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Startup Klaris Diagnostics to Tackle Antibiotic Susceptibility With Phenotypic Single-Cell Technology


The story has been updated to correct the spelling of Nicolas Arab's name, the sample types that can be used with Klaris' test, and the total amount the company has raised. We apologize for the errors. 

NEW YORK (360Dx) – With $3.75 million from its recently completed Series A financing round, Klaris Diagnostics aims to simplify antibiotic selection for drug-resistant infections with its phenotypic single-cell platform.

Founded in 2016, the Austin, Texas-based startup is focused on helping hospitals deal with antimicrobial resistance by reducing the time it can get patients started on targeted antimicrobial therapy. Formerly known as Viasphere, Klaris is developing a method that circumvents some of the drawbacks of existing technology.

Klaris CEO and cofounder Nicolas Arab explained that one of the key issues with developing an effective antimicrobial detection tool is sample isolation. Using traditional culture, researchers must wait at least two days to grow a pure bacterial isolate from a non-sterile sample. Researchers can also determine antimicrobial resistance with molecular testing, which is sensitive, but can miss new mutations that cause different types of resistance.

In contrast, Klaris' technology uses a droplet microfluidics approach for cell isolation and phenotypic detection. During the process, the cells are suspended with the cartridge in an immiscible fluid. The cells then flow through microstructures that partition the suspension and isolate the cells into thousands of microscopic droplets.

Because the reaction occurs in "such small volumes," fluorescence rapidly accumulates and produces optical signals that vary over time according to "unique metabolic and cellular characteristics of the encapsulated cells," Arab said.

Using optical microscopy via a sensor or camera, the system can analyze the fluorescent waveforms linked to specific pathogens, as well as their antibiotic susceptibilities. The system can then quantify the sample by counting droplets that produce a signal indicating the presence of a target cell or microbe, thereby simultaneously performing accurate and precise multiplexed identification and quantification.

According to Arab, the test requires less than four hours to produce a susceptibility profile and can be performed using a variety of samples, including sputum, blood, and urine.

In a hospital setting, a lab personnel can collect the sample from the patient and then ship it to the microbiology lab to run the test.

While Arab declined to provide data on on the test's sensitivity and specificity, in its patent, US Patent No. 9,851,345, issued in December 2017, he and his colleagues noted that the technology is as sensitive as nucleic amplification tests due to its ability to detect single cells.

Based on real-time monitoring of the cell's metabolism and growth, Klaris' approach produces information that is fed into a "neural network, which allows [researchers] to identify the organism and determine phenotypic antibiotic sensitivities," said Arab.

He explained that the firm's neural network acts as computing systems designed to function similarly to the human brain. During the test's development, Klaris generated a comprehensive library of labeled waveforms from the bacteria at various levels of drug resistance. The neural network — a software algorithm built into the phenotypic test — "learn[ed] how to map the stored waveforms to the labeled data (such as bacterial species, family, and susceptibility classification) with remarkable accuracy," Arab said.

Arab said that by using Klaris' test, clinicians would be able to detect all types of gram-positive and gram-negative bacteria besides anaerobic species, which he noted are not part of the firm's focus due to the system's design. Specifically, he highlighted that the test will diagnose Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, as well as species of Enterobacteriaceae.

Compared to current molecular panels developed by competing firms, which focuses on genotypic markers, Klaris' technology, instead, is directed at phenotypic antibiotic susceptibility.

In contrast to genotype-based antibiotic-resistance molecular panels, which are limited to using blood and sterile fluids for testing, the firm's test aims to diagnose "specimens from non-sterile sites, such as the lower respiratory and urinary tracts," Arab said. "These specimens are normally challenging because they are colonized by bacteria that can interfere with and must be distinguished from the bacteria causing the infection."

Arab claims that because Klaris' technology encapsulates individual bacterial cells in tiny droplets, colonizing bacteria are physically isolated from the infectious bacteria, allowing researchers to distinguish the two types and accurately assess the infectious bacteria's antibiotic response.

In addition, Arab said that Klaris is designing the system to be economical across the "spectrum of infection severity, so that clinicians can use a single platform for all infections." He emphasized that while there is a massive demand for antibiotic susceptibility testing, diagnostic tests need to be much less expensive and "hit all the [causes] of those infections [and] be economically justified in the microbiology lab."

Arab also believes that because the neural network does not have to learn "on the fly," the instrument does not depend on high-performance computing or storage requirements. "We can tell you what bacteria are there, how much of them are there, and how they respond to candidate antibiotics being considered for treatment," Arab said.

"When you're trying to identify the bacterial cause of infection, genotypic or molecular technologies are useful for classifying the samples, but are bad at predicting drug response," he said. For that purpose, phenotypic technology works better.

"Rather than marry molecular and phenotypic technology, which is complicated and expensive to do, we discovered a way to take the power of phenotypic technology in terms of drug response, and use artificial intelligence, deep learning, [and] machine learning algorithms to extract information about the metabolic response and phenotypic susceptibility of these cells."

He declined to comment on the price of Klaris' test, saying only that they will be comparable to that of competitive technologies in the antibiotic susceptibility diagnostic space.

He also declined to comment on the technology's commercial timeline, but noted that Klaris is currently working toward filing a 510(k) submission with the US Food and Drug Administration.

If successful in commercializing its technology, Klaris would join a crowded and growing group of firms and organizations working toward antibiotic susceptibility profiling technology. Researchers at Johns Hopkins University, for example, are developing a similar microfluidic assay that identifies pathogens and performs single-cell phenotypic antimicrobial resistance testing. Currently in the proof-of-concept stage, the group's test can produce results within three hours directly from patient blood samples.

In addition, researchers in Sweden have developed an antibiotic susceptibility test that integrates short cultured times and padlock probes to detect species-specific bacterial 16S ribosomal RNA. The team used the assay to detect antibiotic-resistant bacteria in urine samples from urinary tract infection patients in less than four hours.

In February 2017, Accelerate Diagnostics received FDA clearance for its PhenoTest BC Kit and Pheno System. The Accelerate Pheno system uses genotypic technology to identify infectious pathogens and phenotypic technology to conduct antibiotic susceptibility testing, which determines whether live bacterial or fungal cells are resistant or susceptible to an antibiotic.

Klaris has raised more than $4 million between initial seed funding from angel investors and the Series A funding round, which was led by Omnimed Capital earlier this month. The firm plans to raise additional capital in the future as it improves its antibiotic susceptibility technology.

In addition, Klaris plans to establish a foothold in the clinical space by providing clinicians an avenue for detecting all the major antibiotic-resistant pathogens.

Arab envisions the firm's test being used in the clinical space, serving hospitals and intensive care units. By allowing for rapid antibiotic "de-escalation," the firm hopes to help improve antibiotic stewardship and reduce multidrug resistant development in ICUs.