infectious disease dynamics; mathematical models; antibiotic resistance; experimental evolution; contact networks
Igler Claudia, Huisman Jana S., Siedentop Berit, Bonhoeffer Sebastian, Lehtinen Sonja (2022), Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics, in Philosophical Transactions of the Royal Society B: Biological Sciences
, 377(1842), 20200478.
Pires João, Huisman Jana S, Bonhoeffer Sebastian, Van Boeckel Thomas P (2021), Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases, in Journal of Antimicrobial Chemotherapy
Bakkeren Erik, Herter Joana Anuschka, Huisman Jana Sanne, Steiger Yves, Gül Ersin, Newson Joshua Patrick Mark, Brachmann Alexander Oliver, Piel Jörn, Regoes Roland, Bonhoeffer Sebastian, Diard Médéric, Hardt Wolf-Dietrich (2021), Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut, in eLife
, 10, e69744.
Pires João, Huisman Jana S., Bonhoeffer Sebastian, Van Boeckel Thomas P. (2021), Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases, in Microbiology Spectrum
, 9(2), e00495-21.
Uecker Hildegard, Bonhoeffer Sebastian (2021), Antibiotic treatment protocols revisited: the challenges of a conclusive assessment by mathematical modelling, in Journal of The Royal Society Interface
, 18(181), 20210308-20210308.
Lehtinen Sonja, Huisman Jana S., Bonhoeffer Sebastian (2021), Evolutionary mechanisms that determine which bacterial genes are carried on plasmids, in Evolution Letters
, 5(3), 290-301.
Angst Daniel C., Tepekule Burcu, Sun Lei, Bogos Balázs, Bonhoeffer Sebastian (2021), Comparing treatment strategies to reduce antibiotic resistance in an in vitro epidemiological setting, in Proceedings of the National Academy of Sciences
, 118(13), e202346711-e202346711.
Benz Fabienne, Huisman Jana S., Bakkeren Erik, Herter Joana A., Stadler Tanja, Ackermann Martin, Diard Médéric, Egli Adrian, Hall Alex R., Hardt Wolf-Dietrich, Bonhoeffer Sebastian (2021), Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo, in The ISME Journal
, 15(3), 862-878.
Witzany Christopher, Bonhoeffer Sebastian, Rolff Jens (2020), Is antimicrobial resistance evolution accelerating?, in PLOS Pathogens
, 16(10), e1008905-e1008905.
Sun Lei, Ashcroft Peter, Ackermann Martin, Bonhoeffer Sebastian (2020), Stochastic Gene Expression Influences the Selection of Antibiotic Resistance Mutations, in Molecular Biology and Evolution
, 37(1), 58-70.
Tepekule Burcu, Abel zur Wiesch Pia, Kouyos Roger D., Bonhoeffer Sebastian (2019), Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota, in Proceedings of the National Academy of Sciences
, 116(46), 23106-23116.
Bakkeren Erik, Huisman Jana S., Fattinger Stefan A., Hausmann Annika, Furter Markus, Egli Adrian, Slack Emma, Sellin Mikael E., Bonhoeffer Sebastian, Regoes Roland R., Diard Médéric, Hardt Wolf-Dietrich (2019), Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut, in Nature
, 573(7773), 276-280.
Frenoy Antoine, Bonhoeffer Sebastian (2018), Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria, in PLOS Biology
, 16(5), e2005056-e2005056.
Data from "Comparing treatment strategies to reduce antibiotic resistance in an in vitro epidemiological setting"
|Persistent Identifier (PID)
Data and analysis code pertaining to https://www.pnas.org/content/118/13/e2023467118
This is a request for a continuation of grant Nr 155866 under the Bonus of Excellence scheme. The work plan is divided into two parts. Part A makes use of our previously developed software package EndemicPy to simulate diseases spread on the basis of field data of contacts in a wild house mouse population and investigates the social contact structure in that population. Part B builds on the developed robotic liquid handling platform and associated software to investigate the effect of different treatment strategies on the emergence of antibiotic resistance and investigates the conditions selecting for the location of antibiotic resistance genes on plasmids versus chromosomes.