A three-year-old child in the Bay Area was recently admitted to the hospital with a rash. The child was sent home with a diagnosis of hand-foot-and-mouth disease, a common virus that typically resolves in a few weeks.

But the patient continued to get worse and had to be admitted to the hospital. The doctors were stumped, as more and more tests came back negative.

So they called up a stealthy biotechnology start-up in the Bay Area with a novel technology for detecting disease.

Overnight, the company’s lab got a delivery of the child’s blood. Its technology, which can detect the source of an infection — viral, bacterial or fungal — by analyzing fragments of DNA in the patient’s bloodstream, was able to produce a diagnosis in a business day.

Rat-bite fever.

The child had been scratched, likely by a pet rat.

That company, called Karius, is announcing $50 million in financing from investors including Khosla Ventures, Tencent, and Eric Schmidt’s Innovation Endeavors.

This particular patient was involved in one of its early clinical studies, which intended to compare its test to the current gold standard for infectious disease diagnostics. Karius presented its data at a medical conference in June.

The company’s CEO Mickey Kertesz said the U.S. Centers for Disease Control and Prevention delivered the same result of rat bite fever, but it took several months. That’s because current techniques are hypothesis-driven: A physician has an idea for the culprit, takes a sample to culture, and waits for a positive or negative result. If it’s a negative, they move on to the next idea.

This approach has resulted in patients being treated with antibiotics that they do not need and getting misdiagnosed, said Peter Chin-Hong, a doctor who treats patients with infectious diseases at UC San Francisco. That can often lead to patients getting sicker, or ending up with antibiotic resistance.

Kertesz said the company has figured out a way to separate out the disease-causing agent from bacteria that live harmoniously in the body. “We all have gut and skin bacteria that is found in lower levels when you’re healthy,” he said. “It’s different when you’re sick.”

The company’s test doesn’t cover all infections, but it can detect more than 1,000, including rat-bite fever, valley fever and streptococcal infections.

The test is currently available for $2,000, which costs more than traditional diagnostic tests. For that reason, Karius isn’t positioning its test as a first line of defense for doctors. Rather, it’s for those tricky cases where the patient is critically ill, and the first results come back negative.

About 50 percent of cases result in a definitive diagnosis, said Kertesz. Sometimes, it’s not an infection that is making the patient sick, or the infection has already passed and is no longer detectable in the blood.

Karius has tested thousands of patients in clinical studies thus far. It is planning to launch to clinical practices nationwide later this year.

Doctors who have used Karius’ technology say it could be the future for infectious disease diagnostics and treatment.

“I think this technology will revolutionize medicine,” said Chin-Hong.

“People don’t realize that it’s (medicine) an imprecise science and we use a lot of antibiotics to get one infection that we can’t see,” he added.

Chin-Hong said Karius’ test was able to accurately diagnose a patient getting treated for leukemia with a sexually transmitted infection that was wreaking havoc on their health. Getting an answer early can save lives, he said, especially in cases where the patient’s immune system is compromised.

It will be some time before Karius’ test is used in routine medical care. Currently, it is focused on critically ill patients, including those who are recovering from organ transplants or chemotherapy, or infants that don’t have the blood volume for a round of tests.

The company is hoping that it will treat chronically ill patients next. Millions of people are misdiagnosed every year, which presents another opportunity for Karius’ test.

The company is also looking at other sample types beyond blood to broaden its range of detectable infections, as well as generating resistance profiles to better understand whether a patient will respond to a course of therapy.

One dream for the company is to coin new infectious diseases, as it is already finding signals from unknown microbes. It also sees an opportunity to work with public health researchers to track outbreaks.

For Chin-Hong, the current technology already has promise, as it offers more targeted treatment than the status quo.

“It means one blood draw instead of a series of pokes and sticks for the patient,” he said. “And it means one drug rather than a lot of antibiotics that aren’t needed.”