tingjieguo / phage_antibiotic_dynamics

Repository for code and data on the joint impact of phage and antibiotics on bacteria

Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: killers and drivers of resistance evolution - Code Repository

About

This repository contains all the code used to run the analyses outlined in the corresponding paper. Please note that this work is not yet peer-reviewed, and is available here.

For any questions, please contact Quentin Leclerc.

• Email: [email protected]
• Twitter: QuentinLclrc

Data

The "/Data" folder contains the in vitro data generated as part of this project. Please refer to the paper for further details. This includes time-kill curves of three S. aureus strains (NE327, NE201KT7 and DRPET1) exposed to erythromycin or tetracycline.

Model

The core model code is in the "/Model" folder. This folder contains a single R script encoding a function for the model. This relies on the deSolve package.

Parameters

The "/Parameters" folder contains the parameter values. Note that the bacterial growth (bac_params.csv) and phage predation/transduction (pha_params.csv) parameters are derived from a previous study available here. The antibiotic parameters (abx_params.csv) were generated by fitting to the in vitro data, using the estimate_parameters.R script in the "/Analysis" folder.

Analysis

The "/Analysis" folder contains various scripts used to create the figures shown in the paper. Most are explicitly named to indicate the figure they generate, except the following:

• clean_plot_data.R: this is sourced in the fig2_suppfig1.R script. The code here processes the raw datasets in the "/Data" folder.
• estimate_parameters.R: this is sourced in the fig2_suppfig1.R script. The code here uses the summarised in vitro datasets to estimate pharmacodynamic parameters for erythromycin and tetracycline.
• run_model.R: a script to quickly run the model and plot the output for fixed parameter values. Useful to play around with the model under different conditions.

Figures

The "/Figures" folder contains the figures created by the different scripts. Each figure is named according to its position in the paper (e.g. "fig2" is Figure 2 in the paper).

License

This work is distributed under the MIT license (see LICENSE file).