Researchers have developed a new antibiotic that reduced or eliminated drug-resistant bacterial infections in mouse models of acute pneumonia and sepsis, while sparing healthy microbes in the mouse gut. The drug, called lolamicin, also warded off secondary infections with Clostridioides difficile, a common and dangerous hospital-associated bacterial infection, and was effective against more than 130 multidrug-resistant bacterial strains in cell culture.

“People are starting to realize that the antibiotics we’ve all been taking—that are fighting infection and, in some instances, saving our lives—also are having these deleterious effects on us,” said University of Illinois Urbana-Champaign chemistry professor Paul Hergenrother, PhD, who led the study with former doctoral student Kristen Muñoz PhD. “They’re killing our good bacteria as they treat the infection. We wanted to start thinking about the next generation of antibiotics that could be developed to kill the pathogenic bacteria and not the beneficial ones.” Hergenrother and colleagues report on their development in Nature. Their paper is titled “A Gram-negative-selective antibiotic that spares the gut microbiome.”

Infections caused by Gram-negative pathogens are increasingly prevalent and are typically treated with broad-spectrum antibiotics, the authors noted. Gram-positive and gram-negative bacteria differ in the composition of their cell walls. Gram-negative bacteria have a double layer of protection, making them more difficult to kill, Muñoz said.

As Muñoz pointed out, “Most clinically approved antibiotics only kill gram-positive bacteria or kill both gram-positive and gram-negative bacteria.” Numerous studies have found that antibiotic-related disturbances to the gut microbiome increase vulnerability to further infections and are associated with gastrointestinal, kidney, liver and other problems. The authors further noted, “The vast majority of clinically approved antibiotics kill only Gram-positive bacteria (Gram-positive-only antibiotics) or kill both Gram-positive and Gram-negative bacteria (broad-spectrum antibiotics).”

The authors cite figures indicating that the gut microbiome may be composed of up to 47 percent of gram negative bacteria, and so “… compounds that indiscriminately kill Gram-negative bacteria would be expected to induce significant gut dysbiosis.” For example, they point out, colistin, one of the few gram-negative-only antibiotics approved for clinical use, can cause C. difficile-associated diarrhea and pseudomembranous colitis, a potentially life-threatening complication. The drug also has toxic effects on the liver and kidney, and “thus colistin is typically utilized only as an antibiotic of last resort,” the researchers wrote. “There is a critical need for antibiotics that are selective both for Gram-negative bacteria over Gram-positive bacteria, as well as for pathogenic bacteria over commensal bacteria.”

To tackle the many problems associated with indiscriminately targeting gram-negative bacteria, the team focused on a suite of drugs developed by AstraZeneca. These drugs inhibit the Lol system, a lipoprotein-transport system that is exclusive to gram-negative bacteria and genetically different in pathogenic and beneficial microbes. The Lol system comprises five distinct proteins—LolA to LolE—three of which form the LolCDE transporter complex. The drugs were not effective against gram-negative infections unless the researchers first undermined key bacterial defenses in the laboratory.

But because the antibiotics appeared to discriminate between beneficial and pathogenic gram-negative bacteria in cell culture experiments, they represented promising candidates for further exploration, Hergenrother said. “Although the lack of significant antimicrobial activity against wild-type Gram-negative pathogens, lack of in vivo efficacy, poor solubility and high resistance frequencies prevented these inhibitors from being advanced as drugs, resistant-mutant studies provided convincing evidence that these compounds kill E. coli through inhibition of the LolCDE complex,” the authors wrote.

In a series of experiments, Muñoz designed structural variations of the Lol inhibitors and evaluated their potential to fight gram-negative and gram-positive bacteria in cell culture. One of the new compounds, lolamicin, selectively targeted some laboratory strains of gram-negative pathogens including Escherichia coliKlebsiella pneumoniae and Enterobacter cloacae, the researchers found. Lolamicin had no detectable effect on gram-positive bacteria in cell culture. At higher doses, lolamicin killed up to 90 percent of multidrug-resistant E. coliK. pneumoniae and E. cloacae clinical isolates.

When given orally to mice with drug-resistant septicemia or pneumonia, lolamicin rescued 100 percent of the mice with septicemia and 70 percent of the mice with pneumonia, the team reported. Extensive work was also carried out to determine the effect of lolamicin on the gut microbiome. “The mouse microbiome is a good tool for modeling human infections because human and mouse gut microbiomes are very similar,” Muñoz said. “Studies have shown that antibiotics that cause gut dysbiosis in mice have a similar effect in humans.”

Their studies showed that treatment with the antibiotics amoxicillin and clindamycin caused dramatic shifts in the overall structure of bacterial populations in the mouse gut, diminishing the abundance several beneficial microbial groups. “In contrast, lolamicin did not cause any drastic changes in taxonomic composition over the course of the three-day treatment or the following 28-day recovery,” the researchers wrote. In a subsequent experiment in mice, the investigators demonstrated that mice challenged with C. difficile after treatment with lolamicin were able to clear the pathogen—there was little or no C. difficile colonization—whereas mice treated with amoxicillin or clindamycin were unable to clear C. difficile, and demonstrated high-level colonization by the pathogen. “… the intact gut bacterial community in lolamicin-treated mice can successfully clear C. difficile colonization, distinguishing lolamicin from antibiotics that are currently used in the clinic,” the team stated. “Given the known health burden of C. difficile infections (500,000 infections and 30,000 deaths annually, with a 35% recurrence rate in the USA), routine use of microbiome-sparing antibiotics would have a significant positive effect on human health.”

Many more years of research are needed to extend the findings, Hergenrother acknowledged. Lolamicin, or other similar compounds, will need to be tested against more bacterial strains and detailed toxicology studies must be conducted. Any new antibiotics also must be assessed to determine how quickly they induce drug resistance, a problem that arises sooner or later in bacteria treated with antibiotics. “To advance as a translational candidate, the frequency of resistance to lolamicin would probably need to be improved through iterative chemical synthesis and lead optimization, as has been achieved for other antibiotics … and/or it could be used in combination with other antibiotics,” the investigators stated.

The study is a proof-of-concept that antibiotics that kill a pathogenic microbe while sparing beneficial bacteria in the gut can be developed for gram-negative infections—some of the most challenging infections to treat, Hergenrother said. The authors concluded, “Lolamicin has activity against a panel of more than 130 multidrug-resistant clinical isolates, shows efficacy in multiple mouse models of acute pneumonia and septicaemia infection, and spares the gut microbiome in mice, preventing secondary infection with Clostridioides difficile … The intestinal microbiome is central to maintaining host health, and its perturbation can result in many deleterious effects, including C. difficile infection and beyond. Consequently, pathogen-specific antibiotics such as lolamicin will be critical to minimizing collateral damage to the gut microbiome; this microbiome-sparing effect would make such antibiotics superior for patients compared with antibiotics in current clinical practice.”

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