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Infectious disease dynamics: spread along contact networks and experimental evolution of antibiotic resistance

English title Infectious disease dynamics: spread along contact networks and experimental evolution of antibiotic resistance
Applicant Bonhoeffer Sebastian
Number 176401
Funding scheme Project funding
Research institution Gruppe Theoretische Biologie Departement Umweltsystemwissenschaften ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Ecology
Start/End 01.01.2018 - 31.12.2021
Approved amount 899'278.00
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All Disciplines (2)

Discipline
Ecology
Experimental Microbiology

Keywords (5)

infectious disease dynamics; mathematical models; antibiotic resistance; experimental evolution; contact networks

Lay Summary (German)

Lead
This grant is about infectious disease dynamics. The first part addresses the spread of infectious diseases along heterogeneous and time varying contact networks. The second part addresses the experimental evolution of antibiotic resistance.
Lay summary
Dieses Forschungsgesuch behandelt zentrale Aspekte der Dynamik von Infektionskrankheiten. Der erste Teil ist überwiegend theoretisch und befasst sich mit der Ausbreitung von Infektionskrankheiten über heterogene  und zeitlich veränderliche Kontaktnetzwerke. Der zweite Teil befasst sich mit der experimentellen Evolution von Antibiotika-resistenten Bakterien unter epidemiologisch realistischen Populationsdynamiken.
Direct link to Lay Summary Last update: 06.11.2017

Responsible applicant and co-applicants

Employees

Publications

Publication
Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics
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.
Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases
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, dkab451.
Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut
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.
Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases
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.
Antibiotic treatment protocols revisited: the challenges of a conclusive assessment by mathematical modelling
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.
Evolutionary mechanisms that determine which bacterial genes are carried on plasmids
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.
Comparing treatment strategies to reduce antibiotic resistance in an in vitro epidemiological setting
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.
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo
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.
Is antimicrobial resistance evolution accelerating?
Witzany Christopher, Bonhoeffer Sebastian, Rolff Jens (2020), Is antimicrobial resistance evolution accelerating?, in PLOS Pathogens, 16(10), e1008905-e1008905.
Stochastic Gene Expression Influences the Selection of Antibiotic Resistance Mutations
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.
Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota
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.
Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut
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.
Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria
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.

Datasets

Data from "Comparing treatment strategies to reduce antibiotic resistance in an in vitro epidemiological setting"

Author Angst, Daniel
Publication date 12.02.2021
Persistent Identifier (PID) 10.5281/zenodo.4537380
Repository Zenodo
Abstract
Data and analysis code pertaining to https://www.pnas.org/content/118/13/e2023467118

Collaboration

Group / person Country
Types of collaboration
Barbara König Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Tanja Stadler Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Adrian Egli Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Wolf-Dietrich Hardt Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Thomas Van Boeckel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Alex Hall Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure

Awards

Title Year
ETH-Medaille für herausragende Doktorarbeit 2020

Associated projects

Number Title Start Funding scheme
167121 Towards quantification of the contribution of plasmids to the spread of antibiotic resistance 01.03.2017 NRP 72 Antimicrobial Resistance
155866 Evolution and spread of drug resistance: A combined computational and experimental approach 01.01.2015 Project funding

Abstract

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.
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