Infection Detectives Use Metagenomics to Identify Pathogens

When a patient comes into the hospital with severe pneumonia, rat bite fever is not the first thing most doctors think of. In fact, it’s so far down the list of possible infectious causes that most clinicians likely wouldn’t even consider it.

But when metagenomics testing of one patient’s blood came back, there it was: rat bite fever.

“It's like, okay, well how did that happen?” said Bradley Perkins, the chief medical officer at Karius whose metagenomic test identified the infectious microbe in this patient’s sample. “When [the patient’s doctors] went back to talk with him, the patient gave a history of mowing his lawn and accidentally mowing over a dead rat.”

The rat had been infected with Streptobacillus moniliformis, the bacterium that causes rat bite fever. When the patient mowed over the dead animal, the bacteria became aerosolized and entered the man’s lungs. With a definitive answer to what was causing his pneumonia, doctors could finally treat it.

“When you have an agnostic test, you see the full range of things without the limitation of physicians having to think [what] may be a cause of it,” said Perkins. While turning to metagenomics testing first is not the standard protocol for hospitals yet, Perkins and the team at Karius hope that soon it will be.

With their metagenomics technology, Karius aims to return infectious disease diagnoses quickly using a simple blood draw or lung fluid collection for potential lung infections. They are particularly focused on immunocompromised patients, who can have mixed and complex infections on top of a chronic disease, and getting them to care they need to live healthier lives.

Infectious Microbes Leave Behind Cell-Free DNA Footprints

No matter where in the body an infection lurks, cell-free DNA from the microbe will make its way into the bloodstream. “Even if you have a deep-seated infection in your brain, for example, or in remote areas in your bone, in your heart valves, we can pick up those fragments with a plasma sample,” said Perkins.

In the traditional infectious disease diagnostic workflow, a patient comes to the hospital, and doctors have to first decide what they think the infection is and then order a specific test to find out. If the test comes back negative, they must order another and so on. This process takes time, and if the patient is not getting effective treatment, they may become sicker.

“We allow physicians to avoid that by asking the question: Is there any microbial DNA in the bloodstream?” Perkins said.

To use Karius’s test specifically, physicians order a typical blood draw for the patient’s plasma. That sample then gets sent to Karius’s centralized laboratory where the team will send the results back to the clinician the next day. They first enrich for microbial DNA in the sample and run it on a high-throughput sequencer. Then, using their proprietary bioinformatics and artificial intelligence pipeline, the Karius team matches the sequences from the patient’s sample to their database of about 20,000 whole genome sequences. From there, they identify the infectious agent or agents from a list of more than 1,000 different pathogens.

“We need to include a lot more microbes in our dataset than the ones that we report to have confidence that we're really reporting out the ones that are relevant to the physicians,” Perkins explained. “We can actually give them a quantitation of the number of fragments that are present for particular microbes, and that is believed to be useful in characterizing the likelihood that they're causing an infection and potentially the severity of that infection.”

How Fast Metagenomic Testing Helps Immunocompromised Patients

Detecting infections quickly is critical for people who are immunocompromised—not only because they can have multiple infections at once, but because these infections can prevent them from receiving care for conditions such as cancer.

“By better preventing and treating infections, we give them the opportunity to access therapies and get better from their underlying chronic disease, spend better higher quality time with their families, and make physicians more effective in taking care of these people. That's really what motivates us,” said Perkins.

Karius scientists, along with researchers at multiple hospitals and academic institutions, compared Karius’s test to the standard of care in diagnosing infections in people with cancer those who had recently received a stem cell transplant.¹ In the multi-center, prospective, observational study, they found that the Karius test identified more causes of pneumonia than standard non-invasive and invasive tests.

Based on these findings, doctors “can move from empiric antibiotics, which have lots of unintended adverse events, to directed therapy. They can stop doing invasive procedures to get additional samples like broncoscopy or needle biopsies because we have a very fast turnaround time,” Perkins said.

Additionally, the Karius team recently reported that their test could even identify some infections in pediatric cancer patients they got sick.² “Imagine, helping those kids by never having to get sick from an infection in order to treat it,” he said.

As Karius looks ahead, they’re interested in identifying additional antibiotic resistance sequences in the bacteria they identify as well as novel pathogens. With their new ability to test lung fluid for infections, Perkins expects they may also explore sampling other body compartments.³ In the future, the team hopes to use their technology to explore what Perkins calls “microbial dark matter”—the many microbes that live on and inside the body that remain uncharacterized.

But for now, the team’s focus lies squarely on improving outcomes for those most at risk of severe infections.

“There're tens of millions of immunocompromised patients in the United States, and right now we're helping just a small proportion of those,” said Perkins. “Our desire is to continue to improve our ability to do that.”