Inside Precision Medicine
Credit: TUMEGGY / Science Photo Library
A little more than ten years ago, unique fragments of pathogen genomic material were found in the blood of a person fighting off infection. That discovery sent Tim Blauwkamp, PhD, Mickey Kertesz, PhD, and Stephen Quake, PhD, on a journey to develop a diagnostic based on the ability to capture and identify these ultra-rare degraded bits of genomic material from these pathogenic microbes in a blood sample.
The three went on to co-found Karius, where they developed a test (called the Karius Test) that can identify more than 1,000 DNA-based pathogens, including viruses, bacteria, fungi, and parasites, from a single blood draw. Now, Karius has received a contract from the Biomedical Advanced Research and Development Authority (BARDA) to further develop their technology for RNA-based pathogens.
“The vision that we have here is that we’ll be able to detect any infection happening anywhere in the body from a simple blood draw by analyzing those nucleic acids,” Blauwkamp told Insider Precision Medicine. “Since we already have this infrastructure in place for rapid, scalable testing, BARDA has been very interested in partnering with us. This is the first relationship we’ve formalized to develop and bring this RNA capability in-house…to provide a scalable pandemic readiness tool for BARDA and the world.”
Chemistry and compute
The secret sauce to the Karius Test is rooted in two technological innovations in chemistry and computation. Karius developed chemistry that’s optimized for microbial fragments, which have a number of unique features that are different from the fragments of DNA that tumors release, transplanted organs release, or even a developing fetus releases. In essence, Karius developed a liquid biopsy for infectious disease.
The methodology for this infectious disease liquid biopsy is a bit under wraps. “What I can tell you is we’re getting about a thousand times more microbial genomic information out of plasma than we’ve been able to get with any off-the-shelf tools today,” said Blauwkamp. “The current tools have all been optimized for these other liquid biopsy applications in cancer and transplants for human DNA. The microbial DNA differs in several ways and is almost invisible to people using those standard tools. We built different tools and found a very rich microbial DNA signal.”
Capturing the fragments is just half the battle. Karius had to develop the compute support to take sequencing data from the genomic material of these microbes and filter it in a way that sorts out the pathogenic ones from the commensals or environmental background, an endeavor championed by Sivan Bercovici, PhD, Chief Technology and Business Officer.
According to Blauwkamp, their metagenomic process is rooted in having sequenced tens of thousands of patients, including about a thousand healthy patients. This gives the team at Karius a picture of the normal variation in microbial composition and allows them to fish out the outliers.
The next pandemic pathogen
Since its inception in 2014, Karius has been focused on the DNA-based pathogens that are releasing their genomic DNA into the blood. But Blauwkamp said that they’ve known that there’s a very “rich microbial RNA signal,” and that’s what’s at the heart of the contract with BARDA through their DRIVe (Division of Research, Innovation, and Ventures) initiative that funds early-stage companies for life-saving innovation. The BARDA DRIVe initiative is geared towards funding these earlier proof of concept stages for big ideas that can really take those step functions or those leapfrog advances into what’s possible, either for defense or patient care.
Blauwkamp said that the funding from DRIVe is feared at such an early stage in the development process that it’s not even meant to produce a final product—it’s meant to establish the feasibility at a higher level of integrity of being able to detect any pathogen anywhere in the body from these blood specimens using both DNA and RNA. That being said, Blauwkamp is confident that the automated infrastructure at their facility can scale the Karius Test in a pandemic situation.
“I think one of the reasons DRIVe is so interested is that we don’t know what the next pandemic path is going to look like, and there’s a high likelihood that it’s RNA given the past pandemics or near pandemics with viral pathogens,” said Blauwkamp. “There are possibilities of engineered biothreats, so don’t assume you have the exact genomic sequence of whatever’s next. The fact that we don’t have any microbe-specific primers or probes that hybridize in any microbe-specific way; we sequence everything that’s microbial in a specimen, puts you in an ideal situation to adapt within days to a new threat that’s never even been seen before.”
A primer- or pull-down-based approach has the downside of having to be optimized and validated. But Karius does not have to worry about that as long as they can identify the pathogen genome in their liquid biopsies. From the moment the Karius Test picks up on a new reference genome, it can be added to the database and incorporated into the set of other pathogenic genomes to look out for.
Fever pitch
While there is a lot of focus on pandemic preparedness in collaboration with BARDA, there’s a lot of clinical utility for detecting pathogens with RNA genomes. The Karius approach can be a saving grace for an immunocompromised patient or even when clinicians are racing to get the results of an antimicrobial susceptibility test (AST). After all, many ASTs can take 48 to 72 hours, whereas the Karius test takes about 26 once the sample is at their facility.
“The turnaround time is one of the features our customers appreciate most for us,” said Blauwkamp. “They can get their result through either a mobile app notification or secure web portal, and we continue to do the secure electronic fax back to the ordering send-out lab.”
According to Blauwkamp, their test could be a massive help in helping patients with rising or persistent fevers. Today, a fever of unknown origin or neutropenia often requires a sample of the intact infected tissue or fluid. If it’s thought to be caused by a lung infection, the clinician will try to get a sputum or bronchiolar lavage fluid specimen. In the case of endocarditis, a clinician might try to get a piece of the infected heart valve.
“This idea with fevers is you may not have any idea what specimen to get even if you were willing to spend all the money in the world on diagnostics—you still just don’t know where to hunt,” said Blauwkamp. “So, the unique approach we offer here is that the liquid biopsy approach bypasses this need to know where the infection is and offers a great deal of utility from that perspective. In the cases of patients who present with fever, for example, we believe the inclusion of RNA will greatly improve the utility we can offer those patients.”
Soon, the days may be gone where the best thing doctors can do for someone experiencing an alarming fever is to bury them in ice packs and hope that the undiagnosed infection goes away on its own. Every new microbial genome the Karius test detects might serve as the basis for a brand-new antibiotic or antiviral. It may give patients a chance against that particular strain in the never-ending war with the microbial world.
News & FeaturesDNAEmergency medical servicesInfectious diseasesLiquid biopsyMicroorganismsMolecular techniqueRNAKarius Test
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