Klebsiella ecology and genome plasticity compared to E. coli and Gram negative ESKAPE pathogens

This collection contains: (1) R code to parse data downloaded from NCBI to generate plots of genome size, genewise G+C content, AMR gene load and plasmid load for Gram negative opportunistic pathogens K. pneumoniae, E. coli, E. cloaceae, P. aeruginosa and A. baumannii. and (2) Results of querying the IMNGS 16S database (imngs.org) for the above species, and R code to plot the frequency of detection of each species in samples of different source types.

Keywords

Klebsiella, ESKAPE pathogens, E. coli, Plasmids, Antimicrobial resistance