Impressive pan-genomic diversity of E. coli from a wild animal community near urban development reflects human impacts

Data provided here support the findings of this study and code will allow the replication of analyses therein. To do so, first download and unzip the associated data files.

For each analysis, the following files are required:

PCAs: PCA.R, prokka_annotations.zip (and VirulenceFinder_results.csv for virulence factor PCA)

Sankey diagram: Plasmid_AMR_Sankey.R, mlplasmids_results.zip, MOBsuite_results.zip, ResFinder_results.csv

Pathotype assignment: VF_data_analysis.R, VirulenceFinder_results.csv

TableS1_Ecoli_metadata.csv contains the isolate metadata (n=143) for all above analyses.