Innovations: ID Genomics takes the guesswork out of antibiotics

It takes about three days for a lab to identify the exact bacteria that has caused a patient's urinary tract infection, one of the most common infections acquired in U.S. hospitals. Most physicians don't want to leave a patient untreated and in pain for that long, so they make an educated guess when they choose an antibiotic to administer.

The odds the physician will pick the right one should be high. After all, about 80% of UTIs are caused by E. coli. But some E. coli strains have built a resistance to commonly used medications. For example, E. coli strains will fight back in about 30% of patients prescribed the drug Cipro.

“A doctor suspects, but he doesn't have the means to determine right away what species the bug actually belongs to,” said Dr. Evgeni Sokurenko, founder of ID Genomics, a startup company that intends to allow physicians to quickly detect specific types of UTIs and the best antibiotics used to treat them.

Launched in 2013, ID Genomics decodes UTIs in less than 30 minutes by analyzing the genes that are present and those that are not. The test assigns a unique fingerprint to the bacterial strains, allowing physicians to determine the precise makeup of a UTI infection based on the combination of genes. Meanwhile, the company is creating a database of the bacterial fingerprints matched with information about how those strains have responded to particular drugs.

“It is like we are creating a criminal dossier of bacterial strains,” he said. “Just based on the fingerprint we can already say what is the best way to deal with it and what antibiotics should be used.”

Sokurenko began his work assessing antibiotic resistance among infections about 25 years ago. He developed the basis of ID Genomics as a professor of microbiology at the University of Washington, where he still teaches full time. ID Genomics employs 10 people and most of its financial backing has come from a $3 million National Institutes of Health grant awarded last month.

Eight healthcare organizations across the U.S. were selected to participate in the NIH grant and are now contributing to ID Genomics' clinical database. The library has collected more than 8,000 UTI samples so far.

Seattle-based Group Health Cooperative, which became Kaiser Permanente Washington Feb. 1, is now one of the participating providers. Kaiser currently sends patient samples to ID Genomics for its database. The hope is physicians will eventually be able to use ID Genomics in a clinical setting, said Dr. Kim Riddell, director of laboratory services at Kaiser Permanente Washington.

ID Genomics is working with its partners to make the data from the tests more easily understandable to physicians so they can analyze the results quickly and accurately. The test is also awaiting approval from the Food and Drug Administration for clinical use.

Riddell said physicians who work in Kaiser's urgent-care centers would benefit most from ID Genomics' technology because they usually treat the most UTI patients. The technology could also be particularly valuable for providers who care for elderly and chronically ill patients, who are more likely to suffer from antibiotic-resistant infections because their immune systems are weak, Riddell said.

And the more often antibiotics are wrongly used, the weaker they become against the bacteria. “Prescribing the right antibiotic right upfront is absolutely critical when cutting back resistance of these organisms,” Riddell said.

The other organizations contributing data under the NIH grant include Seattle Children's Research Institute, Keck Medical Center of the University of Southern California in Los Angeles and NYU Langone Medical Center in New York City.

Sokurenko said he would like to expand ID Genomics to treat other infections. He said the technology can be used to assess the bacterial strains of various blood infections and infections causing pneumonia.

“Every time a bug causes an infection, it's like they are coming from the moon; no information is being linked to the previous infections,” Sokurenko said. “Sometimes it can take so long to treat, a person can lose his or her life.”