Improved hospital "superbug" detection demonstrated

Microscope image of a glass capillary being used to capture a single bacterial cell during micromanipulation.
Microscope image of a glass capillary being used to capture a single bacterial cell during micromanipulation. — T. Ishoey, courtesy of Roger Lasken

Dangerous microbes in hospitals can be detected in levels low as just one cell, according to a study led by J. Craig Venter Institute scientists. While the study is at the research stage, it could eventually help hospitals identify deadly "superbugs" such as MRSA and CRE before they gain a firm foothold.

Hospitals have been frustrated in stopping superbug invasions because most bacteria don't grow well in cell cultures hospitals use to detect them, said Dr. David Brenner, UCSD's vice chancellor for health sciences and dean of the school of medicine. So such pathogens can stick around hospital environments until they land in a vulnerable patient, perhaps inside someone who has had an operation.

Directly detecting bacteria will help hospitals find the hidden routes these superbugs follow, said Brenner, who has followed the research. Hospitals can use this information to close off these routes.

The study was published Friday as an open access article in the journal Genome Research. Its first author was Jeffrey McLean, a staff scientist at the Venter Institute's La Jolla office. Roger Lasken, director of single cell genomics at the Venter Institute, was the senior author.

Roger Lasken of the J. Craig Venter Institute.— J. Craig Venter Institute

The researchers examined bacteria in a "biofilm" taken from a hospital bathroom sink. Biofilms are sticky masses of bacteria especially resistant to eradication. Researchers found a single cell of a periodontal pathogen, Porphyromonas gingivalis, along with 24 other species of bacteria, some dangerous and some harmless, present in the biofilm.

Moreover, the researchers produced a nearly complete genome sequence of the P. gingivalis bacterium, identifying potentially dangerous differences between it and three other strains that have already been sequenced. These changes may make it easier for the strain to survive outside of its human host and infect people, the researchers said.

The new study is significant because the technology was applied to bacteria in an actual hospital setting, Brenner said. The next step is to do a larger study and identify bacteria throughout the hospital, thus producing the "hospital microbiome," he said.

Jeffrey McLean, J. Craig Venter Institute.

"So what the hope is, if we can understand the flow of bacteria in a hospital, and particularly the flow of drug-resistant bacteria, we can develop novel ways to intervene," Brenner said, listing the questions this research could answer.

"How do bacteria get into the hospital? How do they get transported from one place to another? One patient has drug-resistant bacteria, how does it spread to other patients in the hospital? Is it on the gurneys, is it on the sinks, or the doors? Maybe the way we sterilize things is wrong. Maybe the way we have bacterial-killing lights in certain areas is wrong. It may be the way the plumbing works is wrong."

Answering these questions hasn't been possible because most of the dangerous bacteria are missed by the bacterial culturing methods hospitals now use, Brenner said.

"Right now, we're at the mercy of cultures. If it's culture-negative, we assume it's okay. And this is the breakthrough. It will no longer depend on cultures."

Dr. Dale Lieu, an infectious disease specialist at Kaiser Permanente in San Diego, said the study emphasized some important lessons about microbial hygiene.


