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Day Zero Diagnostics Aiming to Bring Whole-Genome Sequencing Pathogen ID/AST to Clinical Labs


NEW YORK – With a recent new grant and private financing, Day Zero Diagnostics is progressing on a path towards launching a US Food and Drug Administration-cleared sample-to-answer in vitro diagnostic system that uses whole-genome sequencing for same-day, direct-from-blood pathogen identification and antimicrobial susceptibility testing (ID/AST).

Earlier this week, DZD announced completion of a $16 million financing round to support commercialization of an instrument platform for clinical labs. The firm also recently won funding to support new assay development in the other side of its business — an infectious disease testing service focused on sequencing-based hospital-acquired infection tracking.

Jong Lee, CEO and cofounder of Day Zero Diagnostics, said in an interview that the new funds will help the company to move it WGS ID/AST technology to the trial stage.

"We've now got working prototypes in our lab and are striving to complete the cycle of prototype development so that we can go into an FDA clinical study," he said.

The core of the DZD platform consists of a few proprietary technologies, Lee said.

The firm uses an in house-developed "ultra-high enrichment" method called Blood2Bac for the direct-from-blood component of its testing. The recently improved method is able to enrich pathogen DNA such that the firm obtains 10 to 100 times more microbial reads than human DNA reads, Lee said, from samples that start with a billion times more human DNA than bacterial or fungal DNA.

For the WGS, the DZD system performs automated library prep and sequencing and is currently using  Oxford Nanopore Technologies sequencers in its workflow.

For analysis, DZD has developed algorithms using large microbial databases. It uses its KeynomeID algorithm for pathogen species identification based on an internally curated reference genome database, while its Keynome g-AST is a machine learning algorithm for performing genomic AST.

A core database used in the development of these algorithms is DZD's proprietary MicrohmDB, a curated and sourced database that combines the sequences of clinically relevant pathogens with their known phenotypic antimicrobial resistance and susceptibility profiles.

MicrohmDB is "one of the largest databases in the world" of its kind, Lee said, and the DZD strategy also differs from traditional methods for pathogen ID/AST, Lee said.

"We use a machine learning AI approach to this, rather than a more traditional database lookup approach looking for presence or absence of specific resistance genes," Lee explained.

So, while most genomic AST assays target a few dozen known resistance genes, the DZD approach interrogates the entire genome, allowing it to look at both known and unknown drivers of antimicrobial resistance and susceptibility, Lee said.

Lee said the firm has internally demonstrated that its approach can consistently profile both bacteria and fungi in a single assay at concentrations in the low single digits of colony-forming units per milliliter (CFU/ml) using less sample and for a lower cost than other methods.

No other firm has yet commercialized a direct-from-blood ID/AST system, Lee noted. Most commercially available molecular ID/AST assays require positive blood cultures, although T2 Biosystems is developing an ID/AST system based on PCR and miniaturized magnetic resonance technology.

The DZD platform is expected to be differentiated from PCR-based multiplex panels because it will be able to detect many more pathogens and evaluate more possible genetic sources of a resistance phenotype.

Similarly, the WGS approach differs from more traditional targeted-sequencing approaches because, like multiplex PCR, these positive-selection approaches "can only find what they are designed to find," Lee said.

The global push for rapid ID/AST (link) is based in part on an impetus to reduce empiric antimicrobial use in order to improve patient care and slow the burgeoning rates of antimicrobial resistance. The more comprehensive analysis enabled by WGS can essentially eliminate the unknowns that often lead clinicians to hesitate in changing or discontinuing empiric therapies, Lee also said.

In addition to $49 million in venture capital financing so far, the system's development has also been supported in part by three stages of funding from CARB-X totaling $14.4 million.

Lee said CARB-X has helped maintain a constant focus on the growing problem of drug resistance, and he envisions that these efforts will be part of what helps spur a rapid transition to sequencing-based ID/AST in the next five years.

HAI service

In the meantime, DZD also continues to build its testing service, called epiXact, that uses sequencing to track hospital-acquired infections. It is "a really valuable service clinically that's resulted in us being able to work directly with hospital customers," he said, and has also had the benefit of helping the firm build its publication track record.

In the HAI service business, last month Day Zero was also awarded a Phase I Small Business Innovation Research award from the National Institutes of Health's National Institute of Allergy and Infectious Diseases last month to develop a test to trace infections related to fecal microbiome transplants (FMTs).

Mohamad Sater, director of computational biology at DZD, said in an interview that the project was inspired in part by pharmacovigilance work DZD did with a customer of its HAI tracing service that discovered a link between a stool donor and a fatal drug-resistant E. coli infection.

Through shotgun metagenomic sequencing of the donor stool samples and patient blood samples, DZD was able to show that the FMT was the culprit, Sater said.

In a subsequent report in the New England Journal of Medicine, the team also noted that there are more than 300 clinical trials of FMT, and DZD expects to offer its FMT testing service to some of these trials, Sater said.

With the NIH funding, the DZD team hopes to make its existing FMT assay more robust and automated. The firm is also considering developing a sequencing-based FMT donor screening test, Sater said, as transplant material is currently only screening using PCR assays for a few dangerous pathogens.

The FMT infection tracing service is available under the epiXact lab services business, which performs retrospective investigations of infection transmission in clinical settings with a two-day turnaround time. The firm also offers epiXact Pro, a service that develops custom computational biology pipeline for complex of high throughput samples and can also perform prospective investigations through a service called epiXome.

Sequencing clinical samples to create the firm's curated sample collection also offered a window into clonality among hospital infections, Sater said.

"There is a lot of cryptic transmission happening," he said. "The more you sequence, the higher resolution you have, the more you realize how things are interconnected."

Future directions

Although Lee declined to disclose a timeline for its WGS lab system launch, he said that the firm is currently validating its prototype.

"We've demonstrated the capability of working directly from blood, which is something nobody else has been able to do in [sequencing-based] AST," Lee said.

The firm currently has a handful of publications focusing on the HAI service work, but so far has not published details of the direct-from-blood methods or the database.

However, DZD will be presenting work at next month's ID Week meeting in Boston, Lee said, including a study of 36,000 samples that demonstrates the challenges of using resistance gene presence and absence to make clinical decisions. The firm is also preparing to publish this data in a peer-reviewed journal in the future.

Meantime, DZD expects to continue to push on its differentiating factors in the sequencing-based infectious disease diagnostics space.

Favoring this effort is what Lee sees as a current regulatory alignment among different stakeholders in the US that is encouraging FDA-cleared sequencing-based infectious disease diagnostics.

DZD hopes to be at the vanguard here, he said, as no such diagnostic yet exists and the firm has focused on being "regulatory grade" in all of its development work, including the software algorithms.

"Our primary goal is to make sure that we get this in the hands of hospitals … to bring in a new era of sequencing where hospital microbiology labs are using an FDA-cleared test that they can execute locally," said Lee.