When a patient in a hospital gets a new infection—something that happens often when someone’s immune system is compromised—doctors still typically rely on the same tests they’ve used for decades to figure out what’s wrong. Running through a battery of lab tests takes time; to identify bacteria, for example, labs still put samples in a petri dish and wait to see which germ appears, a process that can take days or even weeks.
A startup called Karius, which announced this week that it raised $165 million in a funding round led by SoftBank, uses a different approach, taking a single sample of blood and using genetic testing to quickly identify more than 1,400 pathogens, including bacteria, fungi, viruses, and parasites. The doctor usually gets the results the next day.
“One of the main problems with infectious diseases is that it’s really hard to diagnose which specific microbe is causing the infection,” says Karius CEO Mickey Kertesz. Different microbes can cause the same symptoms. A doctor might guess that it’s a bacterial infection, and a few days later learn that it isn’t. Then they might test for a fungal infection and learn that also is incorrect. “It’s a fairly long and tedious process until the patient is eventually diagnosed.”
The traditional process also typically involves invasive tests such as taking samples of internal tissue, and the new process can avoid that. When microbes infect patients, they shed their DNA into the bloodstream, and that’s what Karius is searching for. In a study at Lurie’s Children Hospital in Chicago, researchers found that using the new process in the first round of testing could have avoided 34 invasive tests.
In some cases, traditional testing may not even be possible. “We had a patient that had a brain mass in an area that neurosurgery would not be able to go and do a biopsy,” says Laila Woc-Colburn, a doctor and associate professor of infectious disease at Baylor College of Medicine in Houston who works with patients with HIV and has used the new testing service. The patient’s symptoms could have been from one of two different diseases. Woc-Colburn was able to use genomic testing to confirm which disease the patient had so treatment could begin.
The company targeted the service first at patients with compromised immune systems, including cancer patients undergoing chemotherapy. “Many cancer patients are lost to infections, not to their underlying cancer, because it is so hard to diagnose what it is that is infecting them,” says Kertesz. In a study last year with St. Jude’s Children Research Hospital involving children who had bone marrow transplants, researchers found that Karius’s tech could identify infections before children felt any symptoms. If this type of testing could be used in a routine way, it could potentially save lives. “The problem is that by the time you know that the child is infected, and by the time you diagnose them, this is in many cases too late,” he says. The fungal or bacterial or viral infection is so strong at that stage.”
The testing is generally as accurate as traditional testing. (Unlike Theranos, a startup that also touted fast analysis of blood samples but was later proven to be fraudulent, more than a dozen peer-reviewed papers have been published demonstrating that Karius works in different patient types.) The technology can also identify pathogens that don’t appear on other tests, such as more than 30 species of the Legionella bacterium. Because the tech uses machine learning, sorting through tens of millions of data points to identify pathogens, it will also get more accurate over time as it’s used more.
The catch: It’s expensive. Hospitals or clinics are billed $2,000 per test. The company argues that this can often be less expensive than the alternative of running multiple tests or keeping someone hospitalized longer. But it’s still a barrier. “Karius is not a cheap test,” says Woc-Colburn. She also says it doesn’t work perfectly yet—in liver transplant patients, for example, who have a disease called “leaky gut” where bacteria may leak from the intestinal wall to the bloodstream, the test picks up that bacteria even though it doesn’t indicate an infection. Still, she says, she expects it to continue to improve and the cost to come down. This type of test “will be the future,” she says. “But we’re still in the early stage.”
Kertesz says that the cost of DNA sequencing is rapidly dropping, and its own cost will continue to come down as it scales up, so this type of testing could become common even in routine cases. “I see a future where genomics and technology like ours are completely displacing most, if not all, existing technologies,” he says.