Genomic virulence biomarkers in Pseudomonas aeruginosa bloodstream infection

Published: 20 October 2023| Version 1 | DOI: 10.17632/3h9gvbzz7x.1
John Karlsson Valik


Code and microbiological data to generate the main findings of the study: "Genomic markers of virulence in Pseudomonas aeruginosa is associated with mortality and septic shock in patients with bloodstream infection". No legal responsibility or warranty comes with the scripts or data. Contact:


Steps to reproduce

LIST OF DATA: Shared data comprises annotated microbiological data. Due to legal restrictions, individual patient-level data cannot be shared. In relevant instances, mock-up data has been created to be able to run the code, but the output will differ from the published paper. For enquirers regarding the output, feel free to contact me. a) b) c) d) LIST OF R-SCRIPTS: 1.) table_1_git.R - code to generate Table 1 2.) PCoA_script_git.R - code to generate clusters and create Figure 4b. NOTE! The clusters are used in subsequent code 3.) phylogenetic_tree_git.R - code to generate the evolutionary tree and create Figure 2a 4.) graph_script_git.R - code to create Figures 2b, 2c, 3a, 3b, 4a and 4c 5.) modelling_git.R - code to generate statistics, logistic regression and create Figure 5a-c 6.) prediction_git.R - code to run the machine learning models and create Figure 5d-f


Karolinska Institutet


Septic Shock, Critical Care of Sepsis, Pseudomonas aeruginosa, Bacterial Virulence, Biomarker in Prognosis