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Pathogenomix Developing Infectious Disease Testing Platform Enabled by Cloud-Based Analytics, NGS


NEW YORK — Pathogenomix is combining sequencer-agnostic, cloud-based analytics software with 16S rRNA gene sequencing to enable hospital laboratories to identify the pathogens behind life-threatening bacterial infections.

Though no NGS-based tests have obtained full US Food and Drug Administration authorization to identify infectious disease pathogens, Pathogenomix said it is on an accelerated path to apply for de novo authorization for Patho-Seq, a test that targets about 400 bacterial pathogens to help diagnose sepsis, bacteremia, joint and implant infections, bacterial meningitis, and tick-borne bacterial infections.

The Santa Cruz, California-based company obtained FDA breakthrough device designation for the test last month and hopes to get de novo authorization in about a year, Chris Risley, Pathogenomix's executive chairman, said in an interview.

If approved, Patho-Seq will become the first authorized system in the US market to identify such a broad panel of pathogens directly from whole blood or cerebrospinal fluid in a single test run, returning results to an ordering clinician within one or two days, Risley said.

The firm will seek de novo authorization for Patho-Seq using cerebrospinal fluid for the diagnosis of bacterial meningitis; synovial fluid for the detection of joint and implant infections; and whole blood for the diagnosis of sepsis, bacteremia, and tick-borne infections.

After applying for de novo authorization, the firm plans to seek authorization to add pathogen targets based on the analysis of additional sample types including urine, tissue, and sputum. In research projects, the platform has identified "any of 2,000 bacteria that might be in a sample," Risley said.

Pathogenomix noted that many other labs are implementing a send-out model where samples are sent to them by hospitals for sequencing. According to Risley, that will continue to be a strong business when laboratory protocols are challenging and sequencers are expensive.

However, "as sequencers fall in price and as lab procedures get easier there is an opportunity to move sequencing" into hospitals, which "saves a day before the clinician gets back pathogen identifications by avoiding shipping," Risley said.

Pathogenomix's model allows a hospital lab to process samples locally and analyze the samples using its software to get fast, accurate pathogen IDs, he said.

One of its key points of differentiation is a pre-processor that accepts 200-megabyte files from a sequencer, reduces the file size to 100 kilobytes, and uploads the file to its cloud server for analysis using its sequencer-agnostic Ripseq analytics software, he said.

Such a test has the potential to complement current commercial molecular and phenotypic tests for pathogen identification and become an important part of the same clinical workflow, Risley added.

Current diagnostic testing panels including those developed by Roche's GenMark Diagnostics, BioMérieux's BioFire Diagnostics, DiaSorin's Luminex,T2 Biosystems, Accelerate Diagnostics, and others, are designed to detect bacterial and other types of pathogens responsible for bloodstream infections.

Though these panels usually include the most prevalent pathogens for bloodstream infections, they have some drawbacks that Patho-Seq can address, Risley said.

With the exception of T2 Biosystems' FDA-cleared fungal and bacterial panels, current IVD tests operate after a blood culture has returned a result indicating an infectious pathogen is in the sample.

Though blood cultures are a vital part of the overall diagnosis of many infections, they can take days to return a result and some important pathogens can't be grown at all, creating diagnostic challenges, Risley noted.

In addition to identifying a broader set of pathogens than current panels, Patho-Seq doesn't require a blood culture, and its ability to operate with different types of samples including blood, cerebrospinal fluid, and urine means it can be used to diagnose different infections, Risley said.

Further, Patho-Seq does not rely on a hypothesis about the specific microorganisms that could be in a sample — something inherent to current ID panels that increases the risk of missing important microorganisms. "A hypothesis-free approach takes the burden off clinicians who can have confidence they will get a comprehensive analysis of the microorganisms in the sample," Risley said.

To obtain validation data for its breakthrough device designation, Pathogenomix collaborated with Mayo Clinic Laboratories to develop NGS wet-lab protocols for Patho-Seq. In an internal study, its collaborators reported obtaining 99 percent sensitivity and 97 percent specificity using 16S NGS to detect bacterial pathogens, Risley said.

According to the Mayo Clinic website, the study consisted of 130 positive patient specimens, 63 negative samples, and additional samples spiked with gram-negative or gram-positive bacteria. However, additional details of the study were not available.

If Patho-Seq is granted de novo authorization, hospitals labs will use Mayo Clinics' wet-lab protocols to prepare samples prior to sequencing, after which they will use Pathogenomix software to reduce the size of the sequencing file. From there, the file will be uploaded to the cloud where it is analyzed using Pathogenomix software prior to the delivery of results to clinicians, Risley said.

Last year, the firm's collaborators at the Mayo Clinic published a study in Clinical Infectious Diseases supporting the utility of 16S rRNA NGS for detecting and identifying bacteria in the plasma of septic patients.

In April, along with US Centers for Disease Control and Prevention researchers, the Mayo Clinic researchers published a study in the Journal of Clinical Microbiology demonstrating the potential for using the approach for the diagnosis of tick-borne bacterial infections from blood.

Using PCR, the investigators amplified a conserved portion of the 16S gene to detect whether there was any bacterial DNA in the sample. They extracted DNA from blood with Roche Diagnostics' MagNA Pure 96 and PCR amplification using dual-priming oligonucleotide primers specific to the V1-V3 region of the 16S rRNA gene. The amplified product underwent modified Illumina 16S metagenomics sequencing library preparation and sequencing on a MiSeq V2 Nano flow cell. Then the investigators conducted sequencing data analysis using Pathogenomix's Ripseq NGS software.

According to Pathogenomix, Ripseq sequence-based analysis reduces the time needed to identify infectious pathogens, in pure- or poly-microbial samples, by up to 90 percent.

Delivering at scale

Many other companies and academic labs are using NGS for infection diagnosis.

For example, researchers at the University of California, San Francisco have launched a clinical metagenomic next-generation sequencing-based test for meningitis and encephalitis.

Redwood City, California-based infectious disease startup Karius offers a laboratory-developed test through its CLIA-certified, CAP-accredited lab where fragments are extracted from a blood sample, which are then sequenced with Illumina next-generation sequencing platforms. The Karius liquid biopsy test uses microbial cell-free DNA to identify pathogens including fungi, parasites, bacteria, and DNA viruses.

In 2020, San Diego-based lllumina and San Francisco-based metagenomics technology firm IDbyDNA announced a strategic partnership and comarketing agreement to provide a streamlined workflow for infectious disease applications of next-generation sequencing, providing pathogen identification as well as information on antimicrobial resistance markers.

TriCore Reference Laboratories is developing a 16S metagenomic assay that it believes will help improve quantitative detection of bacterial pathogens in hospitals and cut down on indirect financial costs. The firm is working with Pathogenomix for sequence-based analysis.

"It’s clearly a technology that works and the question now is for which patients it makes sense, and how to deliver it at scale," said Tim Sweeney, CEO of Inflammatix, which is commercializing a rapid gene expression-based host-response assay for acute infection and sepsis.

Hypothesis-free pathogen identification enabled by NGS provides some benefits over traditional microbiology workflows, such as a faster turnaround time compared to culture and usually higher sensitivity, Sweeney added.

"On the other hand, NGS … is not nearly as fast or cheap as traditional targeted infection diagnostics," he said. "It may be faster than culture, but culture is way too slow for early workflows, and NGS is far more daunting to interpret than standard tests."

As a result, future infectious disease workflows for acutely ill patients may include NGS, but they are likely to first leverage a rapid host response test, such as Inflammatix's, to determine whether further testing is needed, said Sweeney.

Molecular testing is likely to be the next choice for clinicians when additional testing is needed, Sweeney said, adding, "NGS will serve as a backstop for therapy failures or be used for the diagnosis of highly complex patients such as those who are immunocompromised."

Pathogenomix has not yet decided on the pricing for its test, but Risley noted that declining prices for sequencing systems makes them more affordable for microbiology labs.

He added that Pathogenomix intends to engage in discussions with payors about potential reimbursement for Patho-Seq and to clarify the potential cost savings that could result from its implementation.

While it continues pursuing Patho-Seq authorization, the company also analyzes NGS files for reference laboratories as well as hospital labs looking to obtain results for laboratory-developed tests.

Risley said that since the firm was founded in 2016, it has analyzed more than 400,000 sequenced files for laboratories in the US and Europe.

Pathogenomix also eventually plans to seek regulatory approval for Patho-Seq in Europe, and is in discussions with unnamed IVD companies that may be interested in partnering with it to commercialize the platform in the US and abroad, Risley said.