Publications 2026
Journal Articles Review Articles Book Chapters Preprints
Journal articles
Staphylococcus epidermidis implant-associated bone and joint infections: high rates of multiresistance associated with treatment failure
Authors: Schumacher, M., Grob, F., Roth, J.A., Egli, A., Werlen, L., Lemant, J., Morgenstern, M., Clauss, M., Khanna, N., Kuehl, R.
Published in: Int J Antimicrob Agents 2026
DOI: 10.1016/j.ijantimicag.2026.107950
Mucosal BCG vaccination reprograms lung interstitial macrophages and enhances antimicrobial defense in mice
Authors: Forde, A.J., Esposito, M., Kerschbamer, E., Schreiner, D., Moreo, E., Pantouloufos, N., Camarasa, T.M.N., de Lima, J., Soliman, H., Erber, M., Depew, C.E., Naderi, W., King, C.G.
Published in: Mucosal Immunol 2026
DOI: 10.1016/j.mucimm.2026.100391
High-Density E. Coli Cultivation Arrays for Combinatorial Drug Testing With Subsequent Lipid Profiling by MALDI-MS
Authors: Breitfeld, M., Dietsche, C.L., Born, F.L., Onipko, I., Blaase, L., Dittrich, P.S.
Published in: Adv Sci (Weinh) 2026
DOI: 10.1002/advs.76678
A microfluidic hollow-fiber infection model (µHFIM): monitoring bacterial response to dynamic drug treatment with single-cell resolution
Authors: Born, F.L., Dezauzier, R., Zinkernagel, A.S., Dittrich, P.S.
Published in: Microsyst Nanoeng 2026
DOI: 10.1038/s41378-026-01377-z
Opposing range-dependent interactions create complex spatial patterns of antibiotic tolerance in multispecies biofilms
Authors: Bottacin, G., Raach, B., Fröhlich, L., Künnecke, J., Kaczmarczyk, A., Tejada-Arranz, A., Ugolini, G.S., Stocker, R., Jenal, U., Bumann, D., Dittrich, P.S., Schubert, O.T., van Vliet, S.
Published in: Proc Natl Acad Sci 2026
Type VI secretion system-mediated bacterial antagonism in the classroom
Authors: Tejada-Arranz, A., Ringel, P., Lin, L., Basler, M.
Published in: Access Microbiol 2026
Complete genome sequence of Pseudomonas aeruginosa phage OmaKarin
Authors: Ransome, J., Maffei, E., Harms, A.
Published in: Microbiol Resour Announc 2026
DOI: 10.1128/mra.00353-26
Mechanistic basis of teichoic acid transport by a gatekeeper flippase
Authors: Cebrero, G., Chidananda, A.H., Cester, E., Dénéréaz, J., Demir, E.S., Mathew, A.T., Bhowmik, D.R., de Capitani, M., Reymond, J.L., Kannan, N., Avci, F.Y., Veening, J.W., Mehdipour, A.R., Perez, C.
Published in: Nature Communications 2026
DOI: 10.1038/s41467-026-73616-w
Preprint: 10.64898/2026.02.22.707263
Linezolid in addition to standard antibiotic treatment for Staphylococcus aureus bacteraemia: study protocol for a randomised, placebo-controlled trial
Authors: Rose, N., Bernasconi, N.S., Schumacher, M., Werlen, L., Büchel, D., Weisser, M., Vogt, S.B., Wehrle-Wieland, E., Conen, A., Thurnheer, M.C., Martin, Y., Birrer, M., Bongiovanni, M., Albrich, W.C., Karrer, U., Schibli, A., Harbarth, S., Papadimitriou-Olivgeris, M., Briel, M., Hasse, B., Khanna, N., Kuehl, R., Speich, B.
Published in: BMJ Open 2026
DOI: 10.1136/bmjopen-2026-118509
Adaptation of Enterococcus faecalis to intestinal mucus revealed by a human colonic organoid model
Authors: Mikhaleva, S., Hsiao, P.-L., Kurmashev, A., Anderson, C.M., Colomer-Winter, C., Boos, J.A., Choo, P.Y., Willett, J.L.E., Hierlemann, A., Kline, K.A., Persat, A.
Published in: mSystems 2026
DOI: 10.1128/msystems.01304-25
Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira
Authors: Agustoni, E., Mechaly, A., Dalla Rizza, J., Beriashvili, D., Pluhackova, K., Isaikina, P., Trajtenberg, F., Müntener, T., Wunder, E.A. Jr., Ko, A.I., Schirmer, T., Buschiazzo, A., Hiller, S.
Published in: Nature Communications 2026
DOI: 10.1038/s41467-026-71783-4
A modular genetic toolbox for precise gene regulation and multi-color imaging in streptococci
Authors: Mignolet, J., Schmid, A., Staub, J., van der Meer, J.R., Veening, J.W., Libante, V.
Published in: microLife 2026
A microphysiological human mini-bladder reveals urine-urothelium interplay in tissue resilience and UPEC recurrence in urinary tract infections
Authors: Paduthol, G., Nikolaev, M., Sharma, K., Blanc, J., Tomasek, K., Schlunke, L.I.E., Borgeat, V., Ambrosini, G., Kolotuev, I., Clerc-Rosset, S., Gjorevski, N., Knott, G.W., Lütolf, M.P., Thacker, V.V., McKinney, J.D.
Published in: Nature Communications 2026
DOI: 10.1038/s41467-026-68573-3
Preprint: 10.1101/2025.10.28.685030
A Ratiometric pH Sensor for Gram-Positive and Gram-Negative Bacteria
Authors: Kossmann, D., Iizuka, A., Khanna N., Rivera-Fuentes, R.
Published in: Nature Communications 2026
DOI: 10.1021/jacs.5c22321
Preprint: 10.1101/2025.09.09.675137
Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells
Authors: Elsässer, F., Florea, R., Räsch, F., Zedan, M., Sen, N-E., Pflästerer, T., Kleele, T., Loewith, R., Weis, K., de Souza, N., Picotti, P.
Published in: Molecular Systems Biology 2026
DOI: 10.1038/s44320-025-00182-6
Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes
Authors: Jovanovic, A., Bright, F.K., Sadeghi, A., Wicki, B., Caño Muñiz, S.E., Giannini, G.C., Toprak, S., Sauteur, L., Rodoni, A., Wüst, A., Lupien, A., Borrell, S., Grogono, D.M., Wheeler, N.E., Dehio, P., Nemeth, J., Pargger, H., Thomson, R., Bell, S.C., Gagneux, S., Bryant, J.M., Peng, T., Diacon, A.H., Floto, R.A., Abanto, M., Boeck, L.
Published in: Nature Microbiology 2026
DOI: 10.1038/s41564-025-02217-y
Pneumococcal S protein coordinates cell wall modification and repair to resist host antimicrobials
Authors: Burnier, J., Gallay, C., Bruce, K.E., Bjånes, E., Martin, L., Jim, K.K., Tsui, H.T., Cremers, A.J.H., Mignolet, J., Vollmer, D., Biboy, J., Nizet, V., Vollmer, W., Winkler, M.E., Veening, J.W.
Published in: Nature Microbiology 2026
DOI: 10.1038/s41564-025-02184-4
Preprint: 10.1101/2024.11.08.622053
Review articles
Decoding Bistability and Drivers of Phenotypic Variation in Bacteria
Authors: Cámara-Almirón, J., Jaskólska, M., Veening, J.W.
Published in: Annu Rev Microbiol 2026
DOI: 10.1146/annurev-micro-042424-022851
Intracellular Pseudomonas aeruginosa: internalization and survival
Authors: Tejada-Arranz, A., Sunder, V., Basler, M.
Published in: Trends Microbiol 2026
DOI: 10.1016/j.tim.2026.07.004
Book chapters
Preprints
Codon usage determines tRNA-modification requirements for bacterial virulence
Authors: Goormaghtigh Jr, F., Antelo Varela, M., Bumann, D.
Preprint: bioRxiv
Publication date: September 11, 2026
DOI: 10.64898/2026.09.09.750475
A natural glycolipid exposes the outer membrane interface as a tunable regulator of bacterial surface attachment
Authors: Huang, H.-Y., Astorga-Simon, E.N., Adamson, C., Qiao, Y., Navarro, P.P., Persat, A.
Preprint: bioRxiv
Publication date: August 21, 2026
DOI: 10.64898/2026.08.20.745940
A self-regulating dCas9 system enables robust, portable and multiplexed CRISPR interference
Authors: Kaczmarczyk, A., Jenal, U.
Preprint: bioRxiv
Publication date: August 18, 2026
DOI: 10.64898/2026.08.17.745180
Reconstituting Placenta–Embryo Crosstalk in a Microfluidic Chip for Human‑Relevant Developmental Toxicity Studies
Authors: Buerki-Thurnherr, T., Murdeu, M., Wegner, I., Lin, X., Folz, J., Navascués, P., Hierlemann, A., Boos, J.A., Kissling, V.
Preprint: Research Square
Publication date: August 4, 2026
DOI: 10.21203/rs.3.rs-8945339/v1
Staphylococcus aureus Mnh1 cation–proton antiporter promotes phagocytic uptake and intracellular survival in human monocytes
Authors: Iizuka, A., Mazzuoli, M.V., Demirbilek, E., Woischnig, A.-K., Kuehl, R., de Bakker, V., Bumann, D., Zinkernagel, A.S., Veening, J.W., Khanna, N.
Preprint: BioRxiv
Publication date: June 29, 2026
DOI: 10.64898/2026.07.29.730383
Competition against the intestinal microbiota selects for pathoadaptive traits in ESBL E. coli
Authors: Jangir, P.K., Lemos Rocha, L.F., Molari, M., Wenner, N., Fruet, C., Manfredi, P., Flores, C., Sintsova, A., Mouchet, R., Diner, L., Bertola, A., Förster, S., Le, W., Johnson, M., Kunz, M., Rocker, A., Egli, A., Jenal, U., Dehio, C., Bitbol, A., Diard, M.
Preprint: BioRxiv
Publication date: June 29, 2026
DOI: 10.64898/2026.06.25.730905
Stress-adapted codon usage enables efficient virulence-gene expression in Salmonella
Authors: Goormaghtigh, F., Bumann, D.
Preprint: BioRxiv
Publication date: June 18, 2026
DOI: 10.64898/2026.02.22.707322
Pyocyanin disrupts airway regeneration to favor chronic Pseudomonas aeruginosa infection
Authors: Meirelles, L.A., Grigoryan, A., Le Blanc, L., Liaskos, D., Vayena, E., Distler, T., Al-Mayyah, Z., Hatzimanikatis, V., Persat, A.
Preprint: BioRxiv
Publication date: June 18, 2026
DOI: 10.64898/2026.06.15.732350
Epithelial innate immune sensing of pneumococci is inherently restricted to a small cellular minority across species and infection niches
Authors: Minhas, V., de Bakker, V., Jim, K.K., Kurushima, J., Pezoldt, J., Rengifo-Gonzalez, M., Ciolli Mattioli, C., Avraham, R., Deplancke, B., Veening, J.W.
Preprint: BioRxiv
Publication date: June 10, 2026
DOI: 110.64898/2026.06.10.731054
Model-based inference of enzyme inhibitions from perturbation-induced metabolic dynamics
Authors: Liebermeister, W., Pauletti, M., Dorcakova, T., Rahm, C., Zampieri, M.
Preprint: BioRxiv
Publication date: June 3, 2026
DOI: 10.64898/2026.06.01.729220
Persistent Staphylococcus aureus in human musculoskeletal tissues despite targeted antibiotic therapy
Authors: Morin, B., Tripathi, V., Woischnig, A.K., Erdmann, J., Iizuka, A., Baumhoer, D., Rentsch, K., Sauteur, L., Bartoszek, E., Keller, P.M., Jantarug, K., Rivera-Fuentes, P., Hamelin, B., Hosch, S., Mertz, K., Morgenstern, M., Clauss, M., Bumann, D., Kuehl, R., Khanna, N.
Preprint: BioRxiv
Publication date: June 3, 2026
DOI: 10.64898/2026.06.03.728378
Pseudomonas aeruginosa balances cytotoxicity and motility to counter phagocytosis by macrophages
Authors: Distler, T., Tsai, C.-N., Weimann, A., Al-Mayyah, Z., Meirelles, L.A., Floto, R.A., Persat, A.
Preprint: BioRxiv
Publication date: April 3, 2026
DOI: 10.64898/2026.04.02.716043
Lysosomal activation in bladder epithelium enhances intracellular antibiotic clearance of uropathogenic Escherichia coli
Authors: Tomasek, K., Skurvydaite, K., Paduthol, G., Burns, A.M., Schlunke, L., Borgeat, V., Pasquali, C., Romani, M., McKinney, J.D.
Preprint: BioRxiv
Publication date: March 24, 2026
DOI: 10.1101/2025.10.22.683857
Evolved resistance against the type 6 secretion system is toxin specific
Authors: Smith, W., Tejada Arranz, A., Tank, R., Basler, M., Brockhurst, M.
Preprint: BioRxiv
Publication date: March 17, 2026
DOI: 10.64898/2026.03.17.712380v1?ct=
Influence of microbial composition and sample type on antimicrobial resistance in urinary tract infections: a single-centre retrospective cohort study (2015–2023)
Authors: Dubey, A.K., Reyes, J., Rhiner, C., Drescher, K., Dunkel, J., McKinney, J., Egli, A.
Preprint: medRxiv
Publication date: March 02, 2026
DOI: 10.64898/2026.02.23.26344629
A functional genetic landscape of antibiotic sensitivity across the pneumococcal pangenome reveals conserved and lineage-specific vulnerabilities
Authors: Sewgoolam, B., Janssen, A.B., Martin, L.S., Rengifo-Gonzalez, M., de Bakker, V., Rozendal, B., Cremers, A.J.H., Veening, J.W.
Preprint: BioRxiv
Publication date: February 26, 2026
DOI: 10.64898/2026.02.26.708248v1?ct=
Mechanistic basis of teichoic acid transport by a gatekeeper flippase
Authors: Cebrero, G., Chidananda, A.H., Cester, E., Denereaz, J., Demir, E.S., Mathew, A.T., Bhowmik, D.R., de Capitani, M., Reymond, J.-L., Kannan, N., Avci, F., Mehdipour, A.R., Veening, J.-W., Perez, C.
Preprint: BioRxiv
Publication date: February 23, 2026
DOI: 10.64898/2026.02.22.707263v1?ct=
Opposing Range-Dependent Interactions Create Complex Spatial Patterns of Antibiotic Tolerance in Multispecies Biofilms
Authors: Bottacin, G., Raach, B., Fröhlich, L., Künnecke, J., Kaczmarczyk, A., Tejada-Arranz, A., Ugolini, G.S., Stocker, R., Jenal, U., Bumann, D., Dittrich, P.S., Schubert, O.T., van Vliet, S.
Preprint: BioRxiv
Publication date: February 6, 2026
DOI: 10.64898/2026.02.04.703747
Monitoring intracellular antibiotic concentrations in real-time using allosteric biosensors
Authors: Fleckenstein, D., Kaczmarczyk, A., Breitenbach-Netter, N., Rosenberg, G., Jakob, R.P., Sorg, I., Kurmashev, A., Flores, C., Jiménez-Siebert, E., Morris, E., Klimke, S., Tschudin-Sutter, S., Hierlemann, A., Maier, T., Dehio, C., Jenal, U., Drescher, K.
Preprint: BioRxiv
Publication date: February 5, 2026
DOI: 10.64898/2026.02.05.704027
Aeromonas adhesins facilitate kin and non-kin attachment to enable T6SS-mediated antagonism in liquid
Authors: Fridman, C.M., Cohen, H., Keppel, K., Tejada-Arranz, A., Basler, M., Gerlic, M., Salomon, D.
Preprint: BioRxiv
Publication date: January 27, 2026
DOI: 10.64898/2026.01.27.701733
Decoding E. coli’s Gut Survival Strategies: A CRISPRi Approach Across Diets, Inflammatory Environment and Strains
Authors: Maire, A., Tkacz, E., Ortelli, M., Dehio, C., Chassaing, B., Sokol, H., Rolhion, N., Bikard, D.
Preprint: BioRxiv
Publication date: January 5, 2026
DOI: 10.64898/2026.01.05.697630
