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Q&A: Genetic testing can identify antibiotic resistance (Includes interview)

The CDC’s new report on antibiotic resistance in the U.S. indicates that more than 2.8 million antibiotic-resistant infections occur in the United States each year, and more than 35,000 people die as a result, and that the problem is growing.

One of the recommended courses of action in the report is to improve the use and development of diagnostics—laboratory tests that help identify the germ causing an infection, so that resistant infections can be earlier and guide appropriate antibiotic use.

One such test has been developed by LexaGene is a company based in Beverly, Massachusetts, U.S. The method works by by amplifying the genetic material in the sample from the patient to identify it, rather than waiting for a culture which takes 3-5 days.

To learn more about the technology, Digital Journal spoke with Dr. Jack Regan, CEO and Founder of LexaGene.

Digital Journal: What is the current state of antimicrobial resistance?

Jack Regan: To provide some background – the world’s first antibiotic (penicillin) was discovered in 1928 by Sir Alexander Fleming. It was critical in treating WWII patients, and already by the 1950s, resistance to penicillin had become a substantial clinical problem. In response to this, a new type of antibiotic called beta lactam antibiotics was developed, but again – within a decade, resistance to the new beta lactam antibiotics was discovered. Despite this, the number of new antibiotics developed and approved has steadily declined over the last 3 decades.

Today, resistance has been developed to all antibiotics that are commonly prescribed.

Traditional diagnostics involves sending a sample to a lab for a culture to identify not only what the pathogen is, but whether or not it is resistant to antibiotics. This process typically takes several days, leaving healthcare practitioners to prescribe broader-spectrum antibiotics, even though they may not be needed.

This is a problem because, the more broad-spectrum antibiotics in the environment, the greater the selective pressure for bacteria to evolve and develop resistance, which raises the bar for successful clinical treatment.

Antibiotic-resistant bacteria and fungi now cause more than 2.8 million infections and 35,000 deaths in the United States each year. Antibiotic-resistant bacteria are predicted to cause >10M deaths/year by 2050, eclipsing the number of deaths due to cancer

DJ: What are the CDC recommendation for addressing this issue?

Regan: In 2013, the CDC’s National Action Plan for Combating Antibiotic-Resistant Bacteria (CARB) was released. It is a five-year, goal-driven roadmap of actions to detect, prevent, and respond to resistant threats involving an international effort. The CDC has reiterated these proposed five core actions in its most recent report, Antibiotic Resistance Threats in the United States, 2019.

Within the United States effort is spent on:

1. Tracking and Data
2. Infection Prevention and Containment
3. Improving Antibiotic Use
4. Environment and Sanitation
5. Vaccines, Diagnostics, and Therapeutics

DJ: What is the LexaGene solution?

Regan:LexaGene contributes to all 5 aspects of the CDC’s recommended solution. LexaGene provides healthcare practitioners with an automated, easy-to-use instrument that has the ability to rapidly determine the cause of infection while concurrently identifying whether the infection is resistant to commonly prescribed antibiotics, within just one hour.

DJ: What advantages are there over classical culture-dependent methods?

Regan:LexaGene’s method is much faster. Traditional methods generally take at least 48 hours, whereas LexaGene’s automated genetic analyzer provides diagnostic data within just one hour. We are currently working on making this technology available for the human clinical diagnostics market, but of course, FDA clearance takes time, and rightly so.

DJ: How was the technology developed?

Regan:I invented the LexaGene instrument after working on developing a technology that was funded by the Department of Homeland Security (DHS) for Biothreat Detection. That technology was validated by DHS and adopted for use in the government’s BioWatch Program. Despite the successes of this instrument, I was convinced that I could design a better technology that would be more sensitive, more specific, return results more quickly, be capable of processing many samples at once, have lower operating costs, and would have uses aside from biothreat detection, such as human clinical diagnostics. So, I invented a technology to meet these requirements and through Lawrence Livermore National Laboratory, filed for patent protection. And in 2016, I founded LexaGene, and licensed the intellectual property. Since then, my business partner, Daryl Rebeck, and I have raised $18.6M USD, grown the company to a team of 21, built and field-tested beta prototypes, and we are now focused on the instrument’s final design and manufacturing. We are expecting to be commercial by June 2020.

DJ: How is the technology kept up-to-date?

Regan:Like many advanced, computer-driven technologies, LexaGene’s software will be periodically updated to improve functionality. In addition, LexaGene will continue to develop new tests to detect new microbial threats and antibiotic resistance factors. We will also continue to develop new sample preparation methodologies – so that the technology can successfully process multiple sample types across many industries.

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Written By

Dr. Tim Sandle is Digital Journal's Editor-at-Large for science news. Tim specializes in science, technology, environmental, business, and health journalism. He is additionally a practising microbiologist; and an author. He is also interested in history, politics and current affairs.

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