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.
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. BioRxiv 2019, EP EP19177251). We have also developed and tested two non-cross-reactive niche competitors for Samonella Typhimurium infections in mice: one based on a modified apathogenic Salmonella, and one based on a commensal E.coli. Combining these tools allows very robust protection from invasive Salmonellosis and intestinal inflammation.
A successful vaccine scale-up protocol has been developed, allowing us to begin testing of our vaccines in domestic pigs. Vaccination of 12 animals now reveals a strong serum IgG response to the vaccine fed either in liquid form, mixed with food, or fed in capsules. The pigs actively sought the vaccine and showed perfect health and normal growth as well as excellent organ and gut health at autopsy, indicating no adverse effects in the first trials. We therefore conclude that the vaccines are safe and well tolerated in domestic pigs, and that oral inactivated Salmonella is sufficient to induce serological immune responses. This will now be confirmed in a larger cohort of animals and tested for protective efficacy.
In the next phase of the project, we are now expanding our vaccination and niche-competitor technologies to target multi-drug resistant enterotoxigenic and uropathogenic E. coli strains. In contrast to non-Typhoidal Salmonella, this requires induction of not only an anti-O-antigen antibody response, but also an anti-capsular polysaccharide immune response. Virus-like particle-based glycoconjugate vaccines are in development in the group for a set of E.coli capsules commonly associated with enteropathogenic strains. These will then be tested in murine and porcine models of colonization and disease.
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