Interventions targeting the farm environment to control antimicrobial resistance: a mathematical modeling study of resistant Escherichia coli in cattle
Wendy Beauvais, Getahun E. Agga, Terrance Arthur, John W. Schmidt, Rachel Jennings, Renata Ivanek
The objectives of this study were to use tetracycline-resistant E. coli in beef cattle as an exemplar to: (i) elucidate the role of the environment in the persistence of antimicrobial resistant enteric bacteria in farm environments; and (ii) test the hypothesis that generic hygiene measures such as scraping manure from pens more regularly can contribute to reducing the presence of antimicrobial resistant enteric bacteria in farm environments.
This study is currently under peer review.
Basic_model_fitting_procedure.R: R script file for fitting the basic model (without temperature and nutrients) to the observed data.
Figures_230122.R: R script file for producing figures 3 and 4 in the manuscript
Full_model_fitting_procedure_WB_210122.R: R script file for fitting the full model (including temperature and nutrients) to the observed data.
Part2_WB_130421.R: R script file for estimating r-AMR, performing sensitivity analysis and producing figure 2 in the manuscript
Part3_equations_new_dates_130221.R: Difference equations use for fitting the model to observed data.
Weather_data_cleaned_150921_WB.csv: Weather data that was collected during the randomized controlled trial that was used to fit the model. (See manuscript for reference describing methods that were used to record data).
experimental_data_enviro_WB_180520.csv: Microbiological data that was collected from empty pens during the randomized controlled trial that was used to fit the model. (See manuscript for reference describing methods that were used to collect the data).
experimental_data_full_pens_WB_180520.csv: Microbiological data that was collected from populated pens during the randomized controlled trial that was used to fit the model. (See manuscript for reference describing methods that were used to collect the data).
params_enviro_120221.csv: Input parameters used to fit the basic and full models.