Healthcare-associated infections are an intractable problem for hospitals, striking 1 in 38 patients and costing the U.S. healthcare system billions each year.
Startup Claryx, started by brothers Kurt and Dirk Hackenberger, is taking a novel approach to pathogen detection, using environmental and genomic intelligence to support hospital infection prevention programs. The company is building an immune system for hospitals, one that catches transmission while it's happening.
The company launched out of stealth with $3.5 million in pre-seed funding led by Outlander VC. Company Ventures, Boost VC, Neon, Mana Ventures, 640 Oxford and Precursor also backed the round.
The company's technology is being deployed at multiple leading health systems in New York City, Kurt Hackenberger, co-founder and CEO, told Fierce Healthcare in an exclusive interview about the launch and funding round.
The brothers—Kurt is an ex-Carlyle investor and Dirk earned a Ph.D. in infectious disease genomics—were motivated to start the company after their grandmother went to a hospital for a routine procedure, developed C. difficile and then sepsis, turning a few hours into three months in the hospital.
They saw an opportunity to use genomic biosurveillance, what they refer to as genomic intelligence, to read the genomes of confirmed patient infections, link related cases as outbreaks and trace each to its likely source.
"We're trying to find pathogens in hospitals before they get into patients," Dirk Hackenberger, co-founder and chief science officer, told Fierce Healthcare. "The way that we do that is we sequence the genomes of the pathogens themselves, so the things that have actually caused infection in the hospital and are isolated by the clinical microbiology lab, and then we also sequence the metagenome of the environment, so that's that more complicated DNA from things like building-level wastewater, warden room-level air samples and then surface and sink swabs. Once we have those two data sources, we can compare all the genomes against each other. We can see when the same pathogen is causing multiple different infections, essentially guiding the epidemiologist to identify the epidemiological links of what actually makes up an outbreak, and then figure out what the source might be."
"On the other side, and this is novel in the space, we're also going to be comparing those pathogen genomes against the environmental metagenomes to see where they sit in the hospital," he continued. "So, for example, if somebody comes in, they acquire an infection. We see what's the genome of that pathogen, and then we see the exact same sequences in the sink in room 4A and we can raise a flag on that sink to disinfect and remove that potential reservoir before it causes more problems."
Reading a pathogen's genome is the only way to tell a real transmission chain from chance, according to the Hackenbergers, and it's what links scattered cases as one outbreak, points to the likely source, such as another patient, a shared piece of equipment or a reservoir anywhere in the building, and confirms the response worked.
Claryx's technology sequences each patient infection and matches it against a genomic digital twin of the environment, built from its air, its water and its surfaces, using AI to map exactly where it came from and where it might go.
Claryx's co-founders see preventable infections are a solvable problem. Historically, pathogen sequencing has been expensive for hospitals to do at scale.Dirk Hackenberger developed Claryx's core technology, the CloneLink platform, based on proprietary chemistry that cuts certain sequencing costs more than twentyfold. That makes actionable intelligence viable at scale for the first time, according to the co-founders.
"Today we can tell a hospital where an infection came from. We're building toward a future where it never had to happen in the first place," Kurt Hackenberger said.
The estimated direct annual cost of treating hospital-acquired infections in the United States ranges from $28.4 billion to $45 billion. Data from the U.S. Centers for Disease Control and Prevention (CDC) indicates an estimated 518,000 HAIs occurred in U.S. hospitals in 2023, costing billions of dollars and posing significant risks to American lives.
Healthcare-associated infections add an average excess length of stay of 7.8 days per patient, directly reducing bed availability and increasing wait times for incoming patients, studies show. Hospitals with high infection rates face Medicare penalties running into the millions a year, all against operating margins near 2%.
"It's been very difficult up until recently to be able to one align the incentives, and so now with fixed reimbursement Diagnosis-Related Group (DRGs), you actually have real opportunity to then capture the cost that would be associated with those infections. It also comes down to efficiency and being able to enable hospitals to do more with less, with infections being one of the things that clogs us up more than anything else," Kurt Hackenberger said.
There are opportunities for Claryx's technology outside of hospital environments, he noted. Hospitals provide "ground truth" on pathogens in the environment that lead to patient infections. "You can then start training your models on the way the disease manifests inside of the hospital environment to then re-platform those models away from meeting that reference database and towards other places where you don't get those patient infections. There's huge applications for this inside of skilled nursing or elder care," he said.
"When we fast forward a couple years, or even just in the world of today, where you're seeing known threats becoming more antibiotic resistant, you're seeing engineered pathogens becoming potentially more prevalent as a function of AI, with biosecurity being a huge focus area for OpenAI, Anthropic, and others. And then 'unknown unknowns' are showing up with higher degree of prevalence, you're now seeing an opportunity for us to create resilience in the place where people spend 90% of their time, which is indoors. The bigger swing in all this is moving this away from just hospitals and into factories, schools, offices, ships, etc," he said.
There exists meaningful peer-reviewed evidence behind Claryx's approach. In a two-year study at UPMC Presbyterian, published in Clinical Infectious Diseases, a University of Pittsburgh team ran real-time genomic surveillance and found 172 otherwise undetected outbreaks across 476 patients. The study found that 96% of the outbreaks they traced and acted on went no further. The team estimated 62 infections and close to five deaths avoided over the two years, and a 3.2-fold return on the cost of running the program, a figure that excludes the roughly 480 bed-days freed to serve patients who need them.
Claryx deploys continuous genomic intelligence wherever a hospital's risk is highest, whether that's the ICU, the emergency department or transplant and immunocompromised wards, according to the company. AeroScan samples the air continuously, and the Claryx team samples wet reservoirs like sinks, high-touch surfaces and building wastewater. Samples are sequenced at the Claryx lab, where CloneLink compares every infection and environmental sample at the strain level, surfacing matches between patients and the environment around them, the co-founders said.
"We're the ones who are going in doing the swabs and everything else. The whole point of this company is to take as much work off the backs of hospital staff as possible," Kurt Hackenberger said.
With the funding, the company will be able to deploy its technology to more hospitals to continue building the evidence base and prove out the return on investment, the co-founders said.
Kurt Hackenberger sees Claryx operating like an orchestration layer over a hospital’s existing infection prevention programs and capabilities.
“Hospitals spend millions of dollars on infection prevention, cleaning staff and HEPA filters and all this stuff that's not fully optimized in a way that it could be. We can sit over top of all of that and then allocate your resources to their highest and best use. So, you have an outbreak that's happening in your ICU, you'll allocate infection preventionists to go and investigate. You have spiking COVID inside your ED. Let's put a HEPA filter out there. There's a contaminated sink drain inside of the room for 4A. Let's go get a cleaning staff out and be able to rectify that,” he said. “This enables you to take all those resources and allocate them to their highest and best use, which then drives value for the hospital more broadly.”
He added, “The hardest part is getting from the point where we are today to having enough evidence generated to be able to prove exactly that thesis.” The funding will help jumpstart that work over the next 18 to 24 months, he noted.
"Every building people share is a transmission system running invisibly, and Claryx has made it possible to finally see it," said AJ Smith, partner at Outlander VC, in a statement. "We backed Kurt and Dirk because once you can generate this kind of intelligence in a hospital, you can generate it anywhere infection spreads."
Kurt Hackenberger noted that investors from Outlander spent significant time with the company at hospitals to understand the problem and the technology. "They really got deep and really focused on us as founders," he said.
Claryx's scientific advisory board brings together clinicians and researchers from Mayo Clinic, Harvard, Yale, Weill Cornell, Washington University, UCLA and McMaster, alongside former public health leadership from New York City and the CDC.