DeKox: Decolonization of the gut using Klebsiella oxytoca
The progressing global spread of antibiotic-resistant bacteria, particularly Klebsiella pneumoniae and Escherichia coli, poses a massive threat to public health as traditional antibiotics lose their effectiveness. Often, the actual infection is preceded by the asymptomatic colonization of the gut with these resistant bacteria. In cases of immune deficiency, these bacteria may enter the bloodstream through a compromised intestinal barrier and trigger highly virulent infections. Currently, it is not possible to remove these bacteria selectively from the intestine early enough to prevent such colonization to transform into an infection. New treatment options and preventive measures are therefore urgently needed. This is where the DeKox project, launched in September 2025, comes in. The project aims to develop a novel drug based on live bacteria that can specifically replace the dangerous Klebsiella pneumoniae bacteria in the gut with harmless Klebsiella oxytoca bacteria by competing for the same nutrients in the intestine. In the future, this is expected to benefit immunocompromised patients, particularly cancer patients, who are very frequently affected by intestinal colonization with K. pneumoniae and subsequent infection by these bacteria.
Immunosuppressed patients, particularly those with hematologic and oncologic conditions and those who have undergone stem cell transplantation, have a disrupted gut microbiome as a result of treatment with broad-spectrum antibiotics and chemotherapy; and their microbiota community is often colonized by antibiotic-resistant pathogens. In these patients, this otherwise ineffectual colonization may lead frequently to serious infectious diseases, which are often fatal. However, the preexisting and colonized microbiota reservoir in the gut cannot be cleared with medication, so far.
The project "DeKox: Decolonization of the gut using Klebsiella oxytoca" aims to develop a novel solution to this problem. We envision a capsule filled with benign Klebsiella oxytoca bacteria that can be taken orally by the patient and selectively displace Klebsiella pneumoniae in the gut through competitive exclusion. This mechanism has the advantage of sparing the surrounding microbiota community and acting highly selective on K. pneumoniae, since the closely related bacterium K. oxytoca occupies the same ecological niche in the gut. The feasibility of this approach has already been demonstrated in animal models and was published in the high-impact journals Cell Host and Microbe and Nature Microbiology. Following intensive preclinical safety studies at the Helmholtz Centre for Infection Research in Braunschweig using cell culture and mouse models, the safest and most efficient strain from an extensive strain collection is used to produce this pharmaceutical product. This product will then undergo testing in a clinical trial in collaboration with the ↗ University Hospital in Cologne.
