Hospital Transmission Model for Antibiotic-Resistant Bacteria

An R-based epidemiological model simulates the transmission dynamics of antibiotic-resistant and sensitive bacterial strains in a hospital and its catchment area. The model, authored by Esther van Kleef from the University of Oxford, includes functions for running simulations, calculating R0, and generating plots. It was used to test the reasoning behind discordant changes in bacterial strain prevalence relative to infection control measures.

Use Cases

• Simulating hospital transmission dynamics based on the described two-strain competition model.
• Testing hypotheses about the impact of infection control versus antibiotic use on resistance based on the model's reasoning.
• Calculating basic reproduction numbers (R0) for bacterial strains using the provided model functions.
• Reproducing the analysis for the Lancet Infectious Diseases correspondence mentioned in the description.

Strengths

• Includes R code for the full model, plotting, and analysis, facilitating reproducibility.
• Provides specific parameters for baseline scenarios and for reproducing a published correspondence figure.

Limitations

• Row count is unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

University of Oxford

Collection Method

Computational simulation model written in R.