Revolutionizing Infectious Disease Diagnostics Through Genomic Insights

Key Benefits

Business Challenge:
Managing an Evolving, Meticulously Curated Database of Microbial Genomes

Navigating the rapidly changing vast microbial data landscape at Karius demanded a shift from manual, overloaded workflows to a sturdy, automated pipeline capable of handling high-scale data with ease. Initially, for the purpose of its microbial database creation, Karius used a linear and monolithic ETL process, with a solution that soon morphed into a data pipeline behemoth; the core pipeline became larger and larger as new aspects of the data were brought in, resulting in a highly convoluted and unmanageable code. This first solution was less flexible than the evolving operation required.

Technical Challenge:
Transition From a Manual Convoluted Past to an Automated, Streamlined Present

Leveraging Pachyderm has pulled Karius into a future where its data architecture effortlessly ingests diverse data from diverse sources, unveiling an up-to-date panorama of the microbial realm. Pachyderm has been a catalyst for Karius to transition from a manual convoluted past toan automated, streamlined present, where the hypothesis-free technology isn’t justdiagnosing new diseases, but it's doing so with a continuous fresh cut of new data. The Pachyderm datum concept resonates perfectly with the growing volumes of available sequencing data, providing a native solution to unlock incremental data analysis. Pachyderm didn’t just upgrade a technical data asset but ended up aligning nicely with Karius’ visionary stride, ensuring that when it comes to battling infectious diseases, Karius is not just ahead but gets to define the frontier.

Results:
Revolutionizing Infectious Disease Diagnostics Through Genomic Insights

At the heart of Redwood City, California, lies Karius, a trailblazing entity unraveling the mysteries of the microbial world and pioneering liquid biopsy for infectious disease diagnostics. This state-of-the-art technology company is the birthplace of a transformative blood test that empowers physicians with critical microbial insights, helping drive precise diagnostics and treatment.

A timely diagnosis of infections can have a major impact on patient outcomes. Tools that help narrow down the potential cause of infection can decrease antibiotic use (which may potentially help decrease antibiotic resistance), toxicities, and hospitalization costs. But often in clinical practice, physicians struggle to identify the pathogen causing an infection, especially in cases of deep-seated infections such as brain, heart, or lung infections. It is precisely where the Karius Test shines, offering an alternative to biopsy-based diagnosis by providing a diagnosis straight from a blood sample.

The Karius Test is a liquid biopsy that can non-invasively and rapidly detect over 1000 pathogens causing both deep-seated and bloodstream infections from a single blood sample. The Karius Test may help clinicians avoid invasive, low-yield, and sequential diagnostic tests that can delay treatment for vulnerable hospitalized patients. In addition to pathogen identification, the test also detects genotypic antimicrobial resistance (AMR), which may help clinicians to optimize antimicrobial treatment.

Not only does the technology provide a minimally-invasive alternative to biopsy, but the nature of the technology allows physicians to escape the conventional practice of sequential testing, where a doctor orders one test after another to figure out the cause.

The innovation that led to this transformative test stemmed from a Stanford-born revelation: the blood carries residuals of microbial cell-free DNA fragments, a treasure trove of data awaiting deciphering. Equipped with this discovery, Karius developed the equivalent of a microbial DNA “microscope," a confluence of cutting-edge lab chemistries, machine learning algorithms, and robust data platforms capable of rapidly sifting through these DNA fragments, distinguishing microbial signals from noise with unprecedented accuracy. A complex narrative of microbial signals lies in each plasma sample (plasma is the liquid in the blood that carries the cells). The proprietary protocols developed at Karius efficiently harvest the minute amounts of microbial cell-free DNA fragments, which are embedded in a sea of human-derived cell-free DNA, while the computational prowess maps it against an expanding vault of clinical-grade genomic references (the blueprints of the microbial genomes), ensuring precise identification of the underlying microbes, supporting physicians in their identification of disease-causing pathogens.

At the core of Karius’ diagnostic precision is an ever-evolving, meticulously curated database of microbial genomes; it's the bedrock upon which the technology stands. The accuracy and comprehensiveness of the Karius microbial database are paramount, acting as the linchpin that ensures each test's reliability and insightfulness. Moreover, in a realm where the microbial landscape is in constant flux and new discoveries are made daily, the database's agility in adapting to new discoveries while unwaveringly maintaining its accuracy and expansiveness propels Karius' test into a realm of unmatched diagnostic excellence. The continuous, rapid updates are not mere improvements but a commitment to uphold the trust and expectation vested by the medical community and the myriad lives awaiting clearer answers.