Engineered bacteria could help protect ‘good’ gut microbes from antibiotics


Antibiotics are life-saving drugs, but they can also harm the beneficial microbes that live in the human gut. After antibiotic treatment, some patients are at risk of developing inflammatory or opportunistic infections such as: clostridiodes difficile, The indiscriminate use of antibiotics on gut microbes may also contribute to the spread of resistance to drugs.

In an effort to reduce those risks, MIT engineers have developed a new way to help protect the natural flora of the human digestive tract. They took a strain of bacteria that is safe for human consumption and engineered it to safely produce an enzyme that breaks down a class of antibiotics called beta-lactams. These include ampicillin, amoxicillin, and other commonly used drugs.

When it is given with “living biotherapeutic” antibiotics, it protects the microbiota in the gut, but allows the level of antibiotics circulating in the bloodstream to remain high, researchers found in a study of mice.

James Collins, Termeer Professor of Medical Engineering and Science at MIT’s Institute for Medical Engineering and Science (IMES), says, “This work shows how to create a new class of engineered therapeutics to reduce the adverse effects of antibiotics.” synthetic biology can be used for this.” and Department of Biological Engineering, and senior author of the new study.

Andres Cubilos-Ruiz PhD ’15, a research scientist at IMES and the Wyss Institute for Biologically Inspired Engineering at Harvard University, is lead author of the paper, which appears today in Nature Biomedical Engineering, Other authors include MIT graduate students Miguel Alcantar and Pablo Cárdenas, Vice Institute staff scientist Nina Dongia and Broad Institute research scientist Julian Avila-Pacheco.

protect the intestine

Over the past two decades, research has shown that microorganisms in the human gut play important roles not only in metabolism but also in immune function and nervous system function.

“Throughout your life, these gut microbes gather in a highly diverse community that carry out important functions in your body,” says Cubilos-Ruiz. “The problem arises when interventions such as medications or certain types of diet affect the composition of the microbiota and create an altered state, called dysbiosis. Some microbial groups disappear, and the metabolic activity of others increases. This imbalance can lead to various health problems.”

A major complication that can occur is infection of c. difficult, a microbe that normally lives in the gut but does not usually cause harm. When Antibiotics Kill Competing Strains c. difficultHowever, these can carry bacteria and cause diarrhea and colitis. c. difficult Infects about 500,000 people in the United States each year, and causes about 15,000 deaths.

Doctors sometimes prescribe probiotics (a mixture of beneficial bacteria) to people taking antibiotics, but those probiotics are usually also susceptible to antibiotics, and they do not completely replicate the basic microbiota found in the gut. .

“Standard probiotics cannot compare to the diversity that native microbes have,” Cubilos-Ruiz says. “They may not fulfill the same functions as the original microbes that you have nurtured throughout your life.”

To protect the microbiota from antibiotics, the researchers decided to use modified bacteria. He engineered a strain of bacteria called lactococcus lactis, which is commonly used in cheese production, to deliver an enzyme that breaks down beta-lactam antibiotics. These drugs make up about 60 percent of the antibiotics prescribed in the United States.

When these bacteria are delivered orally, they transiently populate the intestines, where they secrete an enzyme, called beta-lactamase. This enzyme then breaks down the antibiotics that reach the intestinal tract. When antibiotics are given orally, the drugs enter the bloodstream primarily from the stomach, so the drugs can still circulate in the body at high levels. This approach can also be used with antibiotics that are injected, which eventually reach the intestine. After their work is finished, the engineered bacteria are excreted through the digestive tract.

Using bacteria engineered to degrade antibiotics presents unique safety requirements: beta-lactamase enzymes harboring cells confer antibiotic resistance and their genes can spread easily between different bacteria. To address this, the researchers used a synthetic biology approach to reconstruct the way the enzyme was synthesized by the bacterium. They broke the gene for beta-lactamase into two fragments, each encoding a fragment of the enzyme. These gene segments are located on different pieces of DNA, making it very unlikely that both gene segments will be transferred to another bacterial cell.

These beta-lactamase fragments are exported outside the cell where they are reassembled, restoring enzymatic function. Since beta-lactamase is now free to circulate in the surrounding environment, its activity becomes a “public good” for the bacterial communities of the gut. This prevents engineered cells from gaining an advantage over native gut microbes.

“Our biocontainment strategy enables other bacteria to deliver antibiotic-degrading enzymes to the gut without the risk of horizontal gene transfer or acquisition of an additional competitive advantage by live biotherapeutics,” says Cubilos-Ruiz.

maintaining microbial diversity

To test their approach, the researchers gave mice two oral doses of the engineered bacteria for each injection of ampicillin. The engineered bacteria made their way into the gut and began to release beta-lactamase. In those mice, the researchers found that the amount of ampicillin circulating in the bloodstream was as high as in mice that did not receive the engineered bacteria.

In the gut, the mice that received the engineered bacteria maintained a higher level of microbial diversity than the mice that received only antibiotics. In those mice, microbial diversity levels dropped dramatically after receiving ampicillin. Furthermore, none of the mice that received the engineered bacteria developed opportunistic c. difficult infection, whereas all mice receiving only antibiotics showed higher levels of c. difficult in the intestine.

“It’s a strong demonstration that this approach can protect the gut microbiota while preserving the efficacy of the antibiotic, because you are not modifying the levels in the bloodstream,” Cubilos-Ruiz says.

The researchers also found that eliminating the evolutionary pressure of antibiotic treatment greatly reduced the chances of gut microbes developing antibiotic resistance after treatment. In contrast, they found several genes for antibiotic resistance in microbes that survived in mice that received antibiotics but not the engineered bacteria. Those genes can be transferred to harmful bacteria, further compounding the problem of antibiotic resistance.

Researchers now plan to begin developing a version of the treatment that can be tested in people at high risk of developing acute diseases resulting from antibiotic-induced gut dysbiosis, and He hopes that eventually, it can be used to protect anyone who needs to take antibiotics for infections outside the gut.

“If the gut doesn’t need antibiotic action, you need to protect the microbiota. It’s like when you get an X-ray, you put on a lead apron to protect the rest of your body from ionizing radiation. wear,” says Cubilos-Ruiz. “No previous intervention could provide this level of protection. With our new technology we can make antibiotics safer by preserving beneficial gut microbes and reducing the likelihood of the emergence of new antibiotic-resistant forms.”

The research was supported by the Defense Threat Reduction Agency, Paul G. Allen Frontiers Group, the Wyse Institute and a National Science Foundation Graduate Research Fellowship.

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