Transcriptomic analysis of Escherichia coli CFT073 colonized in the mammalian intestine

Abstract

Uropathogenic Escherichia coli (UPEC) strain CFT073 is a common cause of hospital acquired urinary tract infections (UTIs) and has been shown to switch metabolic preferences from gluconeogenic to sugar substrates when colonized in the urinary and intestinal tracts, respectively. Interestingly, CFT073 also exhibits a quiescent phenotype when plated below a threshold of 106 CFUs on minimal media in vitro, suggesting a link between the recurrence of CFT073-related UTIs and the ability to remain colonized. This research project used the streptomycin-treated mouse model to first acquire total cellular RNA from E. coli CFT073 colonized in mucosal layer of the mouse cecum. Next, we evaluated whether genes involved in regulation the quiescent phenotype in E. coli CFT073 grown in vitro also play a role in colonization. Lastly, we provide some details of an algorithm-based approach to the analysis of RNA Sequencing (RNA-seq) datasets generated using two mechanistically different sequencing strategies to identifying primary transcripts.