveillance to break the chain of transmission and stem the outbreak.

With a limited number of antibiotics available to fight these highly resistant bacteria, Palmore and Segre are hopeful that using this technology will become a standard approach for hospital infection control.

“We have demonstrated a new approach to hospital infection control based on innovation and genomic technology,” said Segre.