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The Clinical Biofilm Group is associated with the Dept. of Clinical Microbiology, Odense University Hospital and focuses on translating clinical and experimental research to new treatment regimens, diagnostic assays, and medical devices in collaboration with hospital departments and companies. We moreover investigate host-pathogen interactions using innovative, in-house established in vitro cell culture models and animal infection models.

   photo employees 


Thomas Emil Andersen, assoc. prof., MSc,  PhD
Rune Micha Pedersen, clin. assoc. prof., MD, PhD, department specialist
Kristian Stærk, MD, PhD, postdoc
Katrine Pilely, MSc, PhD, postdoc
Jens Sivkær Pettersen, MSc, PhD, postdoc
Line Lundegård Bang, MSc, biomedical laboratory scientist
Ditte Tornby, MSc, PhD student
Jannie Søvsø Hjelmager, MSc, research assistant
Julie May Jensen, animal technician
Benjamin John Veggerskilde Buch, BSc student

Interested in urinary tract infection? See our homepage on this topic here (Danish)

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Research focus

Biofilm-related infections continue to be a major problem at hospitals. Bacteria and fungi are efficient colonizers of implants and indwelling medical devices, which leads to failure of device function and compromised patient treatment. In addition, pathogenic organisms may use biofilm growth as a means of surviving host response in the body’s inner cavities, facilitating invasion and systemic infection.

The research conducted at the Clinical Biofilm Group at the Dept. of Clinical Microbiology, Odense University Hospital, is based on innovative in vitro infection models intended to reproduce keys steps of pathogenesis. Liquid flow-assisted infection models are utilized to create accurate physiological hydrodynamic conditions and to obtain a controlled physicochemical micromilieu that simulates specific infection sites.

To assist the in vitro model research, the group has at its disposal various animal infection models, developed in collaboration with local hospital departments. The combined experimental platform enables detailed studies of infection pathogenesis and functions as a test platform for the development of novel antimicrobials and biocompatible medical devices. 

Our research platform also includes experimental research in SARS-CoV-2 where we, under BSL-3 approved facilities, utilize our experience in cell-culture based infection modelling.

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Ongoing projects

In this project, funded by the European Union and The Innovation Fund Denmark, we collaborate with the Danish Fundamental Metrology Institute, the Danish company LightNovo and the Lithuanian company Standa to develop a miniaturized Raman spectrometer for identification of bacterial infections in wounds. Wound infection is a considerable risk factor especially after surgical procedures and in immune-compromized patients. Fast and reliable identification of pathogenic bacteria in wounds is therefore of utmost importance. This project aims to build a handheld Raman instrument that enables immediate detection of infections in wounds, using novel miniaturized Raman technology coupled with machine learning software.

The project is supported by the EU EUREKA - Eurostars Programme and runs from March 2023 to August 2025.

TELEGRAFT is a multi-disciplinary project involving 10 international partners from, Germany, Lithuania, Portugal, Spain, Sweden, and Denmark. Launched in late 2022, the project aims to develop a novel tissue- and blood compatible vascular graft for dialysis. Our tasks in this project are to co-develop antibacterial and tissue-integration properties of the graft, and assist the development of an integrated Raman sensor. Read more about the project here.

The project is supported with 4.8M€ by the European Union and runs until Dec. 2027.

In the project we analyze the viral load and virus neutralization capacity in COVID-19 hospitalized patients as well as in citizens. To do so, we have established one of DK’s only SARS-CoV-2 experimental laboratories at the facilities of Winsløwparken, Odense, DK. Here, patient/citizen samples are cultured, and viral load and neutralization capacity estimated based on plaque assays and plaque reduction neutralisation tests. Throughout 2020-2023 we have analyzed more than 600 patient samples and assisted the assessment of whether contagious virus is present in these persons. In 2021-23, our focus has been assessments of the effect of the COVID-19 vaccines on neutralization capacity in vulnerable patient groups such as kidney- and cancer patients. Lastly, we have investigated the protection provided by the vaccines in healthy individuals against emerging SARS-CoV-2 variants.

During 2020-2023 the project has been funded by the Novo Nordisk Foundation, the Region of Southern Denmark, and the Danish Ministry og Higher Education and Science. 

In this EU-funded project we collaborate with the SDU-spinoff GlyProVac (DK), Fraunhofer (DE) og Epitopic GmbH (DE) to develop and perform pre-clinical tests of a novel vaccine candidate against recurrent urinary tract infection. Preclinical evaluation is performed in our porcine UTI model. 

The project is supported by the EU EUREKA - Eurostars Programme and runs until March 2024.

This project aims to elucidate the pathogenesis associated with Clostridium difficile intestinal infection. This organism is a major problem at hospitals worldwide, due to its resistance towards many antibiotics. Patients treated with antibiotics often lose their normal intestinal flora, leaving ideal conditions for C. diff. As a consequence, patients may become chronically infected with C. diff., resulting in significant morbidity among these patients. Using the in vitro intestinal infection models developed by the Clinical Biofilm Group, the colonization mechanisms by C. diff. are investigated and novel treatment regimens are developed and tested.

The project is funded by the MICA foundation and the model development by the SDU Research and Innovation Foundation.


Recently finalized projects

The project utilized the research groups’ flow-chamber based intestinal infection model to assess the colonization efficiency of selected outbreak VRE strains. By doing so, we aimed to assess the hypothesis, that certain outbreak VRE strains are specifically competent in rapid colonization of the human intestine, and that this might explain their uncontrolled spread in hospital departments.

The project was funded by the OUH Research Fund and the Region of Southern Denmark.

A project conducted in cooperation with the Dept. of Urology, Odense University Hospital, the Thrombosis Research Unit, Hospital of Southwest Jutland and the Danish medico company Coloplast A/S. The project was supported by the Region of Southern Denmark and Coloplast A/S and aims to elucidate urinary tract infection pathogenesis in high-risk patient groups.

A cross-disciplinary project in which the Clinical Biofilm Group collaborated with the Danish Fundamental Metrology Institute (DK), BacAlert IVS (DK) and art photonics GmbH (DE) with the common goal of developing next generation technology for fast identification of pathogenic bacteria.

The project was funded by the European Union EUREKA programme.

The project was funded by EU’s Horizon 2020 Eurostars program.

Read BacSens news article in "Ingeniøren" here (in Danish).

See BacSens press release here(in Danish).

Project cooperation with Biomodics ApS (DK) and Venair Iberica SA (ES). Funded by the Horizon 2020 Eurostars Programme. In the project, a novel anti-infection balloon urinary catheter was developed.

The project was funded by European Unions’ Horizon 2020 Eurostars programme.

The project has ended. Main results from the project were recently published.



Heidtmann C, Fejer A, Stærk Kristian, Maria P, Asmussen M, Hertz F, Prabhala BK, Frimodt-Møller N, Klitgaard JK, Andersen TE, Nielsen C, Nielsen P. Hit-to-lead Identification and Validation of a Triaromatic Pleuromutilin Antibiotic Candidate. Accepted in Journal of Medicinal Chemistry.

Ilchenko O, Pilhun Y, Kutsyk A, Slobodianiuk D, Goksel Y, Dumont E, Vaut L, Mazzoni C, Morelli L, Rindzevicius T, Andersen TE, Lassen M, Thomsen BL, Mundhada H, Jendresen CB, Philipsen PA, Hædersdal M, Boisen A. Optics miniaturization strategy for demanding Raman spectroscopy applications. Accepted in Nature Communications.

Beagan ML, Dreyer CH, Jensen LK, Jensen HE, Andersen TE, Overgaard SO, Ding M. The potential of sheep in preclinical models for bone infection research – a systematic review. Accepted in Journal of Orthopaedic Translation.

Riber SS, Clausen LL, Dahl M, Riber LP, Andersen TE, Lindholt JS. Experimental comparative study of a novel drug-eluting arteriovenous graft in a sheep model. Accepted in Frontiers in Cardiovascular Medicine.

Schrøder B, Tentor F, Miclăuș T, Stærk K, Andersen TE, Spinelli M, Rendeli C, Del Popolo G, Bagi P, Nielsen, LF. New micro-hole zone catheter reduces residual urine and mucosal microtrauma in a lower urinary tract model. Sci Rep. 2024, 14, 2268.

Grønnemose RB, Tornby DR, Riber SS, Hjelmager JS, Riber LPS, Lindholt JS, Andersen TE. An antibiotic-loaded silicone-hydrogel interpenetrating polymer network for prevention of surgical site infections. Gels. 2023; 9(10):826.

Kern K, Delaroque N, Boysen A, Puder M, Wendt R, Kölsch A, Ehrentreich-Förster E, Stærk K, Andersen TE, Andersen K, Lund L and Szardenings M. Glycosylation of bacterial antigens changes epitope patterns. Front. Immunol. 2023. 14:1258136.

Stærk K, Schrøder B, Jensen LK, Andersen TE, Nielsen LF. Catheter-associated bladder mucosal trauma during intermittent voiding: an experimental study in pigs. BJUI Compass. 2024;5:217–223.

Rasmussen M, Møller FT, Baig S, Bennedbæk M, Christiansen LE, Cohen AS, Ellegaard K, Fomsgaard A, Franck KT, Gunalan V, Larsen NB, Larsen TG, Lassaunière R, Polacek C, Qvesel AG, Sieber RN,  Rasmussen LD, Stegger M, Spiess K, Tang ME, Vestergaard LS, Andersen TE, Hoegh SV, Pedersen RM, Skov MN, Steinke K, Sydenham TV, Hoppe M, Nielsen L, Krause TG, Ullum H, Jokelainen P. First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023. Eurosurveillance. 2023 Sep 7; 28(36): 2300460.

Stærk K, Jensen, LK, Andersen TE. Evaluation of urine dipstick tests in experimental porcine urinary tract infection with uropathogenic Escherichia coli. Sci Rep 13, 12404 (2023).

Pedersen RM, Bang LL, Holm DK, Madsen LW, Johansen IS, Jensen TG, Justesen US, Bistrup C, Andersen TE. Serum Neutralization of Omicron XBB.1.5 in Kidney Transplant Recipients After Bivalent mRNA Booster Vaccination. Kidney International Reports. 2023 May 26;8(8):1665–8. doi: 10.1016/j.ekir.2023.05.020.

Ehmsen S, Pedersen RM, Bang LL, Asmussen A, Kragh A, Holm DK, Sydenham TV, Jensen TG, Jeppesen SS, Frederiksen H, Andersen TE, Ditzel HJ. BQ.1.1, XBB.1, and XBB.1.5 neutralization after bivalent mRNA COVID-19 booster in patients with cancer. Cancer Cell. 2023 Apr 10;41(4):649-650

Stærk K, Langhorn L, Andersen TE. Clean-catching urine from pigs: A method for collecting quality specimens for urinalysis and microbiological culturing in a laboratory environment. Lab Anim. 2023;57(3):293-303

Stærk K, Langhorn L, Palarasah Y, Andersen TE. A method for collecting high numbers of blood samples in standard vacuum tubes from non-heparinized pigs. Lab Anim. 2023;57(3):336-340

Pedersen RM, Bang LL, Tornby DS, et al. Serum Neutralization of Omicron BA.5, BA.2 and BA.1 in Triple Vaccinated Kidney Transplant Recipients. Kidney Int Rep. 2023;8(3):667-671

Stærk K, Grønnemose RB, Palarasah Y, Lund L, Andersen TE. Intracellular Uropathogenic Escherichia coli are undetectable in urinary bladders after oral mecillinam treatment: an experimental study in a pig model of cystitis. Microbial Pathogenesis 2022;173(Pt A):105817.

Pedersen RM, Bang LL, Tornby DS, Madsen LW, Holm DK, Sydenham TV, Johansen IS, Jensen TG, Justesen US, Andersen TE. Omicron BA.5 Neutralization among Vaccine-Boosted Persons with Prior Omicron BA.1/BA.2 Infections. Emerging Infectious Diseases 2022;28(12):10.3201/eid2812.221304.

Thomsen BL, Christensen JB, Usenov I, Grønnemose RB, Andersen TE, Lassen M. Accurate and fast identification of minimally prepared bacteria phenotypes using Raman spectroscopy assisted by machine learning. Scientific Reports 2022;12(1):16436.

Tentor F, Schrøder BG, Nielsen S, Schertiger L, Stærk K, Andersen TE, Bagi P, Nielsen LF. Development of an ex-vivo porcine lower urinary tract model to evaluate the performance of urinary catheters. Scientific Reports 2022;12:17818.

García V, Stærk K, Alobaidallah MSA, Grønnemose RB, Guerra PR, Andersen TE, Olsen JE, Herrero-Fresno A. Genome-wide analysis of fitness factors in uropathogenic Escherichia coli in a pig UTI model. Microbiological Research. 2022 Sep 15;265:127202.

Pedersen RM, Bang LL, Tornby DS, Kierkegaard H, Nilsson AC, Johansen IS, Sydenham TV, Jensen TG, Justesen US, Bistrup C, Andersen TE*. Neutralization of SARS-CoV-2 Omicron and Delta variants in relation to vaccine-induced antibody levels in kidney transplant recipients and healthy controls. Microbiology Spectrum. 2022 Sep 28;e0131422.

Stærk K, Hjelmager JS, Alm M, Thomsen P, Andersen TE. A new catheter-integrated drug-delivery system for controlled intravesical Mitomycin C release. Urologic Oncology. 2022 Jun 23:S1078-1439(22)00193-4.

Pedersen RM, Bang LL, Madsen LW, Sydenham TV, Johansen IS, Jensen TG, Justesen US, Andersen TE. Serum Neutralization of SARS-CoV-2 Omicron BA.1 and BA.2 after BNT162b2 Booster Vaccination. Emerging Infectious Diseases. 2022;28:1274-1275.

Stærk KS, Andersen MØ, Andersen TE. Uropathogenic Escherichia coli can cause cystitis at extremely low inocula in a pig model. J. Med. Microbiol. 2022;71(4). doi: 10.1099/jmm.0.001537.

Torres-Puiga S, García V, Stærk K, Andersen TE, Møller-Jensen J, Olsen JE, Herrero-Fresno A. 'Omics'-technologies -What have they told us about Uropathogenic Escherichia coli fitness and virulence during urinary tract infection? Frontiers in Cellular and Infection Microbiology. 2022;12:824039.

Guo Y, Contesini F, Wang X, Ghidinelli S, Tornby D, Andersen, TE, Mortensen U, Larsen TO. Biosynthesis of Calipyridone A Represents a Fungal 2-pyridone Formation without Ring Expansion in Aspergillus californicus. Organic Letters. 2022;24(3):804-808.

Pedersen RM, Tornby DS, Bang LL, Madsen LW, Skov MN, Sydenham TV, Steinke K, Jensen TG, Johansen IS, Andersen TE. Rectally shed SARS-CoV-2 in COVID-19 inpatients is consistently lower than respiratory shedding and lacks infectivity. Clin Microbiol Infect. 2022;28(2):304.e1-304.e3.

García V, Grønnemose RB; Torres-Puig S, Kudirkiene E, Piantielli M, Ahmed S, Andersen TE, Møller-Jensen J, Olsen JE, Herrero-fresno A. Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections. Microb Genom. 2021;7(12):000719.

Stærk K, Grønnemose RB, Nielsen TK, Petersen NA, Palarasah Y, Torres-Puig S, Møller-Jensen J, Kolmos HJ, Lund L, Andersen TE. Escherichia coli type-1 fimbriae are critical to overcome initial bottlenecks of infection upon low-dose inoculation in a porcine model of cystitis. Microbiology. 2021;167(10).

Marbjerg L, Stougaard CL, Sørensen S-AG, Thomsen AV, Wang L, Andersen L, Andersen TE, Kallipolitis B and Kemp M. A New Tool for Analyses of Whole Genome Sequences Reveals Dissemination of Specific Strains of Vancomycin-Resistant Enterococcus faecium in a Hospital. Front. Med. 2021; 8:733676. doi: 10.3389/fmed.2021.733676.

Pedersen RM, Bang LL, Tornby DS, Kierkegaard H, Nilsson AC, Johansen IS, Bistrup C, Jensen TG, Justesen US, Andersen TE. The SARS-CoV-2-neutralizing capacity of kidney transplant recipients 4 weeks after receiving a second dose of the BNT162b2 vaccine. Kidney International. 2021;100:1129-1131.

Trink J, Li R, Palarasah Y, Troyanov S, Andersen TE, Sidelmann JJ, Inman MD, Pizzo SV, Gao B, Krepinsky JC. Activated alpha 2-macroglobulin is a novel mediator of mesangial cell profibrotic signaling in diabetic kidney disease. Biomedicines 2021, 9(9), 1112.

Pedersen RM, Tornby DS, Bistrup C, Johansen IS, Andersen TE, Justesen US. Negative SARS-CoV-2 antibodies, T-cell response and virus neutralization following full vaccination in a renal transplant recipient: a call for vigilance. Clin Microbiol Infect. 2021:S1198-743X(21)00290-1.

Pedersen RM, Tornby DS., Bang LL, Madsen LW, Skov MN, Jensen TG, Johansen IS, Andersen TE. Rectally shed SARS-CoV-2 lacks infectivity: time to rethink faecal–oral transmission? Nature Reviews Gastroenterology and Hepatology. 18, 669 (2021).


Last Updated 06.12.2023