NCCR Microbiome

1. Community coalescence, function, and immune response in successful CDI treatment

Clostridioides difficile infections (CDI) stand as the primary cause of nosocomial antibiotic-associated diarrhea, and reports of community-acquired CDI are also on the rise. Antibiotic treatment serves as both the first-line intervention and the primary risk factor for infection. The disruption of the intestinal microbiota creates an ideal environment for C. difficile to thrive. Consequently, recurrent CDI, the most prevalent complication occurring in up to 30% of patients, can be effectively treated through fecal microbiota transplantation (FMT).

Our findings in phase 1 confirm that patients with CDI exhibit lower bacterial diversity compared to healthy individuals. However, this diversity is better maintained in patients treated with fidaxomicin compared to vancomycin. We also confirmed in a mice model that microbiota engrafted from fidaxomicin treated patients were more resistant to C. difficile challenge than vancomycin treated patients. Finally, patients who underwent fecal microbiota transplantation (FMT) demonstrated effective restoration of microbial community structure. The response to CDI encompasses various parameters, as discussed earlier, such as the microbiota structure, microbiota function, and the host immune response. Currently, numerous molecules are proposed for CDI treatment, targeting the pathogen, its virulence factors, the immune response, or the microbiota. Gaining a clear understanding of the interrelation among these different factors will enable us to recommend the most effective treatment for the patient based on the characteristics of the episode, including the number, severity, risk factors, and immune profile.

Specific objectives:

• Identify factors (structure and functions) associated to the increased resilience in fidaxomicin treated compared vancomycin treated patients
• Evaluate the immune response and biliary acid profile in these 2 groups
• Build hypothetic synthetic communities to treat CDI based on the profiles obtained previously
• Propose personalized therapeutic options in CDI

2. Stability of structure and function of lyophilized gastro-resistant formulation for fecal microbiota transplantation compared to capsules and fresh stools.

Fecal Microbiota Transplantation (FMT) stands as the benchmark treatment for recurrent Clostridioides difficile infection, boasting an efficacy rate of 90%. Nevertheless, the current standard-of-care formulation, FMT in oral capsules, is susceptible to optimization. Limited research has assessed the bacterial load, viability, or composition of the microbiota in FMT, as well as its stability during storage. In collaboration with the Geneva Pharmacy laboratory (led by Professor E. Alleman), we have developed a new formulation using alginate beads. Our preliminary results indicate that the novel alginate formulation is comparable to oral capsules in terms of the Chao1 index, Shannon index, or Bray-Curtis distance. Additionally, the composition and viability of the frozen alginate particles remained stable over a 12 months evaluation. This novel formulation holds promise as it not only compares favorably to FMT oral capsules but is also more easily consumable and requires less volume. It has the potential to revolutionize FMT treatment accessibility for various indications.

Specific objectives:

• Develop a gastro-resistant formulation of alginate beads
• Ensure the stability of the obtained material over a 24 months period in both frozen and room temperature preservation
• Characterize the group of healthy volunteers for control in the current studies performed in other cohorts of the NCCR
• Initiate a pilot trial in human to test tolerance and efficacy of this new gastro-resistant lyophilized formulation

3. Protective microbiota in Salmonella infection

Non-typhoidal Salmonella infections (NTSi) occur worldwide. S. enteritidis subsp. Enteritidis and S. enteritidis subsp. Typhimurium are the two most common causes of NTSi. We need novel strategies for therapy of prevention. The major reservoirs of Salmonella are poultry and livestock; most human infections occur through the consumption of contaminated food products. Importantly, only a small percentage of infected humans develop enteric disease. We hypothesize that so far uncharacterized features of the microbiota determine if a colonized person develops disease. Here, we want to identify such disease-preventing features (e.g. competing species, phages etc.).

We have recruited a total of 27 individuals so far, with 8, 11, and 8 samples belonging to the symptomatic Salmonella, asymptomatic Salmonella, and healthy groups, respectively. Samples were performed at day 0 and day 30. Additionally, we obtained samples from patients infected with Campylobacter and Shigella infections.

Preliminary 16S analysis from phase 1 revealed similar alpha and beta diversity profiles within and between symptomatic patients and asymptomatic carriers, supporting the hypothesis that the presence of protective bacteria may be the differentiating factor. We identified three species as differentially abundant, an uncultured Ruminococcaceae species, and two additional interesting species: Bifidobacterium longum and Romboutsia timonensis. They were statistically more prevalent and abundant in asymptomatic carriers compared to symptomatic patients. These results provide a unique opportunity to identify potential innovative therapeutic solutions respecting the gut microbiota in Salmonella infection combining direct microbiota manipulation or phage targeted modifications. This approach will also be expanded to other classical pathogens, such as Campylobacter and Shigella, already included in our cohort.

Specific objectives:

• Explore potential virulence differences in colonizing and infecting Salmonella strains
• Identify and develop a protective strain combination targeting Salmonella-infected patients
• Identify protective microbiota-related functions in Salmonella asymptomatic carriers
• Explore an alternative approach to bacterial microbiota targeted therapeutics using Salmonella lytic phages to restore eubiosis

• Prof. Claire Bertelli, IMUL, Lausanne
• Dre Tatiana Galpérine (FMT Center), CHUV, Lausanne
• Elena Montenegro Borbolla, PhD Student
• Carmen Chen, PhD student