Data and code from: "Building multidimensional tolerance landscapes to predict the population dynamics of bacteria exposed to antibiotics in urban sewers"

City sewers harbor diverse bacterial communities exposed to various antibiotic residues resulting from human consumption and excretion. Although these residues typically occur at sub-inhibitory concentrations, they can still impact the growth rate and yield of susceptible wastewater bacteria. Many bacteria exhibit antibiotic tolerance through transient phenotypic changes. Antibiotic residues, combined with complex environmental factors like temperature and salinity, especially in coastal cities, contribute to non-additive interactions that modulate antibiotic tolerance and affect population dynamics.

To better understand these interactions, we developed continuous multivariate tolerance landscapes for three bacterial species: Escherichia coli, the emerging pathogen Streptococcus suis, and the sewer-inhabiting Arcobacter cryaerophilus. We modeled their intrinsic growth rates and carrying capacities across complex environments, incorporating temperature, salinity, and concentrations of two antibiotics (ciprofloxacin and azithromycin). Using these multivariate tolerance curves, we predicted microbial population dynamics in two sewers of Barcelona, highlighting the importance of environmental complexity in shaping microbial responses to antibiotic stressors.

Usage

Users can perform the analysis by running the R script (TC3D.R) after the installation of all

package mentioned in the preamble, 

This folder contains:

- 3 datasets with OD measures for the 3 species:

              * data_acrya.xlsx

              * data_ecoli.xlsx

              * data_ssuis.xlsx

- 1 excel files with metadata (plate, well, species, environmental conditions)

              * map_plate_all.xlsx

- 4 datasets giving time series of the flow and several measures including  conductivity and   temperaturefor 2 sewers of Barcelona obtained from sample cabines  set during the implementation of SCOREWATER (ID:820751)

              * carmel_flow.csv

              * carmel_quality.csv

              * poblenou_flow.csv

              * poblenou_quality.csv

- 1 C++ script compiled and run with the R TMB package:

              * fit_growth_r_K_SS_treatment.cpp : computes the negative loglikelihood for r and K, and state DOs, given the observed DO, for the populations under one same environmental treatment (salinity * temperature * antibiotic), and computes the density-dependence parameter alpha from r and K using the Delta Method.