NEW YORK – On the back of a new $28.7 million Series C funding round, infectious disease firm Pattern Bioscience is preparing to commercialize its rapid phenotypic antibiotic susceptibility platform.
The platform, which was developed in-house but also uses some licensed intellectual property, combines single-cell isolation and machine learning to both identify a pathogen causing an infection and determine the antibiotic susceptibility of that pathogen, said Pattern Cofounder and CEO Nick Arab. The test can be run directly from a specimen for most specimens and returns a result in four to six hours without the need for an upfront culture, which is the current gold standard for antibiotic susceptibility testing.
Conducting the test requires an upfront sample preparation step, with about five minutes of hands-on time, that involves a centrifuge to create a cell suspension that is then placed into the platform's consumable. Because the preparation method is proprietary, Arab declined to describe it in detail but he noted the firm — formerly known as Klaris Diagnostics — is still optimizing its sample prep procedure to improve the speed.
The disposable consumable inserted into the instrument contains two microfluidic chips, each with 20 droplet arrays that use microfluidics to isolate the cells: Some of those arrays are used for pathogen identification, others contain a specific antibiotic used for susceptibility testing, and one contains a control. The instrument uses fluorescence and optical microscopy to detect metabolic patterns from the cells in the pathogen identification arrays, which are then analyzed by Pattern's artificial intelligence-based software to determine what pathogen is present. The system is also able to quantify the sample by counting the number of droplets that produce a fluorescent signal, which indicates the presence of the target cell.
By isolating the cells, the platform is also able to detect polymicrobial infections caused by more than one type of pathogen, Arab noted.
Antibiotic response causes changes in the metabolic patterns within the susceptibility testing arrays, and those changes are measured by the instrument to determine whether a pathogen is susceptible, intermediate, or resistant to the antibiotic. According to Arab, the firm's technology is "measuring the live response of the cells to … the candidate antibiotics that are being considered for treatment."
The pathogen identification and antibiotic susceptibility testing are performed simultaneously within the instrument, he noted, and a full system includes 11 test modules, each of which can run two cartridges at a time. The platform can also be used on all sample types.
The company's next step is a clinical trial to validate the platform and its first assay — a pneumonia test for hospitalized patients — that received breakthrough device designation from the US Food and Drug Administration in 2021. The clinical validation will be funded through the Series C financing round, and Pattern plans to publish externally reviewed data this year, Arab said.
In an internal study conducted for its breakthrough device designation application, the pneumonia test showed 98 percent sensitivity and nearly 100 percent specificity for pathogen identification. It also showed nearly 97 percent categorical agreement for antibiotic susceptibility testing.
After the platform has been clinically validated, the company intends to seek 510(k) clearance from the FDA, although Arab declined to disclose the exact timeline for regulatory submission and approval. Once the platform is approved, Pattern's target customers at launch are large US hospitals, with the goal to eventually add further tests. The next assays in the company's pipeline are a positive blood culture test and a urinary tract infection test.
The price of the test will be comparable to other rapid syndromic tests, he added, which are about $75 to $150. For the US market, the company plans to distribute the platform and test directly, but as it expands globally it will likely seek distribution partners. Pattern also expects to tackle the European market after the US, Arab said.
In throwing its hat into the rapid susceptibility testing arena, Pattern will be joining a crowded field as the market continues its recovery from the COVID-19 pandemic when any diagnostic testing being done was almost exclusively for SARS-CoV-2, especially in the pandemic's early days. Major players such as Accelerate Diagnostics and BioMérieux have long been in the AST space but are putting more emphasis on rapid testing: Accelerate's Pheno system was the first rapid identification and antibiotic susceptibility platform granted FDA de novo approval, although the system's rollout has encountered its share of hurdles. Meantime, BioMérieux's recent acquisition of Specific Diagnostics brought the rapid Specific Reveal platform into its fold.
Smaller companies that are also gaining prominence in the space include Selux Diagnostics, which received 510(k) clearance from the FDA in January for its Next Generation Phenotyping System and Gram-positive bacteria panel, and SpeeDx, an Australian firm developing a phenotypic test to determine the antibiotic susceptibility of gonorrhea infections.
Arab noted that many existing or in-development rapid AST platforms, such as Accelerate's Pheno system and the Specific Reveal platform, can only be used with positive blood cultures, while Pattern's instrument can be used with a variety of sample types, including positive blood culture, urine, skin, and soft tissue.
"Our platform is able to parse the heterogeneity that is present in those other specimen types that are more complex," he said.
In an email, however, Accelerate Chief Strategy Officer John Meduri clapped back and noted that during the single-cell digital imaging step of the Pheno workflow, "we often visualize the heterogeneity, [such as] subpopulations of resistance cells, of an individual bacterial species in the presence of an antibiotic." The system has been developed to "directly correlate the final susceptibility test results with the gold standard, broth microdilution, to best interpret this heterogeneity to deliver the accurate and needed minimum inhibitory concentration result for each and every antimicrobial/organism combination," he added.
The system can also differentially identify up to three different species. Accelerate is currently working on a next-generation system, called Wave, that will address additional sample types, Meduri added.
BioMérieux did not respond to a request for comment.