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Evolutionary Traps and Niche Competitors to Eliminate Salmonella from Livestock – Microbials 2017


Für den Inhalt der Angaben zeichnet die Projektleitung verantwortlich.


This project is one of the five winners of the call 2017 «Microbials – Direct Use of Micro-Organisms». Project partners: University Pierre and Marie Curie UPMC, Paris, France; ETH Zürich, Institute for Microbiology, Switzerland

Project data

  • Project no: GRS-073/17 
  • Amount of funding: CHF 410'000 
  • Approved: 30.10.2017 
  • Duration: 04.2018 - 09.2022 
  • Area of activity:  Microbials, seit 2016

Project management

Project description

Antibiotic multi-resistant (AMR) bacteria, that frequently inhabit the intestinal tract of humans and livestock, are a serious threat, either directly as opportunistic pathogens, or as a reservoir of antibiotic resistance genes. Novel antibiotics are challenging to develop to clinical application and an alternative solution is therefore urgently required.
Our recent work has demonstrated that vaccine-induced intestinal antibodies cannot kill bacteria per se, but they can dramatically decrease their ability of targeted bacteria to compete. Oral vaccination combined with precisely engineered "probiotic" competitors therefore has the potential to eliminate AMR-carrying species from the gut microbiota. Critically, the same antibodies also inhibit horizontal gene transfer, i.e. prevent the spread of antibiotic resistance between gut bacterial strains in the gut. Thus we expect vaccination to simultaneously decrease the frequency of AMR bacteria in the environment, and to slow the spread of remaining AMR genes between bacterial strains/species.
In this project we will test a vaccination/benign competitor protocol for targeted drug-free removal of an individual bacterial strain from the microbiota of mice. Subsequently, we will extend this protocol to domestic pigs, providing a solid framework for subsequent large-scale trials and extension to more diverse bacterial species and hosts.

What is special about the project?

This project brings together three novel concepts, namely inactivated oral vaccines, engineered benign competitor bacteria and our recent understanding of the function of intestinal antibodies. We hope that the elimination of AMR bacteria by these combined techniques will provide a potent alternative to antibiotic usage in livestock rearing and will buy valuable time for the development of next-generation antibiotics. Combining the expertise of mucosal immunologists (ETH Zürich), evolutionary microbiologists (ETH Zürich/Biozentrum Basel), biomathematicians (UPMC, Paris) and veterinarians (Agrovet, Zürich) allows us to develop these technologies in a highly systematic manner.


The first aim of this project was to establish proof-of-principle in mice. Here we have optimized our inactivated oral vaccine protocol, including developing an oligo-valent vaccine that can drive an evolutionary trade-off in Salmonella (Diard et al. Nature Microbiology 2021, EP EP19177251). We have also developed and tested two non-cross-reactive niche competitors for Salmonella Typhimurium infections in mice: one based on a modified apathogenic Salmonella, and one based on a commensal E.coli. A patent application based on the Salmonella niche competitor is about to be submitted. Via a combination of mathematical modeling and optimization in vivo, we have developed a combined vaccine/niche competitor protocol that can completely eradicate Salmonella from the gut lumen. This is the first demonstration of a sterilizing immunization against non-Typhoidal Salmonellosis in any animal model.
We have also made major progress in translating these vaccines into domestic pigs. A GMP-compatible scale-up protocol for vaccine production has been developed and is in routine use. First experimental trials have demonstrated that the vaccine is safe and well tolerated even at very high doses. Additionally, pigs will consume it voluntarily, making application simple. The vaccine induces a robust antibody response against Salmonella Typhimurium with only two applications. Therefore, we have proven safety and immunogenicity of our vaccines, as well as optimized oral dosing in domestic pigs. The next stage of this translation will be to carry out a Salmonella challenge infection in vaccinated pigs, which is being done in collaboration with a major veterinary vaccine producer. If successful, we hope to see rapid application to prevent Salmonella disease in domestic pigs worldwide.
We have extended this project to develop vaccines and examine potential niche-competitors for pathogenic E.coli. An early observation in these experiments is that E.coli capsules are poorly immunogenic when delivered as whole-cell oral vaccines, despite being abundantly present in the vaccine prep. While two common capsules are in fact autoantigens and are not suitable for vaccine targeting, the remaining serovars may be effectively targeted by glycoconjugate vaccines. A follow-up project (SNF Bridge Discovery) aims to develop biochemical synthesis for such vaccines that could then be added to our inactivated whole-cells to generate robust selective pressures. Follow-up projects in the Diard group will also consider combining vaccination and therapeutic bacteriophage to eliminate E.coli carrying autoantigen capsular polysaccharides.


Diard M, Bakkeren E, Lentsch V, Rocker A, Bekele NA, Hoces D, Aslani S,Arnoldini M, Böhi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude MW, Hockenberry A, Viollier PH, Falquet L, Wüthrich D, Bonfiglio F, Loverdo C, Egli A, Zandomeneghi G, Mezzeng R, Holst O, Meier BH, Hardt WD, Slack E*. A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nat Microbiol. 2021 May 27. doi.org/10.1038/s41564-021-00911-1;
Kathrin Moor, Médéric Diard, Mikael E. Sellin, Boas Felmy, Sandra Y. Wotzka, Albulena Toska, Erik Bakkeren, Markus Arnoldini, Florence Bansept, Alma Dal Co, Tom Völler, Andrea Minola, Blanca Fernandez-Rodriguez, Gloria Agatic, Sonia Barbieri, Luca Piccoli, Costanza Casiraghi, Davide Corti, Antonio Lanzavecchia, Roland R. Regoes, Claude Loverdo, Roman Stocker, Douglas R. Brumley*, Wolf-Dietrich Hardt*, Emma Slack*. High-avidity IgA protects the intestine by enchaining growing bacteria. Nature. 2017. 544(7651):498-502;
Médéric Diard, Erik Bakkeren, Jeffrey K. Cornuault, Kathrin Moor, Annika Hausmann, Mikael E. Sellin, Claude Loverdo, Abram Aertsen, Martin Ackermann, Marianne De Paepe, Emma Slack, Wolf- Dietrich Hardt. Inflammation boosts bacteriophage transfer between Salmonella. Science. 2017. Mar 17;355(6330):1211-1215;
Bansept F, Schumann-Moor K, Diard M, Hardt WD, Slack E, Loverdo C. Enchained growth and cluster dislocation: A possible mechanism for microbiota homeostasis. PLoS Comput Biol. 2019 May 3;15(5):e1006986. doi: 10.1371/journal.pcbi.1006986;
Herp S, Brugiroux S, Garzetti D, Ring D, Jochum LM, Beutler M, Eberl C, Hussain S, Walter S, Gerlach RG, Ruscheweyh HJ, Huson D, Sellin ME, Slack E, Hanson B, Loy A, Baines JF, Rausch P, Basic M, Bleich A, Berry D, Stecher B. Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis. Cell Host Microbe. 2019 May 8;25(5):681-694.e8. doi: 10.1016/j.chom.2019.03.004
Diard M, Bakkeren E, Hoces D, Lentsch V, Arnoldini M, Böhi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude M, Hockenberry A, Viollier PH, Falquet L, Wüthrich D, Bonfiglio F, Egli A, Zandomeneghi G, Mezzenga R, Holst O, Meier BH, Hardt WD, Slack E*. Rationally designed oral vaccines can set and evolutionary trap for Salmonella Typhimurium
Daniel Hoces, Markus Arnoldini, Médéric Diard, Claude Loverdo and Emma Slack. Growing, evolving and sticking in a flowing environment: Understanding IgA interactions with bacteria in the gut. 2019 Nov Immunology. 2020 Jan;159(1):52-62
Oliver Pabst, Emma Slack. IgA and the intestinal Microbiota: The importance of being specific. Mucosal Immunol. 2020 Jan;13(1):12-21
Sterlin D, Fadlallah J, Slack E, Gorochov G. Antibody/microbiota interface in health and disease. Mucosal Immunol. 2020 Jan;13(1):3-11.
Bakkeren E, Huisman JS, Fattinger SA, Hausmann A, Furter M, Egli A, Slack E, Sellin ME, Bonhoeffer S, Regoes RR, Diard M, Hardt WD. Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut. Nature. 2019 Sep;573(7773):276-280
Wotzka SY, Kreuzer M, Maier L, Arnoldini M, Nguyen BD, Brachmann AO, Berthold DL, Zünd M, Hausmann A, Bakkeren E, Hoces D, Gül E, Beutler M, Dolowschiak T, Zimmermann M, Fuhrer T, Moor K, Sauer U, Typas A, Piel J, Diard M, Macpherson AJ, Stecher B, Sunagawa S, Slack E, Hardt WD. Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice. Nat Microbiol. 2019 Dec;4(12):2164-2174


Persons involved in the project

Dr. Emma Wetter-Slack, project leader
Verena Lentsch, PhD student
Dr. Claude Loverdo; Collaborator
Prof. Médéric Diard, Collaborator
Dr. Aurore Woller, Postdoctoral researcher

Last update to this project presentation  20.10.2022