by Wendy Plump, Princeton University

Transcriptional and translational changes of one-carbon metabolite genes in response to low-dose TMP. FolE2 is transcriptionally the most induced gene and translationally the second-most induced protein in the presence of low-dose TMP. Credit: Mo Lab

Melioidosis—a bacterial infection that causes fever, pneumonia, and sepsis—presents two enormous challenges for infectious disease experts: It kills roughly half the people who contract it and it is extremely tough to treat even in countries with advanced health care systems.

The pathogen that causes melioidosis is so virulent it was used as a biologic warfare agent in World Wars I and II. Treatment demands an expensive, long-term IV and antibiotic regimen that is difficult to enact in southeast Asia and northern Australia where melioidosis is prevalent. And while the disease itself is rare in the United States, the first known case of environmental transmission occurred here in 2022.

Princeton Chemistry's Seyedsayamdost Lab offers a promising treatment for this neglected tropical disease with a combination of low-dose antibiotics that targets the pathogen but leaves gut microbiome bacteria unscathed.

The researchers' approach could herald a shift in the way we use antibiotics. By attacking the pathogen's unique and hidden metabolic "vulnerabilities," the lab offers a new tool in the global challenge to counteract antibiotic resistance and uncover similar combination therapies for other diseases.

"Virtually all antibiotics are A-bombs. They are broad-spectrum and we use them in such high doses that they eradicate nearly everything in and around them, notably bacteria that protect us. That's a problem," said Mohammad Seyedsayamdost, professor of chemistry. "We found that even low doses of antibiotics reveal susceptibilities that are difficult to detect but can be leveraged, once known. That was the 'aha' moment.

"Low-dose or subinhibitory doses of antibiotics don't affect growth of the pathogen but have a significant impact on its physiology and metabolism. And once we noticed that, we took advantage of this very unique response to combat an organism that is really difficult to kill."

The lab's research, titled "Combatting melioidosis with chemical synthetic lethality," was published in the Proceedings of the National Academy of Sciences in collaboration with the Davis Lab at Emory University and the Chandler lab at the University of Kansas.

"To me, the most exciting part of this paper is its potential to change how we think about antibiotic development," said the paper's lead author and former Mo Lab graduate student Yifan Zhang.

"We've known for a long time that antimicrobial resistance is a growing global crisis, and yet the pipeline for new antibiotics has been alarmingly slow. With this study, our goal was to take a different approach—one that doesn't just focus on finding a new 'silver bullet," but instead looks at how we can outsmart pathogens by exploiting their metabolic vulnerabilities."

"This work also reinforces how important it is to think beyond traditional boundaries in science," added Zhang, now a medical student at Robert Wood Johnson. "Combining ideas from the oncology space with our knowledge of microbiology and microbial metabolism required us to challenge a lot of assumptions about how antibiotics 'should' work. It's exciting to see those risks pay off with a discovery that could genuinely help patients."

Looking at the pathogen through HiTES

Melioidosis is caused by the bacterium Burkholderia pseudomallei. One traditional method of determining antibiotic efficacy against it is by looking for signs of Burkholderia growth with the unaided eye or through a simple assay, and then treating it with a broad-spectrum antibiotic that kills everything in its path: an antibiotic as a blunt instrument.

But the Mo Lab used another method, High Throughput Elicitor Screening (HiTES), a technology for which Seyedsayamdost was awarded a 2020 MacArthur Prize, to peer deeply into the metabolome for clues to bacterial vulnerability.

HiTES revealed that this pathogen's metabolism is altered dramatically with low-dose antibiotics. In essence, low-dose trimethoprim opens up a secondary, previously unknown metabolite stress response in the pathogen. Under these conditions, the researchers found the folate biosynthetic enzyme FolE2 to be conditionally essential, an enzyme that's not widely found in bacteria and that—ironically—makes it easy to exploit.

By using an approach called chemical synthetic lethality, they were able to successfully combine trimethoprim with a natural product, dehydrocostus lactone (DHL), to inhibit the function of FolE2, cutting off this secondary response on which the bacteria relies for survival … and doing it in a way that selectively kills the pathogen without annihilating the gut's essential bacteria.

"That selectivity is something I'm particularly proud of because it aligns with the growing understanding that our microbiome isn't just a bystander—it's crucial for our overall health," said Zhang.

"Basically we accomplished the molecular version of synthetic lethality, a well-known genetics phenomenon, wherein two mutations are only deadly when combined," said Seyedsayamdost. "You add one molecule, it has no effect. You add a second molecule, it has no effect. But you combine the two molecules—in this case, trimethoprim and DHL—and the combination is deadly. We mixed genetics and chemistry, and it worked."

The research also suggests that this combination therapy can be used against any organism to find treatments that are less destructive systemically.

"Ultimately, I hope this research doesn't just stop at Burkholderia pseudomallei," said Zhang. "If we can expand this strategy to other pathogens, I believe we can open up entirely new avenues for developing treatments that are not only effective but also respect the delicate balance of our microbiomes.

"Knowing that our work has the potential to contribute to targeted, life-saving treatments for such a devastating disease is both humbling and deeply fulfilling. That's the bigger picture that keeps me motivated and excited about where this work can lead."

More information: Yifan Zhang et al, Combatting melioidosis with chemical synthetic lethality, Proceedings of the National Academy of Sciences (2024). DOI: 10.1073/pnas.2406771121

Journal information: Proceedings of the National Academy of Sciences 

Provided by Princeton University