This repository contains the analysis for a manuscript published at Open Forum Infectious Disease in January 2020. The focus of this work is the analysis of the association between trehalose utilization variants in clinical C. difficile isolates and infection severity outcome in patients.

The paper is available at Open Forum Infectious Diseases.

Genetic determinants of trehalose utilization are not associated with severe Clostridium difficile infection outcome

Katie Saund, Krishna Rao, Vince Young, and Evan Snitkin.

This repository includes the R code necessary for figures, supplementary tables, and statistical analyses.
NOTE: If running the code, users must (1) unzip the zipped data file and (2) add an directory named "outputs" inside the data/ directory.

C. difficile genome sequences are available under the NCBI BioProject PRJNA561087.

Katie Saund ([email protected]) and Krishna Rao contributed code to this project.