Exploring the complexity of infectious disease spread
I’m an infectious disease modeller and group leader of the Quantitative and Predictive Infectious Disease Epidemiology (QUPI) group at the Institute for Infection Prevention and Hospital Epidemiology (IIK) of the Uniklinik Freiburg.
Main research interests
I work on a main topics in the field of infectious diseases
Antibiotic resistance
Resistance to antibiotics forms a threat to patients, as treatment options become fewer, and otherwise treatable infections become potentially life-threatening.
Healthcare networks
Healthcare networks are formed by shared patients between healthcare facilities. Each patient exchange forms a potential transmission route between facilities for healthcare-associated pathogens (such as resistant bacteria).
Nowcasting and forecasting
Up-to-date information on the epidemiology of a disease is crucial during pandemics, epidemics, and local outbreaks. Nowcasting can help create a current situational overview, while forecasting provides an overview of the (near) future
Visualisation of complex data
Infectious disease epidemiology revolves around the analysis of complex, and often dirty, data. Visualising these data in an understandable way is important to understanding disease spread.
Genomic analysis
Genomic Analysis has become an important part of infectious disease epidemiology, allowing for the linking of cases, as well as understanding the wider processes underlying a pathogen’s success.
Evolutionary trajectories
Pathogen evolution can nowadays be closely monitored through whole genome sequencing. The amount of information resulting from these efforts require new approaches to optimally track evolutionary trajectories of pathogens.
Teaching activities
I’ve taught, and teach, multiple courses on infectious diseases, epidemiology, and related topics.
Introduction to infectious disease epidemiology
- Bachelor’ course
- University College Freiburg
Pandemics II
CAS infectious disease epidemiology for WEA healthworkers
- Certificate of advanced studies
- In collaboration with University of Lagos
Publications
The 5 most recent publications:
- MJ Lydeamore, D Wu, T Donker, C Gorrie, CK Higgs, M Easton, et al. Changes in isolation guidelines for CPE patients results in only mild reduction in required hospital beds, Infection, Disease & Health 2024
- MJ Lydeamore, T Donker, D Wu, C Gorrie, A Turner, M Easton, et al. Carbapenemase-producing enterobacterales colonisation status does not lead to more frequent admissions: a linked patient study Antimicrobial Resistance & Infection Control 13 (1), 82, 2024
- T Donker, A Papathanassopoulos, H Ghosh, R Kociurzynski, M Felder, et al. Estimation of SARS-CoV-2 fitness gains from genomic surveillance data without prior lineage classification Proceedings of the National Academy of Sciences 121 (25), e2314262121 2024
- D Pople, T Kypraios, T Donker, N Stoesser, AC Seale, R George, et al. Model-based evaluation of admission screening strategies for the detection and control of carbapenemase-producing Enterobacterales in the English hospital setting BMC medicine 21 (1), 492 2023
- R Kociurzynski, A D’Ambrosio, A Papathanassopoulos, F Bürkin, et al. Forecasting local hospital bed demand for COVID-19 using on-request simulationsScientific Reports 13 (1), 21321 2023
A choice of 5 key publications:
- Donker T, Wallinga J, Grundmann H (2010) Patient Referral Patterns and the Spread of Hospital-Acquired Infections through National Health Care Networks. PLoS Comput Biol 6(3): e1000715. doi:10.1371/journal.pcbi.1000715
- Ciccolini M, Donker T, Grundmann H, Bonten MJM, Woolhouse MEJ. Efficient surveillance for healthcare-associated infections spreading between hospitals. Proceedings of the National Academy of Sciences. 2014 Jan 27;1–6.
- Donker T, Smieszek T, Henderson KL, Johnson AP, Walker AS, Robotham JV. Measuring distance through dense weighted networks: The case of hospital-associated pathogens. PLoS Computational Biology. 2017;13(8):e1005622
- Donker T, The dangers of using large language models for peer review. The Lancet Infectious Diseases 2023;23 (7), 781
- T Donker, A Papathanassopoulos, H Ghosh, R Kociurzynski, M Felder, et al. Estimation of SARS-CoV-2 fitness gains from genomic surveillance data without prior lineage classification Proceedings of the National Academy of Sciences 121 (25), e2314262121 2024
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