Prof. Dr. Dirk Bumann

Roche, Béatrice, Claudi, Beatrice, Cunrath, Olivier, Bleck, Christopher K.E., Antelo-Varela, Minia, Li, Jiagui, & Bumann, Dirk. (2025). A Salmonella subset exploits erythrophagocytosis to subvert SLC11A1-imposed iron deprivation. Cell Host and Microbe, 33(5), 632–642. https://doi.org/10.1016/j.chom.2025.04.013

Fanous, Joseph, Claudi, Beatrice, Tripathi, Vishwachi, Li, Jiagui, Goormaghtigh, Frédéric, & Bumann, Dirk. (2025). Limited impact of Salmonella stress and persisters on antibiotic clearance. Nature, 639(8053), 181–189. https://doi.org/10.1038/s41586-024-08506-6

Erdmann, Joana, Kuehl, Richard, Morgenstern, Mario, Bumann, Dirk, Clauss, Martin, Khanna, Nina, & Rentsch, Katharina M. (2025). Amoxicillin Concentrations in Samples of Musculoskeletal Infections. Helvetica Chimica Acta, 108(2). https://doi.org/10.1002/hlca.202400178

Antelo-Varela, Minia, Bumann, Dirk, & Schmidt, Alexander. (2024). Optimizing SureQuant for Targeted Peptide Quantification: a Technical Comparison with PRM and SWATH-MS Methods [Journal-article]. Analytical Chemistry, 96(45), 18061–18069. https://doi.org/10.1021/acs.analchem.4c03622

Nordmann, Patrice, Helsens, Nicolas, Poirel, Laurent, Sadek, Mustafa, Bumann, Dirk, & Findlay, Jacqueline. (2024). The OprF porin as a potential target for the restoration of carbapenem susceptibility in Pseudomonas aeruginosa expressing acquired carbapenemases. Antimicrobial Agents and Chemotherapy, 68(10). https://doi.org/10.1128/aac.00761-24

Jantarug, Krittapas, Tripathi, Vishwachi, Morin, Benedict, Iizuka, Aya, Kuehl, Richard, Morgenstern, Mario, Clauss, Martin, Khanna, Nina, Bumann, Dirk, & Rivera-Fuentes, Pablo. (2024). A Far-Red Fluorescent Probe to Visualize Gram-Positive Bacteria in Patient Samples. ACS Infectious Diseases, 10(5), 1545–1551. https://doi.org/10.1021/acsinfecdis.4c00060

Huessy, Benjamin, Bumann, Dirk, & Ebert, Dieter. (2024). Ectopical expression of bacterial collagen-like protein supports its role as adhesin in host–parasite coevolution. Royal Society Open Science, 11(4). https://doi.org/10.1098/rsos.231441

Li, Jiagui, Alhayek, Alaa, Wang, Heng, & Bumann, Dirk. (2024). High-Resolution Three-dimensional Whole-organ Tomography of Microbial Infections. Journal of Visualized Experiments, 2024(205). https://doi.org/10.3791/66469

Forrer, Pascal, Palianina, Darya, Stühler, Claudia, Kreuzaler, Matthias, Roux, Julien, Li, Jiagui, Schmutz, Christoph, Burckhardt, David, Franzeck, Fabian, Finke, Daniela, Schmidt, Alexander, Bumann, Dirk, & Khanna, Nina. (2024). Unveiling signaling pathways inducing MHC class II expression in neutrophils. Frontiers in Immunology, 15. https://doi.org/10.3389/fimmu.2024.1444558

Sollier, Julie, Basler, Marek, Broz, Petr, Dittrich, Petra S., Drescher, Knut, Egli, Adrian, Harms, Alexander, Hierlemann, Andreas, Hiller, Sebastian, King, Carolyn G., McKinney, John D., Moran-Gilad, Jacob, Neher, Richard A., Page, Malcolm G. P., Panke, Sven, Persat, Alexandre, Picotti, Paola, Rentsch, Katharina M., Rivera-Fuentes, Pablo, et al. (2024). Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions. Nature Microbiology, 9(1), 1–3. https://doi.org/10.1038/s41564-023-01566-w

Hauswirth, Patrick, Buck, Jonas, Puligilla, Ramya, Alter, Claudio, Sieber, Sandro, Claudi, Beatrice, Fanous, Joseph, Bumann, Dirk, & Huwyler, Jörg. (2023). Zebrafish Larvae as an in vivo Model for Antimicrobial Activity Tests against Intracellular Salmonella. IMR Press, FBL, 28(5), 99. https://doi.org/10.31083/j.fbl2805099

Huessy, Benjamin, Bumann, Dirk, & Ebert, Dieter. (2023). Ectopical expression of bacterial collagen-like protein supports its role as adhesin in host-parasite coevolution. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.07.14.549037

Dogga, Sunil Kumar, Lunghi, Matteo, Maco, Bohumil, Li, Jiagui, Claudi, Beatrice, Marq, Jean-Baptiste, Chicherova, Natalia, Kockmann, Tobias, Bumann, Dirk, Hehl, Adrian B., Soldati-Favre, Dominique, & Hammoudi, Pierre-Mehdi. (2022). Importance of aspartyl protease 5 in the establishment of the intracellular niche during acute and chronic infection of Toxoplasma gondii. Molecular Microbiology, 118(6), 601–622. https://doi.org/10.1111/mmi.14987

Hinnu, Mariliis, Putrinš, Marta, Kogermann, Karin, Bumann, Dirk, & Tenson, Tanel. (2022). Making Antimicrobial Susceptibility Testing More Physiologically Relevant with Bicarbonate? Antimicrobial Agents and Chemotherapy, 66(5), e0241221. https://doi.org/10.1128/aac.02412-21

Luscher, Alexandre, Gasser, Véronique, Bumann, Dirk, Mislin, Gaëtan L. A., Schalk, Isabelle J., & Köhler, Thilo. (2022). Plant-Derived Catechols Are Substrates of TonB-Dependent Transporters and Sensitize Pseudomonas aeruginosa to Siderophore-Drug Conjugates. mBio, 13(4), e0149822. https://doi.org/10.1128/mbio.01498-22

Bhamidimarri, Satya Prathyusha, Young, Tessa R., Shanmugam, Muralidharan, Soderholm, Sandra, Baslé, Arnaud, Bumann, Dirk, & van den Berg, Bert. (2021). Acquisition of ionic copper by the bacterial outer membrane protein OprC through a novel binding site. PLoS Biology, 19(11), e3001446. https://doi.org/10.1371/journal.pbio.3001446

Dehinwal, Ruchika, Cooley, Danielle, Rakov, Alexey V., Alugupalli, Akhil S., Harmon, Joey, Cunrath, Olivier, Vallabhajosyula, Prashanth, Bumann, Dirk, & Schifferli, Dieter M. (2021). Increased Production of Outer Membrane Vesicles by Salmonella Interferes with Complement-Mediated Innate Immune Attack. mBio, 12(3), e0086921. https://doi.org/10.1128/mbio.00869-21

Haschka, David, Tymoszuk, Piotr, Petzer, Verena, Hilbe, Richard, Heeke, Simon, Dichtl, Stefanie, Skvortsov, Sergej, Demetz, Egon, Berger, Sylvia, Seifert, Markus, Mitterstiller, Anna-Maria, Moser, Patrizia, Bumann, Dirk, Nairz, Manfred, Theurl, Igor, & Weiss, Guenter. (2021). Ferritin H deficiency deteriorates cellular iron handling and worsens Salmonella typhimurium infection by triggering hyperinflammation. JCI insight, 6(13), e141760. https://doi.org/10.1172/jci.insight.141760

Huemer, Markus, Mairpady Shambat, Srikanth, Bergada-Pijuan, Judith, Söderholm, Sandra, Boumasmoud, Mathilde, Vulin, Clément, Gómez-Mejia, Alejandro, Antelo Varela, Minia, Tripathi, Vishwachi, Götschi, Sandra, Marques Maggio, Ewerton, Hasse, Barbara, Brugger, Silvio D., Bumann, Dirk, Schuepbach, Reto A., & Zinkernagel, Annelies S. (2021). Molecular reprogramming and phenotype switching in; Staphylococcus aureus; lead to high antibiotic persistence and affect therapy success. Proceedings of the National Academy of Sciences of the United States of America, 118(7), e2014920118. https://doi.org/10.1073/pnas.2014920118

Li, Jiagui, Claudi, Beatrice, Fanous, Joseph, Chicherova, Natalia, Cianfanelli, Francesca Romana, Campbell, Robert A. A., & Bumann, Dirk. (2021). Tissue compartmentalization enables; Salmonella; persistence during chemotherapy. Proceedings of the National Academy of Sciences of the United States of America, 118(51), e2113951118. https://doi.org/10.1073/pnas.2113951118

Ude, Johanna, Tripathi, Vishwachi, Buyck, Julien M., Söderholm, Sandra, Cunrath, Olivier, Fanous, Joseph, Claudi, Beatrice, Egli, Adrian, Schleberger, Christian, Hiller, Sebastian, & Bumann, Dirk. (2021). Outer membrane permeability: Antimicrobials and diverse nutrients bypass porins in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America, 118(31), e2107644118. https://doi.org/10.1073/pnas.2107644118

Cianfanelli, Francesca Romana, Cunrath, Olivier, & Bumann, Dirk. (2020). Efficient dual-negative selection for bacterial genome editing. BMC Microbiology, 20(1). https://doi.org/10.1186/s12866-020-01819-2

Bumann, Dirk. (2020). Salmonella single-cell metabolism and stress responses in complex host tissues. In Cossart, Pascale;Roy, Craig R.;Sansonetti, Philippe (ed.), Bacteria and Intracellularity (pp. 167–177). wiley. https://doi.org/10.1128/9781683670261.ch12

Cianfanelli, Francesca Romana, Cunrath, Olivier, & Bumann, Dirk. (2020). Efficient Dual-Negative Selection for Bacterial Genome Editing. bioRxiv. https://doi.org/10.1101/2020.03.03.974816

Cunrath, Olivier, Graulier, Gwenaëlle, Carballido-Lopez, Ana, Pérard, Julien, Forster, Anne, Geoffroy, Valérie A., Saint Auguste, Pamela, Bumann, Dirk, Mislin, Gaetan L. A., Michaud-Soret, Isabelle, Schalk, Isabelle J., & Fechter, Pierre. (2020). The pathogen; Pseudomonas aeruginosa; optimizes the production of the siderophore pyochelin upon environmental challenges. Metallomics, 12(12), 2108–2120. https://doi.org/10.1039/d0mt00029a

Hausmann, Annika, Böck, Desirée, Geiser, Petra, Berthold, Dorothée L., Fattinger, Stefan A., Furter, Markus, Bouman, Judith A., Barthel-Scherrer, Manja, Lang, Crispin M., Bakkeren, Erik, Kolinko, Isabel, Diard, Médéric, Bumann, Dirk, Slack, Emma, Regoes, Roland R., Pilhofer, Martin, Sellin, Mikael E., & Hardt, Wolf-Dietrich. (2020). Intestinal epithelial NAIP/NLRC4 restricts systemic dissemination of the adapted pathogen Salmonella Typhimurium due to site-specific bacterial PAMP expression. Mucosal Immunology, 13(3), 530–544. https://doi.org/10.1038/s41385-019-0247-0

Mas, Guillaume, Burmann, Björn M., Sharpe, Timothy, Claudi, Beatrice, Bumann, Dirk, & Hiller, Sebastian. (2020). Regulation of chaperone function by coupled folding and oligomerization. Science advances, 6(43), eabc5822. https://doi.org/10.1126/sciadv.abc5822

Roche, Béatrice, & Bumann, Dirk. (2020). Single-cell reporters for pathogen responses to antimicrobial host attacks. Current opinion in microbiology, 59, 16–23. https://doi.org/10.1016/j.mib.2020.07.013

Rosas-Ballina, Mauricio, Guan, Xue Li, Schmidt, Alexander, & Bumann, Dirk. (2020). Classical Activation of Macrophages Leads to Lipid Droplet Formation Without; de novo; Fatty Acid Synthesis. Frontiers in Immunology, 11, 131. https://doi.org/10.3389/fimmu.2020.00131

Wolf, Tobias, Jin, Wenjie, Zoppi, Giada, Vogel, Ian A., Akhmedov, Murodzhon, Bleck, Christopher K. E., Beltraminelli, Tim, Rieckmann, Jan C., Ramirez, Neftali J., Benevento, Marco, Notarbartolo, Samuele, Bumann, Dirk, Meissner, Felix, Grimbacher, Bodo, Mann, Matthias, Lanzavecchia, Antonio, Sallusto, Federica, Kwee, Ivo, & Geiger, Roger. (2020). Dynamics in protein translation sustaining T cell preparedness. Nature immunology, 21(8), 927–937. https://doi.org/10.1038/s41590-020-0714-5

Balaban, Nathalie Q., Helaine, Sophie, Lewis, Kim, Ackermann, Martin, Aldridge, Bree, Andersson, Dan I., Brynildsen, Mark P., Bumann, Dirk, Camilli, Andrew, Collins, James J., Dehio, Christoph, Fortune, Sarah, Ghigo, Jean-Marc, Hardt, Wolf-Dietrich, Harms, Alexander, Heinemann, Matthias, Hung, Deborah T., Jenal, Urs, Levin, Bruce R., et al. (2019). Publisher Correction: Definitions and guidelines for research on antibiotic persistence (Nature Reviews Microbiology, (2019), 17, 7, (441-448), 10.1038/s41579-019-0196-3). Nature Reviews Microbiology, 17(7), 460. https://doi.org/10.1038/s41579-019-0207-4

Bumann, Dirk. (2019). Salmonella; Single-Cell Metabolism and Stress Responses in Complex Host Tissues. Microbiology Spectrum, 7(2). https://doi.org/10.1128/microbiolspec.bai-0009-2019

Napolitani, Giorgio, Kurupati, Prathiba, Teng, Karen Wei Weng, Gibani, Malick M., Rei, Margarida, Aulicino, Anna, Preciado-Llanes, Lorena, Wong, Michael Thomas, Becht, Etienne, Howson, Lauren, de Haas, Paola, Salio, Mariolina, Blohmke, Christoph J., Olsen, Lars Rønn, Pinto, David Miguel Susano, Scifo, Laura, Jones, Claire, Dobinson, Hazel, Campbell, Danielle, et al. (2019). Publisher Correction: Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses (Nature Immunology, (2018), 19, 7, (742-754), 10.1038/s41590-018-0133-z). Nature Immunology, 20(4), 514. https://doi.org/10.1038/s41590-019-0357-6

Balaban, Nathalie Q., Helaine, Sophie, Lewis, Kim, Ackermann, Martin, Aldridge, Bree, Andersson, Dan I., Brynildsen, Mark P., Bumann, Dirk, Camilli, Andrew, Collins, James J., Dehio, Christoph, Fortune, Sarah M., Ghigo, Jean-Marc, Hardt, Wolf-Dietrich, Harms, Alexander, Heinemann, Matthias, Hung, Deborah T., Jenal, Urs, Levin, Bruce R., et al. (2019). Definitions and guidelines for research on antibiotic persistence. Nature Reviews Microbiology, 17(7), 441–448. https://doi.org/10.1038/s41579-019-0196-3

Bhamidimarri, Satya Prathyusha, Zahn, Michael, Prajapati, Jigneshkumar Dahyabhai, Schleberger, Christian, Söderholm, Sandra, Hoover, Jennifer, West, Josh, Kleinekathöfer, Ulrich, Bumann, Dirk, Winterhalter, Mathias, & van den Berg, Bert. (2019). A Multidisciplinary Approach toward Identification of Antibiotic Scaffolds for Acinetobacter baumannii. Structure (London, England : 1993), 27(2), 268–+. https://doi.org/10.1016/j.str.2018.10.021

Bumann, Dirk, Fanous, Joseph, Li, Jiagui, & Goormaghtigh, Frédéric. (2019). Antibiotic chemotherapy against heterogeneous pathogen populations in complex host tissues. F1000Research, 8, 1781. https://doi.org/10.12688/f1000research.19441.1

Carballido Lopez, Ana, Cunrath, Olivier, Forster, Anne, Pérard, Julien, Graulier, Gwenaëlle, Legendre, Rachel, Varet, Hugo, Sismeiro, Odile, Perraud, Quentin, Pesset, Bénédicte, Saint Auguste, Pamela, Bumann, Dirk, Mislin, Gaëtan L. A., Coppee, Jean Yves, Michaud-Soret, Isabelle, Fechter, Pierre, & Schalk, Isabelle J. (2019). Non-specific interference of cobalt with siderophore-dependent iron uptake pathways. Metallomics : Integrated Biometal Science, 11(11), 1937–1951. https://doi.org/10.1039/c9mt00195f

Cunrath, Oliver, & Bumann, Dirk. (2019). Host resistance factor SLC11A1 restricts Salmonella growth through magnesium deprivation. Science, 366(6468), 995–999. https://doi.org/10.1126/science.aax7898

Cunrath, Olivier, Meinel, Dominik M., Maturana, Pauline, Fanous, Joseph, Buyck, Julien M., Saint Auguste, Pamela, Seth-Smith, Helena M. B., Körner, Jonas, Dehio, Christoph, Trebosc, Vincent, Kemmer, Christian, Neher, Richard, Egli, Adrian, & Bumann, Dirk. (2019). Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains. EBioMedicine, 41, 479–487. https://doi.org/10.1016/j.ebiom.2019.02.061

Eren, Elif, Planes, Rémi, Buyck, Julien, Bordignon, Pierre-Jean, Colom, André, Cunrath, Olivier, Dreier, Roland F., Santos, José C., Duplan-Eche, Valérie, Näser, Emmanuelle, Peixoto, Antonio, Bumann, Dirk, Cougoule, Céline, Coste, Agnès, Neyrolles, Olivier, Broz, Petr, & Meunier, Etienne. (2019). Type-3 Secretion System-induced pyroptosis protects Pseudomonas against cell-autonomous immunity. bioRxiv. https://doi.org/10.1101/650333

Jayachandran, Rajesh, Gumienny, Aleksandra, Bolinger, Beatrice, Ruehl, Sebastian, Lang, Mathias Jakob, Fucile, Geoffrey, Mazumder, Saumyabrata, Tchang, Vincent Sam Yong, Woischnig, Anne-Kathrin, Stiess, Michael, Kunz, Gabriele, Claudi, Beatrice, Schmaler, Mathias, Siegmund, Kerstin, Li, Jianping, Dertschnig, Simone, Hollaender, George, Medina, Eva, Karrer, Urs, et al. (2019). Disruption of Coronin 1 Signaling in T Cells Promotes Allograft Tolerance while Maintaining Anti-Pathogen Immunity. Immunity, 50(1), 152–165. https://doi.org/10.1016/j.immuni.2018.12.011

Trebosc, Vincent, Gartenmann, Sarah, Tötzl, Marcus, Lucchini, Valentina, Schellhorn, Birgit, Pieren, Michel, Lociuro, Sergio, Gitzinger, Marc, Tigges, Marcel, Bumann, Dirk, & Kemmer, Christian. (2019). Dissecting Colistin Resistance Mechanisms in Extensively Drug-Resistant Acinetobacter baumannii Clinical Isolates. mBio, 10(4), e01083–19. https://doi.org/10.1128/mbio.01083-19

Wu, Aimin, Tymoszuk, Piotr, Haschka, David, Heeke, Simon, Dichtl, Stefanie, Petzer, Verena, Seifert, Markus, Hilbe, Richard, Sopper, Sieghart, Talasz, Heribert, Bumann, Dirk, Lass-Flörl, Cornelia, Theurl, Igor, Zhang, Keying, & Weiss, Guenter. (2018). Correction: Wu et al., “Salmonella utilizes zinc to subvert antimicrobial host defense of macrophages via modulation of NF-κB signaling” [Infection and Immunity, 85, 12, (2017), (e00418-17)] doi: 10.1128/IAI.00418-17. Infection and Immunity, 86(3). https://doi.org/10.1128/IAI.00881-17

Lim, Daejin, Kim, Kwang Soo, Jeong, Jae-Ho, Marques, Oriana, Kim, Hyun-Ju, Song, Miryoung, Lee, Tae-Hoon, Kim, Jae Il, Choi, Hueng-Sik, Min, Jung-Joon, Bumann, Dirk, Muckenthaler, Martina U., & Choy, Hyon E. (2018). The hepcidin-ferroportin axis controls the iron content of Salmonella-containing vacuoles in macrophages. Nature Communications, 9(1), 2091. https://doi.org/10.1038/s41467-018-04446-8

Luscher, Alexandre, Moynié, Lucile, Auguste, Pamela Saint, Bumann, Dirk, Mazza, Lena, Pletzer, Daniel, Naismith, James H., & Köhler, Thilo. (2018). TonB-Dependent Receptor Repertoire of Pseudomonas aeruginosa for Uptake of Siderophore-Drug Conjugates. Antimicrobial Agents and Chemotherapy, 62(6), e00097–18. https://doi.org/10.1128/aac.00097-18

Napolitani, Giorgio, Kurupati, Prathiba, Teng, Karen Wei Weng, Gibani, Malick M., Rei, Margarida, Aulicino, Anna, Preciado-Llanes, Lorena, Wong, Michael Thomas, Becht, Etienne, Howson, Lauren, de Haas, Paola, Salio, Mariolina, Blohmke, Christoph J., Olsen, Lars Rønn, Pinto, David Miguel Susano, Scifo, Laura, Jones, Claire, Dobinson, Hazel, Campbell, Danielle, et al. (2018). Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses. Nature Immunology, 19(7), 742–754. https://doi.org/10.1038/s41590-018-0133-z

Samanta, Susruta, Bodrenko, Igor, Acosta-Gutiérrez, Silvia, D’Agostino, Tommaso, Pathania, Monisha, Ghai, Ishan, Schleberger, Christian, Bumann, Dirk, Wagner, Richard, Winterhalter, Mathias, van den Berg, Bert, & Ceccarelli, Matteo. (2018). Getting Drugs through Small Pores: Exploiting the Porins Pathway in Pseudomonas aeruginosa. ACS Infectious Diseases, 4(10), 1519–1528. https://doi.org/10.1021/acsinfecdis.8b00149

Abellón-Ruiz, Javier, Kaptan, Shreyas S., Baslé, Arnaud, Claudi, Beatrice, Bumann, Dirk, Kleinekathöfer, Ulrich, & van den Berg, Bert. (2017). Structural basis for maintenance of bacterial outer membrane lipid asymmetry. Nature Microbiology, 2(12), 1616–1623. https://doi.org/10.1038/s41564-017-0046-x

Bumann, Dirk, & Cunrath, Olivier. (2017). Heterogeneity of Salmonella-host interactions in infected host tissues. Current Opinion in Microbiology, 39, 57–63. https://doi.org/10.1016/j.mib.2017.09.008

Bumann, Dirk, & Schothorst, Joep. (2017). Intracellular Salmonella metabolism. Cellular Microbiology, 19(10), e12766. https://doi.org/10.1111/cmi.12766

Dehio, Christoph, & Bumann, Dirk. (2017). Editorial overview: Bacterial systems biology. Current Opinion in Microbiology, 39, viii–vixi. https://doi.org/10.1016/j.mib.2017.11.024

Schürmann, Nura, Forrer, Pascal, Casse, Olivier, Li, Jiagui, Felmy, Boas, Burgener, Anne-Valérie, Ehrenfeuchter, Nikolaus, Hardt, Wolf-Dietrich, Recher, Mike, Hess, Christoph, Tschan-Plessl, Astrid, Khanna, Nina, & Bumann, Dirk. (2017). Myeloperoxidase targets oxidative host attacks to Salmonella and prevents collateral tissue damage. Nature Microbiology, 2(4), 16268. https://doi.org/10.1038/nmicrobiol.2016.268

Wu, Aimin, Tymoszuk, Piotr, Haschka, David, Heeke, Simon, Dichtl, Stefanie, Petzer, Verena, Seifert, Markus, Hilbe, Richard, Sopper, Sieghart, Talasz, Heribert, Bumann, Dirk, Lass-Flörl, Cornelia, Theurl, Igor, Zhang, Keying, & Weiss, Guenter. (2017). Salmonella Utilizes Zinc To Subvert Antimicrobial Host Defense of Macrophages via Modulation of NF-κB Signaling. Infection and Immunity, 85(12), e00418–17. https://doi.org/10.1128/iai.00418-17

Freed, Nikki E., Bumann, Dirk, & Silander, Olin K. (2016). Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality. BMC Microbiology, 16(1), 203. https://doi.org/10.1186/s12866-016-0818-0

Gasser, Véronique, Baco, Etienne, Cunrath, Olivier, Saint August, Pamela, Perraud, Quentin, Zill, Nicolas, Schleberger, Christian, Schmidt, Alexander, Paulen, Aurélie, Bumann, Dirk, Mislin, Gaëtan L. A., & Schalk, Isabelle J. (2016). Catechol siderophores repress the pyochelin pathway and activate the enterobactin pathway in Pseudomonas aeruginosa: an opportunity for siderophore-antibiotic conjugates development. Environmental Microbiology, 18(3), 32–819. https://doi.org/10.1111/1462-2920.13199

Trebosc, Vincent, Gartenmann, Sarah, Royet, Kevin, Manfredi, Pablo, Tötzl, Marcus, Schellhorn, Birgit, Pieren, Michel, Tigges, Marcel, Lociuro, Sergio, Sennhenn, Peter C., Gitzinger, Marc, Bumann, Dirk, & Kemmer, Christian. (2016). A novel genome editing platform for drug resistant Acinetobacter baumannii revealed an AdeR-unrelated tigecycline resistance mechanism. Antimicrobial Agents and Chemotherapy, 60(12), 7263–7271. https://doi.org/10.1128/aac.01275-16

Abu Kwaik, Yousef, & Bumann, Dirk. (2015). Host delivery of favorite meals for intracellular pathogens. PLoS Pathogens, 11(6), e1004866. https://doi.org/10.1371/journal.ppat.1004866

Bumann, Dirk. (2015). Heterogeneous Host-Pathogen Encounters: Act Locally, Think Globally [Review of Heterogeneous Host-Pathogen Encounters: Act Locally, Think Globally]. Cell Host & Microbe, 17, Article 1. https://doi.org/10.1016/j.chom.2014.12.006

Martano, Giuseppe, Delmotte, Nathanaël, Kiefer, Patrick, Christen, Philipp, Kentner, David, Bumann, Dirk, & Vorholt, Julia A. (2015). Fast sampling method for mammalian cell metabolic analyses using liquid chromatography-mass spectrometry. Nature Protocols, 10(1), 1–11. https://doi.org/10.1038/nprot.2014.198

McEwan, David G., Richter, Benjamin, Claudi, Beatrice, Wigge, Christoph, Wild, Philipp, Farhan, Hesso, McGourty, Kieran, Coxon, Fraser P., Franz-Wachtel, Mirita, Perdu, Bram, Akutsu, Masato, Habermann, Anja, Kirchof, Anja, Helfrich, Miep H., Odgren, Paul R., Van Hul, Wim, Frangakis, Achilleas S., Rajalingam, Krishnaraj, Macek, Boris, et al. (2015). PLEKHM1 Regulates Salmonella-Containing Vacuole Biogenesis and Infection. Cell Host & Microbe, 17(1), 58–71. https://doi.org/10.1016/j.chom.2014.11.011

Bumann, Dirk. (2014). Identification of protective antigens for vaccination against systemic salmonellosis. Frontiers in Immunology, 5(381), 381. https://doi.org/10.3389/fimmu.2014.00381

Burton, Neil A., Schürmann, Nura, Casse, Olivier, Steeb, Anne K., Claudi, Beatrice, Zankl, Janine, Schmidt, Alexander, & Bumann, Dirk. (2014). Disparate Impact of Oxidative Host Defenses Determines the Fate of Salmonella during Systemic Infection in Mice. Cell Host & Microbe, 15(1), 72–83. https://doi.org/10.1016/j.chom.2013.12.006

Claudi, Beatrice, Spröte, Petra, Chirkova, Anna, Personnic, Nicolas, Zankl, Janine, Schürmann, Nura, Schmidt, Alexander, & Bumann, Dirk. (2014). Phenotypic variation of salmonella in host tissues delays eradication by antimicrobial chemotherapy. Cell, 158(4), 722–733. https://doi.org/10.1016/j.cell.2014.06.045

Kentner, David, Martano, Giuseppe, Callon, Morgane, Chiquet, Petra, Brodmann, Maj, Burton, Olga, Wahlander, Asa, Nanni, Paolo, Delmotte, Nathanaël, Grossmann, Jonas, Limenitakis, Julien, Schlapbach, Ralph, Kiefer, Patrick, Vorholt, Julia A., Hiller, Sebastian, & Bumann, Dirk. (2014). Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth. Proceedings of the National Academy of Sciences of the United States of America, 111(27), 34–9929. https://doi.org/10.1073/pnas.1406694111

Maze, Alain, Glatter, Timo, & Bumann, Dirk. (2014). The central metabolism regulator EIIAGlc switches Salmonella from growth arrest to acute virulence through activation of virulence factor secretion. Cell reports, 7(5), 1426–1433. https://doi.org/10.1016/j.celrep.2014.04.022

Meunier, Etienne, Dick, Mathias S., Dreier, Roland F., Schürmann, Nura, Kenzelmann Broz, Daniela, Warming, Søren, Roose-Girma, Merone, Bumann, Dirk, Kayagaki, Nobuhiko, Takeda, Kiyoshi, Yamamoto, Masahiro, & Broz, Petr. (2014). Caspase-11 activation requires lysis of pathogen-containing vacuoles by IFN-induced GTPases. Nature, 509(7500), 70–366. https://doi.org/10.1038/nature13157

Kwaik, Yousef Abu, & Bumann, Dirk. (2013). Microbial quest for food in vivo : “Nutritional virulence” as an emerging paradigm. Cellular Microbiology, 15(6), 882–890. https://doi.org/10.1111/cmi.12138

Steeb, Benjamin, Claudi, Beatrice, Burton, Neil A., Tienz, Petra, Schmidt, Alexander, Farhan, Hesso, Mazé, Alain, & Bumann, Dirk. (2013). Parallel exploitation of diverse host nutrients enhances salmonella virulence. PLoS Pathogens, 9(4), e1003301. https://doi.org/10.1371/journal.ppat.1003301

Barat, Somedutta, Steeb, Benjamin, Mazé, Alain, & Bumann, Dirk. (2012). Extensive in vivo resilience of persistent Salmonella. PLoS ONE, 7(7), e42007. https://doi.org/10.1371/journal.pone.0042007

Barat, Somedutta, Willer, Yvonne, Rizos, Konstantin, Claudi, Beatrice, Mazé, Alain, Schemmer, Anne K., Kirchhoff, Dennis, Schmidt, Alexander, Burton, Neil, & Bumann, Dirk. (2012). Immunity to intracellular Salmonella depends on surface-associated antigens. PLoS Pathogens, 8(10), e1002966. https://doi.org/10.1371/journal.ppat.1002966

Leschner, Sara, Deyneko, Igor V., Lienenklaus, Stefan, Wolf, Kathrin, Bloecker, Helmut, Bumann, Dirk, Loessner, Holger, & Weiss, Siegfried. (2012). Identification of tumor-specific Salmonella Typhimurium promoters and their regulatory logic. Nucleic Acids Research, 40(7), 94–2984. https://doi.org/10.1093/nar/gkr1041

Mary, Camille, Duek, Paula, Salleron, Lisa, Tienz, Petra, Bumann, Dirk, Bairoch, Amos, & Lane, Lydie. (2012). Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway. PLoS ONE, 7(12), e52877. https://doi.org/10.1371/journal.pone.0052877

Schrimpf, Sabine P., von Mering, Christian, Bendixen, Emøke, Heazlewood, Joshua L., Bumann, Dirk, Omenn, Gil, & Hengartner, Michael O. (2012). The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland [Review of The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland]. Proteomics, 12, Article 3. https://doi.org/10.1002/pmic.201290015

Willer, Yvonne, Müller, Beatrice, & Bumann, Dirk. (2012). Intestinal inflammation responds to microbial tissue load independent of pathogen/non-pathogen discrimination. PLoS ONE, 7(5), e35992. https://doi.org/10.1371/journal.pone.0035992

Crull, K., Bumann, D., & Weiss, S. (2011). Influence of infection route and virulence factors on colonization of solid tumors by Salmonella enterica serovar Typhimurium. FEMS Immunology and Medical Microbiology, 62(1), 75–83. https://doi.org/10.1111/j.1574-695x.2011.00790.x

Hänisch, J., Kolm, R., Wozniczka, M., Bumann, D., Rottner, K., & Stradal, T. E. B. (2011). Activation of a RhoA/Myosin II-Dependent but Arp2/3 Complex-Independent Pathway Facilitates Salmonella Invasion. Cell Host & Microbe, 9(4), 85–273. https://doi.org/10.1016/j.chom.2011.03.009

Pawelczyk, S., Bumann, D., & Abraham, W. R. (2011). Kinetics of carbon sharing in a bacterial consortium revealed by combining stable isotope probing with fluorescence-activated cell sorting. Journal of Applied Microbiology, 110(4), 73–1065. https://doi.org/10.1111/j.1365-2672.2011.04964.x

Stelter, C., Kappeli, R., Konig, C., Krah, A., Hardt, W. -D., Stecher, B., & Bumann, D. (2011). Salmonella-Induced Mucosal Lectin RegIIIbeta Kills Competing Gut Microbiota. PLoS ONE, 6(6), e20749. https://doi.org/10.1371/journal.pone.0020749

Thiele, I., Hyduke, D. R., Steeb, B., Fankam, G., Allen, D. K., Bazzani, S., Charusanti, P., Chen, F. -C., Fleming, R. M. T., Hsiung, C. A., De Keersmaecker, S. C. J., Liao, Y. -C., Marchal, K., Mo, M. L., Ozdemir, E., Raghunathan, A., Reed, J. L., Shin, S. -il, Sigurbjornsdottir, S., et al. (2011). A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Systems Biology, 5(8), 1–9. https://doi.org/10.1186/1752-0509-5-8

Wild, P., Farhan, H., McEwan, D. G., Wagner, S., Rogov, V. V., Brady, N. R., Richter, B., Korac, J., Waidmann, O., Choudhary, C., Dötsch, V., Bumann, D., & Dikic, I. (2011). Phosphorylation of the Autophagy Receptor Optineurin Restricts Salmonella Growth. Science, 333(6039), 33–228. https://doi.org/10.1126/science.1205405

Bumann, Dirk. (2010). Pathogen proteomes during infection : a basis for infection research and novel control strategies. Journal of Proteomics, 73(11), 76–2267. https://doi.org/10.1016/j.jprot.2010.08.004

Bumann, D., Behre, C., Behre, K., Herz, S., Gewecke, B., Gessner, J. E., von Specht, B. U., & Baumann, U. (2009). Systemic, nasal and oral live vaccines against Pseudomonas aeruginosa : a clinical trial of immunogenicity in lower airways of human volunteers. Vaccine, 28(3), 13–707. https://doi.org/10.1016/j.vaccine.2009.10.080

Bumann, Dirk. (2009). System-level analysis of Salmonella metabolism during infection. Current Opinion in Microbiology, 12(5), 67–559. https://doi.org/10.1016/j.mib.2009.08.004

de Buhr, M. F., Hedrich, H. J., Westendorf, A. M., Obermeier, F., Hofmann, C., Zschemisch, N. H., Buer, J., Bumann, D., Goyert, S. M., & Bleich, A. (2009). Analysis of Cd14 as a genetic modifier of experimental inflammatory bowel disease (IBD) in mice. Inflammatory Bowel Diseases, 15(12), 36–1824. https://doi.org/10.1002/ibd.21030

Hänisch, J., Ehinger, J., Ladwein, M., Rohde, M., Derivery, E., Bosse, T., Steffen, A., Bumann, D., Misselwitz, B., Hardt, W. D., Gautreau, A., Stradal, T. E., & Rottner, K. (2009). Molecular dissection of Salmonella-induced membrane ruffling versus invasion. Cellular Microbiology, 12(1), 84–98. https://doi.org/10.1111/j.1462-5822.2009.01380.x

Aebischer, T., Bumann, D., Epple, H. J., Metzger, W., Schneider, T., Cherepnev, G., Walduck, A. K., Kunkel, D., Moos, V., Loddenkemper, C., Jiadze, I., Panasyuk, M., Stolte, M., Graham, D. Y., Zeitz, M., & Meyer, T. F. (2008). Correlation of T cell response and bacterial clearance in human volunteers challenged with Helicobacter pylori revealed by randomised controlled vaccination with Ty21a-based Salmonella vaccines. Gut, 57(8), 72–1065. https://doi.org/10.1136/gut.2007.145839

Bumann, D. (2008). Has nature already identified all useful antibacterial targets? Current Opinion in Microbiology, 11(5), 387–392. https://doi.org/10.1016/j.mib.2008.08.002

Bumann, D., & Buss, L. (2008). Nutritional physiology and colony form in Podocoryna carnea (Cnidaria: Hydrozoa). Invertebrate Biology, 127(4), 368–380. https://doi.org/10.1111/j.1744-7410.2008.00135.x

Bumann, D., & Valdivia, R. H. (2007). Identification of host-induced pathogen genes by differential fluorescence induction reporter systems. Nature Protocols, 2(4), 7–770. https://doi.org/10.1038/nprot.2007.78

Halle, S., Bumann, D., Herbrand, H., Willer, Y., Dahne, S., Forster, R., & Pabst, O. (2007). Solitary intestinal lymphoid tissue provides a productive port of entry for Salmonella enterica serovar Typhimurium. Infection and Immunity, 75(4), 85–1577. https://doi.org/10.1128/iai.01392-06

Kirchhoff, D., Frentsch, M., Leclerk, P., Bumann, D., Rausch, S., Hartmann, S., Thiel, A., & Scheffold, A. (2007). Identification and isolation of murine antigen-reactive T cells according to CD154 expression. European Journal of Immunology, 37(9), 7–2370. https://doi.org/10.1002/eji.200737322

Thone, F., Schwanhausser, B., Becker, D., Ballmaier, M., & Bumann, D. (2007). FACS-isolation of Salmonella-infected cells with defined bacterial load from mouse spleen. Journal of Microbiological Methods, 71(3), 4–220. https://doi.org/10.1016/j.mimet.2007.08.016

Becker, D., Selbach, M., Rollenhagen, C., Ballmaier, M., Meyer, T. F., Mann, M., & Bumann, D. (2006). Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature, 440(7082), 7–303. https://doi.org/10.1038/nature04616

Rollenhagen, C., & Bumann, D. (2006). Salmonella enterica highly expressed genes are disease specific. Infection and Immunity, 74(3), 60–1649. https://doi.org/10.1128/iai.74.3.1649-1660.2006

Sabarth, N., Hurvitz, R., Schmidt, M., Zimny-Arndt, U., Jungblut, P. R., Meyer, T. F., & Bumann, D. (2005). Identification of Helicobacter pylori surface proteins by selective proteinase K digestion and antibody phage display. Journal of Microbiological Methods, 62(3), 9–345. https://doi.org/10.1016/j.mimet.2005.04.030

Arnold, H., Bumann, D., Felies, M., Gewecke, B., Sorensen, M., Gessner, J. E., Freihorst, J., von Specht, B. U., & Baumann, U. (2004). Enhanced immunogenicity in the murine airway mucosa with an attenuated Salmonella live vaccine expressing OprF-OprI from Pseudomonas aeruginosa. Infection and Immunity, 72(11), 53–6546. https://doi.org/10.1128/iai.72.11.6546-6553.2004

Bumann, D., Habibi, H., Kan, B., Schmid, M., Goosmann, C., Brinkmann, V., Meyer, T. F., & Jungblut, P. R. (2004). Lack of stage-specific proteins in coccoid Helicobacter pylori cells. Infection and Immunity, 72(11), 42–6738. https://doi.org/10.1128/iai.72.11.6738-6742.2004

Bumann, D., Jungblut, P. R., & Meyer, T. F. (2004). Helicobacter pylori vaccine development based on combined subproteome analysis. Proteomics, 4(10), 8–2843. https://doi.org/10.1002/pmic.200400909

Metzger, W. G., Mansouri, E., Kronawitter, M., Diescher, S., Soerensen, M., Hurwitz, R., Bumann, D., Aebischer, T., Von Specht, B. -U., & Meyer, T. F. (2004). Impact of vector-priming on the immunogenicity of a live recombinant Salmonella enterica serovar typhi Ty21a vaccine expressing urease A and B from Helicobacter pylori in human volunteers. Vaccine, 22(17-18), 7–2273. https://doi.org/10.1016/j.vaccine.2003.11.020

Rollenhagen, C., Sorensen, M., Rizos, K., Hurvitz, R., & Bumann, D. (2004). Antigen selection based on expression levels during infection facilitates vaccine development for an intracellular pathogen. Proceedings of the National Academy of Sciences of the United States of America, 101(23), 44–8739. https://doi.org/10.1073/pnas.0401283101