Resistance evolution in microbial communities
Anti-resistance strategies
Research
The evolution of antimicrobial resistance is strongly reducing our options for antimicrobial treatment, both in agriculture, industry and medicine. At the same time regulatory demands on microbial safety, waste water limitation, and biocides have never been so strict. We urgently need new antimicrobial strategies, therefore, but most importantly we need strategies where the evolution of resistance is less rapid.
Most current antimicrobials have been designed to act against free-living bacteria. Over the last decades it became clear, however, that microbes commonly live together in dense and genetically-diverse communities. If these communities are surface-associated and embedded in a self-produced slime-layer they are generally called biofilms. Microbial communities often show a strongly increased tolerance against antimicrobials. New antimicrobial strategies, therefore, should take this community mode-of-life into account.
The MICA Lab studies microbial community behaviour and develops antimicrobials targeting communities. Our main goal is to obtain a better understanding of social interaction in microbial communities, resistance development in communities and methodologies to monitor communities in situ. This should allow us to develop novel types of antimicrobials that interfere with social interactions (socio-active strategies), resistance development (anti-resistance strategies) or take benefit of improved monitoring (observation-guided strategies). To support this research, we have set up an integrated development platform for antimicrobial compounds.
Resistance evolution
We aim to understand how resistance development in microbial communities differs from resistance development in isolated, free-living microbes. Our recent experiments indeed indicate that different aspects of the microbial community mode-of-life can promote the evolution of resistance against conventional antimicrobials. This demonstrates the potential of 'anti-resistance strategies' that interfere with community behaviour to enhance the longevity of conventional antibiotics. Our current research mainly focuses on resistance development in Salmonella biofilms, in brewery biofilms and biofilms on orthopedic implants and catheters.
Publications
- Brepoels, P., Appermans, K., Perez-Romero, C.A., Lories, B., Marchal, K., Steenackers, H.P. with Steenackers, H.P. (corresp. author) (2022). Antibiotic Cycling Affects Resistance Evolution Independently of Collateral Sensitivity. Molecular Biology and Evolution, 39 (12), Art.No. ARTN msac257. doi: 10.1093/molbev/msac257
- Dieltjens, L., Appermans, K., Lissens, M., Lories, B., Kim, W., Van der Eycken, E., Foster, K., Steenackers, H. (2020). Inhibiting bacterial cooperation is an evolutionarily robust anti-biofilm strategy. Nature Communications, 11 (1), 107. doi: 10.1038/s41467-019-13660-x Open Access
- Steenackers, H., Parijs, I., Foster, K., Vanderleyden, J. (2016). Experimental Evolution in Biofilm Populations. FEMS Microbiology Reviews, 40(3), 373-397. doi: 10.1093/femsre/fuw002
- Roberfroid, S., Vanderleyden, J., Steenackers, H. (2016). Gene expression variability in clonal populations: causes and consequences. Critical Reviews in Microbiology, 42 (6), 969-984. doi: 10.3109/1040841X.2015.1122571
- Pulido-Tamayo, S., Sánchez-Rodríguez, A., Swings, T., Van den Bergh, B., Dubey, A., Steenackers, H., Michiels, J., Fostier, J., Marchal, K. (2015). Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations. Nucleic Acids Research, 43 (16), e105. doi: 10.1093/nar/gkv478
In situ monitoring of microbial communities
Observation-guided strategies
In situ monitoring
The tolerance of a particular biofilm to antimicrobial treatment is highly dependent on its specific structure. Hence, rapid detection of biofilms and accurate monitoring of the biofilm structure, thereby predicting its tolerance to antimicrobial treatment, is of utmost importance. Today, however, no technologies exist that allow for in depth in situ biofilm characterization. In collaboration with several research partners, we aim to develop a novel sensor technology, based on impedance measurement by microelectrode arrays, that allows for in situ biofilm monitoring and prediction of its susceptibility to different types of antimicrobials.
Publications
- Shastry, A., Villanueva, X., Steenackers, H., Cnudde, V., Robles, E., Boone, M.N. (2020). Study on the Effect of Contrast Agent on Biofilms and Their Visualization in Porous Substrate Using X-ray mu CT. Applied Sciences-Basel, 10 (16), 5435. doi: 10.3390/app10165435 Open Access
- Maes, S., Vackier, T., Nguyen Huu, S., Heyndrickx, M., Steenackers, H., Sampers, I., Raes, K., Verplaetse, A., De Reu, K. (2019). Occurrence and characterization of biofilms in drinking water systems of broiler houses. BMC Microbiology, 19 (77). doi: 10.1186/s12866-019-1451-5 Open Access
- Maes, S., Heyndrickx, M., Vackier, T., Steenackers, H., Verplaetse, A., De Reu, K. (2019). Identification and Spoilage Potential of the Remaining Dominant Microbiota on Food Contact Surfaces after Cleaning and Disinfection in Different Food Industries. Journal of Food Protection, 82 (2), 262-275. doi: 10.4315/0362-028X.JFP-18-226 Open Access
- Goikoetxea, E., Routkevitch, D., De Weerdt, A., Green, J., Steenackers, H., Braeken, D. (2018). Impedimetric fingerprinting and structural analysis of isogenic E. coli biofilms using multielectrode arrays. Sensors And Actuators B: Chemical, 263, 319-326. doi: 10.1016/j.snb.2018.01.188 Open Access
Development platform for antimicrobial compounds
To support the above described research lines, the MICA Lab is coordinating an interdisciplinary platform for the development of antimicrobials, which is based on several collaborations with research groups within and outside the KU Leuven. This platform includes in silico and in vitro screening of antimicrobial agents, chemical synthesis and structure-activity-relationship studies, mode of action studies and evaluation of resistance development, and design of combination therapies and delivery strategies. More detailed information on this platform can be found here.
Publications
Chemical synthesis and in vitro screenings of anti-biofilm compounds
- Villanueva, X., Zhen, L., Ares, J.N., Vackier, T., Lange, H., Crestini, C., Steenackers, H.P. (2023). Effect of chemical modifications of tannins on their antimicrobial and antibiofilm effect against Gram-negative and Gram-positive bacteria. Front Microbiol 13:987164. doi:10.3389/fmicb.2022.987164
- Idir, F., Van Ginneken, S., Coppola, G.A., Grenier, D., Steenackers, H.P., Bendali, F. Origanum vulgare ethanolic extracts as a promising source of compounds with antimicrobial, anti-biofilm, and anti-virulence activity against dental plaque bacteria. Frontiers in Microbiology 13, (2022). doi:10.3389/fmicb.2022.999839
- Lissens, M., Joos, M., Lories, B., Steenackers, H.P. (2022). Evolution-proof inhibitors of public good cooperation: a screening strategy inspired by social evolution theory. FEMS Microbiology Reviews (Online ahead of print). doi: 10.1093/femsre/fuac019
- Jacobs, L., Meesters, J., Parijs, I., Hooyberghs, G., Van der Eycken, E.V., Lories, B., Steenackers, H.P. (2021). 2-Aminoimidazoles as potent inhibitors of contaminating brewery biofilms. Biofouling, 37 (1), 61-77. doi: 10.1080/08927014.2021.1874366 Open Access
- Pertusati, F., Pileggi, E., Richards, J., Wootton, M., Van Leemputte, T., Persoons, L., De Coster, D., Villanueva, X., Daelemans, D., Steenackers, H., McGuigan, C., Serpi, M. (2020). Drug repurposing: phosphate prodrugs of anticancer and antiviral FDA-approved nucleosides as novel antimicrobials. Journal of Antimicrobial Chemotherapy, 75 (10), 2864-2878. doi: 10.1093/jac/dkaa268 Open Access
- Lories, B., Belpaire, T., Yssel, A., Ramon, H., Steenackers, H. (2020). Agaric acid reduces Salmonella biofilm formation by inhibiting flagellar motility. Biofilm, 2, 100022. doi: 10.1016/j.bioflm.2020.100022 Open Access
- Trang, T.T T., Dieltjens, L., Hooyberghs, G., Waldrant, K., Ermolat'ev, D., Van der Eycken, E., Steenackers, H. (2018). Enhancing the anti-biofilm activity of 5-aryl-2-aminoimidazoles through nature inspired dimerisation. Bioorganic & Medicinal Chemistry, 26 (8), 1470-1480. doi: 10.1016/j.bmc.2018.01.005
- Gill, R.K., Kumar, V., Robijns, S.C A., Steenackers, H.P L., Van der Eycken, E., Bariwal, J. (2017). Polysubstituted 2-aminoimidazoles as anti-biofilm and antiproliferative agents: Discovery of potent lead. European Journal of Medicinal Chemistry, 138, 152-169. doi: 10.1016/j.ejmech.2017.06.043 Open Access
- Yssel, A., Vanderleyden, J., Steenackers, H. (2017). Repurposing of nucleoside- and nuclebase-derivative drugs as antibiotics and biofilm inhibitors. Journal of Antimicrobial Chemotherapy, 72 (8), 2156-2170. doi: 10.1093/jac/dkx151
- Peeters, E., Hooyberghs, G., Robijns, S., Waldrant, K., De Weerdt, A., Delattin, N., Liebens, V., Kucharikova, S., Tournu, H., Verstraeten, N., Dovgan, B., Girandon, L., Fröhlich, M., De Brucker, K., Van Dijck, P., Michiels, J., Cammue, B., Thevissen, K., Vanderleyden, J., Van der Eycken, E., Steenackers, H.P. (2016). Modulation of the substitution pattern of 5-aryl-2-aminoimidazoles allows fine-tuning of their anti-biofilm activity spectrum and toxicity. Antimicrobial Agents and Chemotherapy, 60 (11), 6483-6497. doi: 10.1128/AAC.00035-16
- Mishra, N.M., Briers, Y., Lamberigts, C., Steenackers, H., Robijns, S., Landuyt, B., Vanderleyden, J., Schoofs, L., Lavigne, R., Luyten, W., Van der Eycken, E. (2015). Evaluation of the antibacterial and antibiofilm activities of novel CRAMP-vancomycin conjugates with diverse linkers. Organic & Biomolecular Chemistry, 13 (27), 7477-7486. doi: 10.1039/c5ob00830a
- Liebens, V., Gerits, E., Knapen, W., Swings, T., Beullens, S., Steenackers, H., Robijns, S., Lippell, A., O’Neill, A., Veber, M., Fröhlich, M., Krona, A., Lövenklev, M., Corbau, R., Marchand, A., Chaltin, P., De Brucker, K., Thevissen, K., Cammue, B., Fauvart, M., Verstraeten, N., Michiels, J. (2014). Identification and characterization of an anti-pseudomonal dichlorocarbazol derivative displaying anti-biofilm activity. Bioorganic & Medicinal Chemistry Letters, 24 (23), 5404-5408. doi: 10.1016/j.bmcl.2014.10.039
- Steenackers, H., Dubey, A., Robijns, S., Ermolatev, D., Delattin, N., Dovgan, B., Girandon, L., Fröhlich, M., De Brucker, K., Thevissen, K., Balzarini, J., Van der Eycken, E., Vanderleyden, J. (2014). Evaluation of the toxicity of 5-aryl-2-aminoimidazole-based biofilm inhibitors against eukaryotic cell lines, bone cells and the nematode Caenorhabditis elegans. Molecules, 19 (10), 16707-16723. doi: 10.3390/molecules191016707 Open Access
- De Brucker, K., Delattin, N., Robijns, S., Steenackers, H., Verstraeten, N., Landuyt, B., Luyten, W., Schoofs, L., Dovgan, B., Fröhlich, M., Michiels, J., Vanderleyden, J., Cammue, B., Thevissen, K. (2014). Derivatives of the mouse cathelicidin-related antimicrobial peptide (CRAMP) inhibit fungal and bacterial biofilm formation. Antimicrobial Agents and Chemotherapy, 58 (9), 5395-5404. doi: 10.1128/AAC.03045-14
- Steenackers, H., Ermolat'ev, D., Trang, T.T T., Savalia, B., Sharma, U.K., De Weerdt, A., Shah, A., Vanderleyden, J., Van der Eycken, E. (2014). Microwave-assisted one-pot synthesis and anti-biofilm activity of 2-amino-1H-imidazole/triazole conjugates. Organic & Biomolecular Chemistry, 12 (22), 3671-3678. doi: 10.1039/c3ob42282h
- Robijns, S., De Pauw, B., Loosen, B., Marchand, A., Chaltin, P., De Keersmaecker, S., Vanderleyden, J., Steenackers H. (2012). Identification And Characterization Of 4-[4-(3-Phenyl-2-propen-1-yl)-1-Piperazinyl]-5H-Pyrimido[5,4-B]Indole Derivatives As Salmonella Biofilm Inhibitors. FEMS Immunology and Medical Microbiology, 65 (2), 390-394. doi: 10.1111/j.1574-695X.2012.00973.x Open Access
- Steenackers, H., Ermolat'ev, D., Savaliya, B., De Weerdt, A., De Coster, D., Shah, A., Van der Eycken, E., De Vos, D., Vanderleyden, J., De Keersmaecker, S. (2011). Structure-activity relationship of 2-hydroxy-2-aryl-2,3-dihydro-imidazo[1,2-a]pyrimidinium salts and 2N-substituted 4(5)-aryl-2-amino-1H-imidazoles as inhibitors of biofilm formation by Salmonella Typhimurium and Pseudomonas aeruginosa. Bioorganic & Medicinal Chemistry 19 (11), 3462-3473. doi: 10.1016/j.bmc.2011.04.026
- Steenackers, H., Ermolat'ev, D., Savaliya, B., De Weerdt, A., De Coster, D., Shah, A., De Vos, D., Vanderleyden, J., De Keersmaecker, S., Van der Eycken, E. (2011). Structure-Activity Relationship of 4(5)-Aryl-2-amino-1H-imidazoles, N1-Substituted 2-Aminoimidazoles and Imidazo[1,2-a]pyrimidinium Salts as Inhibitors of Biofilm Formation by Salmonella Typhimurium and Pseudomonas aeruginosa. Journal of Medicinal Chemistry, 54 (2), 472-484. doi: 10.1021/jm1011148
- Ermolat'ev, D., Bariwal, J., Steenackers, H., De Keersmaecker, S., Van der Eycken, E. (2010). Concise and diversity-oriented route toward polysubstituted 2-aminoimidazole alkaloids and their analogues. Angewandte Chemie - International Edition, 49 (49), 9465-9468. doi: 10.1002/anie.201004256
- Steenackers, H., Levin, J., Janssens, J., De Weerdt, A., Balzarini, J., Vanderleyden, J., De Vos, D., De Keersmaecker, S. (2010). Structure-activity relationship of brominated 3-alkyl-5-methylene-2(5H)-furanones and alkylmaleic anhydrides as inhibitors of Salmonella biofilm formation and quorum sensing regulated bioluminescence in Vibrio harveyi. Bioorganic & Medicinal Chemistry, 18 (14), 5224-5233. doi: 10.1016/j.bmc.2010.05.055 Open Access
- Janssens, J., Steenackers, H., Robijns, S., Gellens, E., Levin, J., Zhao, H., Hermans, K., De Coster, D., Verhoeven, T., Marchal, K., Vanderleyden, J., De Vos, D., De Keersmaecker, S. (2008). Brominated furanones inhibit biofilm formation by Salmonella enterica serovar Typhimurium. Applied and Environmental Microbiology, 74 (21), 6639-6648. doi: 10.1128/AEM.01262-08
In silico screenings of anti-biofilm compounds
- Qing, X., De Weerdt, A., De Maeyer, M., Steenackers, H., Voet, A. (2018). Rational design of small molecules that modulate the transcriptional function of the response regulator PhoP. Biochemical and Biophysical Research Communications, 495 (1), 375-381. doi: 10.1016/j.bbrc.2017.11.037
- Qing, X., Steenackers, H., Venken, T., De Maeyer, M., Voet, A. (2017). Computational studies of the active and inactive regulatory domains of response regulator PhoP using molecular dynamics simulations. Molecular Informatics, 36 (11). 10.1002/minf.201700031
Mode of action determination of anti-biofilm compounds
- Lories, B., Belpaire, T., Yssel, A., Ramon, H., Steenackers, H. (2020). Agaric acid reduces Salmonella biofilm formation by inhibiting flagellar motility. Biofilm, 2, 100022. doi: 10.1016/j.bioflm.2020.100022 Open Access
- Robijns, S., Roberfroid, S., Van Puyvelde, S., De Pauw, B., Uceda Santamaría, E., De Weerdt, A., De Coster, D., Hermans, K., De Keersmaecker, S., Vanderleyden, J., Steenackers, H. (2014). A GFP promoter fusion library for the study of Salmonella biofilm formation and the mode of action of biofilm inhibitors. Biofouling, 30 (5), 605-625. doi: 10.1080/08927014.2014.907401
Anti-biofilm coatings
- Mufty, H., Van Den Eynde, J., Meuris, B., Metsemakers, W-J., Van Wijngaerden, E., Vandendriessche, T., Steenackers, H.P., Fourneau, I. (2021). Pre-clinical In Vitro Models of Vascular Graft Coating in the Prevention of Vascular Graft Infection: A Systematic Review. European Journal Of Vascular And Endovascular Surgery, 63 (1), 119-137. doi: 10.1016/j.ejvs.2021.07.015
- Mufty, H., Van den Eynde, J., Steenackers, H.P., Metsemakers, W-J., Meuris, B., Fourneau, I. (2021). A systematic review of preclinical data regarding commercial silver-coated vascular grafts. Journal of Vascular Surgery, 74 (4), 1386-1393. doi: 10.1016/j.jvs.2021.04.055 Open Access
- Coppola, G.A., Onsea, J., Moriarty, T.F., Nehrbass, D., Constant, C., Zeiter, S., Aktan, M.K., Braem, A., Van der Eycken, E.V., Steenackers, H.P., Metsemakers, W-J. (2021). An Improved 2-Aminoimidazole Based Anti-Biofilm Coating for Orthopedic Implants: Activity, Stability, and in vivo Biocompatibility. Frontiers in Microbiology, 12, 658521. doi: 10.3389/fmicb.2021.658521 Open Access
- Mufty, H., Van den Eynde, J., Meuris, B., Metsemakers, W-J., Van Wijngaerden, E., Vandendriessche, T., Steenackers, H.P., Fourneau, I. (2021). Pre-clinical in vivo Models of Vascular Graft Coating in the Prevention of Vascular Graft Infection: A Systematic Review. European Journal of Vascular and Endovascular Surgery, 62 (1), 99-118. doi: 10.1016/j.ejvs.2021.02.054
- Peeters, E., Hooyberghs, G., Robijns, S., De Weerdt, A., Kucharíková, S., Tournu, H., Braem, A., Čeh, K., Majdič, G., Španič, T., Pogorevc, E., Claes, B., Dovgan, B., Girandon, L., Impellizzeri, F., Erdtmann, M., Krona, A., Vleugels, J., Fröhlich, M., Garcia-Forgas, J., De Brucker, K., Cammue, B.P. A., Thevissen, K., Van Dijck, P., Vanderleyden, J., Van der Eycken, E., Steenackers, H.P. (2019). An antibiofilm coating of 5-aryl-2-aminoimidazole covalently attached to a titanium surface. Journal of Biomedical Materials Research Part B: Applied Biomaterials, 107 (6), 1908-1919. doi: 10.1002/jbm.b.34283 Open Access
- Claes, B., Boudewijns, T., Muchez, L., Hooyberghs, G., Van der Eycken, E., Vanderleyden, J., Steenackers, H.P., De Vos, D. (2017). Smart metal-organic framework coatings: triggered anti-biofilm compound release. ACS Applied Materials & Interfaces, 9 (5), 4440-4449. doi: 10.1021/acsami.6b14152
- Gerits, E., Kucharíková, S., Van Dijck, P., Erdtmann, M., Krona, A., Lövenklev, M., Fröhlich, M., Dovgan, B., Impellizzeri, F., Braem, A., Vleugels, J., Robijns, S.C., Steenackers, H.P., Vanderleyden, J., De Brucker, K., Thevissen, K., Cammue, B.P., Fauvart, M., Verstraeten, N., Michiels, J. (2016). Antibacterial activity of a new broad-spectrum antibiotic covalently bound to titanium surfaces. Journal of Orthopaedic Research, 34 (12), 2191-2198. doi: 10.1002/jor.23238 Open Access
Salmonella biofilms as a model system
- Coppens, B., Belpaire, T. E. R., Pešek, J., Steenackers, H. P., Ramon, H., & Smeets, B. (2023). Anomalous diffusion of nanoparticles in the spatially heterogeneous biofilm environment. iScience, 26(6), 106861. https://doi.org/10.1016/j.isci.2023.106861
- Hermans, K., Roberfroid, S., Thijs, I., Kint, G., De Coster, D., Marchal, K., Vanderleyden, J., De Keersmaecker, S., Steenackers, H. (2016). FabR regulates Salmonella biofilm formation via its direct target FabB. BMC Genomics, 17, 253. doi: 10.1186/s12864-016-2387-x Open Access
- Van Assche, E., Van Puyvelde, S., Vanderleyden, J., Steenackers, H. (2015). RNA-binding proteins involved in post-transcriptional regulation in bacteria. Frontiers in Microbiology, 6, 141. doi: 10.3389/fmicb.2015.00141 Open Access
- Van Puyvelde, S., Steenackers, H.P., Vanderleyden, J. (2013). Small RNAs regulating biofilm formation and outer membrane homeostasis. RNA Biology, 10 (2), 185-191. doi: 10.4161/rna.23341
- Steenackers, H., Hermans, K., Vanderleyden, J., De Keersmaecker, S. (2012). Salmonella biofilms: An overview on occurrence, structure, regulation and eradication. Food Research International, 45 (2), 502-531. doi: 10.1016/j.foodres.2011.01.038 Open Access
Screening platform
- In vitro biofilm & toxicity
- In silico: molecular modelling and datamining
Chemical synthesis
- Novel synthesis pathways
- Upscaling
- Immobilization
Mode of action & resistance
- GFP promoter fusions
- Omics approaches
- Experimental evolution
Towards application
- Anti-biofilm coatings
- Delivery (magnetic nanoparticles)
- Combination therapy
- Real life biofilms
Social interactions in microbial communities
Socio-active strategies
Social interactions
We aim to understand how microbes within communities interact with each other. It is increasingly recognized that social interactions between microbes can strongly enhance the tolerance and pathogenicity of communities. Social interactions therefore present an interesting target for novel types of antimicrobials (socio-active strategies), especially because in some cases resistance development is not expected. Our current research mainly focuses on social interactions within bacterial communities containing Salmonella, within contaminating biofilms in breweries and greenhouses and within biofilms on orthopedic implants and urinary catheters.