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Publications from the Beyond Antibiotics programme, Institute of Biomedical Engineering, University of Oxford

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Publications

  • Böhning, J., Bharat, T.A.M., & Collins, S.M. (2022) Compressed sensing for electron cryotomography and high-resolution subtomogram averaging of biological specimens. Structure 30(3): 408-417.
  • Böhning, J., Graham, M., Letham, S.C., Davis, L.K., Schulze, U., Stansfeld, P.J., Corey, R.A., Pearce, P., Tarafder, A.K. and Bharat, T.A. (2023). Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa. Nature Communications, 14(1), 8429.
  • Böhning, J., Tarafder, A. K., & Bharat, T. A. (2024). The role of filamentous matrix molecules in shaping the architecture and emergent properties of bacterial biofilms. Biochemical Journal, 481(4), 245-263.
  • Campbell, C. K. (2024). Ultrasound-activated agents for the treatment of chronic wound biofilms (Doctoral dissertation, University of Oxford).
  • Campbell, C.K., O’Brien, K., Kosk, D., Rumney, R.M., Glynne-Jones, P., Birkin, P.R., LuTheryn, G.,
  • Webb, J.S., Stride, E., Carugo, D. and Evans, N.D. (2025). Optimising the manufacture of perfluorocarbon nanodroplets through varying sonication parameters. Ultrasonics Sonochemistry, 118, 107332.
  • Caspy, I., Wang, Z., & Bharat, T. A. (2025). Structural biology inside multicellular specimens using electron cryotomography. Quarterly reviews of biophysics, 58, e6.
  • Choi, V., Carugo, D., & Stride, E. Biofilm Drug Delivery: Repurposing Antimicrobials through Ultrasound-Triggered Nanoscale Systems Against Clinical Isolates. npj Antimicrobials and Resistance, 3(1), 22-38.
  • Choi, V., Rohn, J.L., Stoodley, P., Carugo, D. and Stride, E., (2023). Drug delivery strategies for antibiofilm therapy. Nature Reviews Microbiology, 1-18.
  • Chun ALM, Mosayyebi A, Butt A, Carugo D, & Salta M. (2022). Early biofilm and streamer formation is mediated by wall shear stress and surface wettability: A multifactorial microfluidic study. MicrobiologyOpen, 11(4), 1310.  
  • Crowther, A., LuTheryn, G., Garcia-Maset, R., Parhizkar, M., Sutton, J. M., Hind, C., & Carugo, D. (2025). Efficacy of nitric oxide donors and EDTA against Pseudomonas aeruginosa biofilms: Implications for antimicrobial therapy in chronic wounds. Biofilm, 9, 100280.
  • De Grandi D, Meghdadi A, LuTheryn G, & Carugo D. (2022). Facile production of quercetin nanoparticles using 3D printed centrifugal flow reactors. RSC Advances, 2, 696-713.  
  • Doukkali A.L., Lorenzi, T., Parcell, BJ, Rohn, J.L. and Bowness, R., (2023). A hybrid individual-based mathematical model to study bladder infections. Frontiers in Applied Mathematics and Statistics, 9. 
  • Esser, T.K., Böhning, J., Fremdling, P., Bharat, T., Gault, J., & Rauschenbach, S. (2022). Cryo-EM samples of gas-phase purified protein assemblies using native electrospray ion-beam deposition. Faraday Discuss 240(0): 67-80.
  • Flores, C. and Rohn, J. L. (2025). Bacterial adhesion strategies and countermeasures in urinary tract infection. Nature microbiology, 10(3), 627-645.
  • Flores, C., Ling, J., Loh, A., Maset, R.G., Aw, A., White, I.J., Fernando, R. and Rohn, J.L., (2023). A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and asymptomatic bacteria. bioRxiv, 2023-06.
  • Garcia-Maset, R., Chu, V., Yuen, N., Blumgart, D., Yoon, J., Murray, B. O., Joseph, A.A., and Rohn, J. L. (2025). Effect of host microenvironment and bacterial lifestyles on antimicrobial sensitivity and implications for susceptibility testing. npj Antimicrobials and Resistance, 3(1), 42.
  • Guyon, R., Bau, L., Reinke, S., Hill, A., Stride, E., Sims, L., Truby, A. and Milicic, A. (2024). Injectable core-shell microcapsules deliver prime-boost immunisation against malaria in a single shot.
  • Guyon, R., Reinke, S., Truby, A., Sims, L., Hill, A.V., Bau, L., Stride, E. and Milicic, A. (2025). Core-shell microcapsules compatible with routine injection enable prime/boost immunization against malaria with a single shot. Science translational medicine, 17(804), eadw2256.
  • Hammond, F., Pearson, C., Araujo, E. B. N., & Powrie, F. (2025). P51 Enrichment of drug resistant Klebsiella pneumoniae in the gut following antibiotics alters the colonic immune landscape. JAC-Antimicrobial Resistance, 7(Supplement_4), dlaf230-058.
  • He, Y.; Grandi, D.D.; Chandradoss, S.; LuTheryn, G.; Cidonio, G.; Nunes Bastos, R.; Pereno, V.; Carugo, D., (2023). Rapid Production of Nanoscale Liposomes Using a 3D-Printed Reactor-In-A-Centrifuge: Formulation, Characterisation, and Super-Resolution Imaging. Micromachines,14, 1763. 
  • Herdman, M., von Kügelgen, A., Kureisaite-Ciziene, D., Duman, R., El Omari, K., Garman, E.F., Kjaer, A., Kolokouris, D., Löwe, J., Wagner, A. and Stansfeld, P.J. (2022). High-resolution mapping of metal ions reveals principles of surface layer assembly in Caulobacter crescentus cells. Structure, 30(2), 215-228.
  • Jafari, N.V. and J. L. Rohn (2022). The urothelium: a multi-faceted barrier against a harsh environment, Mucosal Immunology 15(6):1127-1142.
  • Jafari, N.V. and J.L. Rohn, (2023). An immunoresponsive three-dimensional urine-tolerant human urothelial (3D-UHU) model to study urinary tract infection. Frontiers in Infection Cell Microbiology, 13, 269.10.3389/FCIMB.2023.1128132.
  • Keller, S., LuTheryn, G., Gray, M., Lyons, B., Cleveland, R.O., Stride, E., and Coussios, C.C., (2024). Quantitative evaluation of anti-biofilm cavitation activity seeded from microbubbles or protein cavitation nuclei by passive acoustic mapping. Physics in Medicine & Biology, 69: 215008
  • Krause, S., Gfrerer, S., von Kügelgen, A., Reuse, C., Dombrowski, N., Villanueva, L., Bunk, B., Spröer, C., Neu, T.R., Kuhlicke, U., Schmidt-Hohagen, K., Hiller, K., Bharat, T.A.M., Rachel, R., Spang, A., and Gescher, J. (2022). The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host. Nature Communications 13(1): 1735.  
  • LuTheryn, G., Hind, C., Campbell, C., Crowther, A., Wu, Q., Keller, S.B., Glynne-Jones, P., Sutton, J.M., Webb, J.S., Gray, M. Wilks, S.A., Stride, E., Carugo, D., (2022). Bactericidal and anti-biofilm effects of uncharged and cationic ultrasound-responsive nitric oxide microbubbles on Pseudomonas aeruginosa biofilms. Frontiers in Cellular and Infection Microbiology, 12: 956808.
  • LuTheryn, G., Ho, E.M., Choi, V. & Carugo, D., (2023). Cationic Microbubbles for Non-Selective Binding of Cavitation Nuclei to Bacterial Biofilms. Pharmaceutics, 15(5), 1495.
  • Marcotulli, M., Barbetta, A., Scarpa, E., Bini, F., Marinozzi, F., Ruocco, G., Casciola, C.M., Scognamiglio, C., Carugo, D. and Cidonio, G. (2024). Jingle cell rock: steering cellular activity with low-intensity pulsed ultrasound (LIPUS) to engineer functional tissues in regenerative medicine. Ultrasound in medicine & biology, 50(12), 1973-1986.
  • Maset, R. G., Crowther, A., Chu, V., Di Grande, D., Jariah, R. O., Yoon, J., Blumgart, D., Hodek, M.A., Yuen, N., Murray, B.O., Pasquina-Lemonche, L., and Rohn, J. L. (2025). Effect of human urinary microenvironment and fluid flow on antibiotic and phage therapy efficacy against uropathogenic Escherichia coli. bioRxiv, 2025-11.
  • Morris C.J., Rohn, J. L., Glickman, S., & Mansfield K.J., (2023). Effective treatments of UTI – Is intravesical therapy the future? Pathogens,12(3), 417.
  • Murray, B.O., Flores, C., Williams, C., Flusberg, D.A., Marr, E.E, Kwiatkowska, K.M., Charest, J.L., Isenberg, B.C., & Rohn, J.L., (2021).  Recurrent urinary tract infection: a mystery in search of better model system. Frontiers in Cellular and Infection Microbiology, 1, 691210. 
  • Ochner, H., Böhning, J., Wang, Z., Tarafder, A. K., Caspy, I., & Bharat, T. A. (2024). Structure of the Pseudomonas aeruginosa PAO1 Type IV pilus. PLoS pathogens, 20(12), e1012773.
  • Ochner, H., Isbilir, B., Blasche, S., Scheidweiler, D., Zhang, Y., Wang, Z., Smith, T., Franco, C., Bradley, R., Patil, K.R. and Bharat, T. A. (2025). Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging. bioRxiv, 2025-08.
  • Piedad, J. C. P., & Yang, B. (2025). Sublingual MV140 vaccine: a promising noninvasive approach for recurrent urinary tract infections in women. Future Microbiology, 20(7-9), 513-521.
  • Plazonic, F., LuTheryn, G., Hind, C., Clifford, M., Gray, M., Stride, E., Glynne-Jones, P., Hill, M., Sutton, J.M. & Carugo, D., (2022). Bactericidal effect of ultrasound-responsive microbubbles and sub-inhibitory gentamicin against Pseudomonas aeruginosa biofilms on substrates with differing acoustic impedance. Ultrasound in Medicine & Biology, 48(9): 1888-1898.
  • Recino, A., Rayner, M. L., Rohn, J. L., Della Pasqua, O., Carter, B., Cupani, A., Dahlmann-Noor, A., Foltynie, T., Furman, J., Hobbiger, S. and Lugarà, E. and Spingardi, P. (2025). Therapeutic innovation in drug repurposing: challenges and opportunities. Drug Discovery Today, 30(7), 104390.
  • Sathiananthamoorthy, S., Florman, F., Richard, D., Cheng, K.K., Torri, V., McCaig, F., Harber. M., & Rohn, J.L., (2023). Application of various techniques to gain insights into the complex urinary tract microbial communities of renal transplant recipients. Transplantation Direct, 69(2),1418.
  • Smith, O. E., & Bharat, T. A. (2024). Architectural dissection of adhesive bacterial cell surface appendages from a “molecular machines” viewpoint. Journal of Bacteriology, 206(12), e00290-24.
  • Teng, G., Cleveland, R., Keller, S., & Stride, E., Characterization and rapid identification of bacteria using polarized multi-spectral imaging, Light: Science & Applications (under review). 
    von Kügelgen, A., van Dorst, S., Alva, V., & Bharat, T.A.M. (2022). A multidomain connector links the outer membrane and cell wall in phylogenetically deep-branching bacteria. Proceedings of the National Academy of Science USA, 119(33): 6119  
  • Wang, Z., & Bharat, T. A. (2024). Serial lift-out for in situ structural biology of multicellular specimens. nature methods, 21(9), 1587-1588.
  • Wright, J., Logan, K., McKaig, T., Kamila, S., McClenaghan, C., Nesbitt, H., Taylor, M.A., Love, M., Stride, E., Ruan, J.L., McHale, A.P. and Callan, J.F. (2025). Paclitaxel and rose bengal loaded microbubbles for the ultrasound targeted chemo-sonodynamic therapy of pancreatic cancer. European Journal of Pharmaceutics and Biopharmaceutics, 114937.
  • Wu, Q., Choi, V., Bau, L., Carugo, D., Evans, N. D., & Stride, E. (2024). Investigation of Ultrasound Mediated Extravasation of a Model Drug by Perfluorobutane Nanodroplets. Ultrasound in Medicine & Biology, 50(10), 1573-1584.
  • Wu, Q., Gray, M. D., Smith, C. A., Bau, L., Coussios, C. C., Cleveland, R. O., & Stride, E. P. (2026). Subharmonics are not an infallible safety metric for cavitation dynamics. International Journal of Hyperthermia, 43(1), 2620728.
  • Wu, Q., Gray, M., Smith, C. A., Bau, L., Cleveland, R. O., Coussios, C., & Stride, E. (2024). Challenges in classifying cavitation: Correlating high-speed optical imaging and passive acoustic mapping of cavitation dynamics. The Journal of the Acoustical Society of America, 156(5), 3608-3620.
    Wu, Q., Gray, M., Smith, C., Bau, L., Coussios, C., & Stride, E. P. (2022). Correlating high-speed optical imaging and passive acoustic mapping of cavitation dynamics. The Journal of the Acoustical Society of America, 151(4), 174.
  • Yang, B., Lavigne, A., Carugo, D., Turney, B., Somani, B., & Stride, E. (2024). Mitigating infections in implantable urological continence devices: risks, challenges, solutions, and future innovations. A comprehensive literature review. Current Opinion in Urology, 34(6), 495-508.
  • Yuen, N., Maset, R. G., Wang, W., Kubal, M., Chen, Z., Chu, V., White, I.J., Gao, J., Torelli, F., Crowther, A., Pasquina-Lemonche, L., and Rohn, J. L. (2026). Gut-relevant short-chain fatty acids modulate host-pathogen dynamics of uropathogenic Escherichia coli at the colonic epithelial interface. bioRxiv, 2026-01.