Poster Presentation BACPATH 2022

Transcriptome profiling of uropathogenic Escherichia coli in response to infection-relevant stress (#162)

Minh-Duy Phan 1 2 , Daniel G Mediati 3 , Kate M Peters 1 2 , Nguyen Thi Khanh Nhu 1 2 , Brandon M Sy 3 , Ignatius Pang 4 , Jai Tree 3 , Jay CD Hinton 5 , Mark A Schembri 1 2
  1. Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
  2. School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
  3. School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
  4. Bioinformatics Scientific Core Facility, Children's Medical Research Institute, Sydney, NSW, Australia
  5. Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom

The globally disseminated multidrug resistant uropathogenic E. coli ST131 clone is a major cause of urinary tract infection and life-threatening sepsis. A representative strain of ST131, EC958, has been used extensively to characterise this clone in the quest to understand the adaptive features that have led to its overriding dominance. EC958 is resistant to human serum killing, grows well in human urine, and is an effective gut coloniser. In this study, we investigated the transcriptomic changes (using RNA-seq) of EC958 following exposure to a suite of in vitro conditions relevant to infection, including two growth phases (mid-exponential and early stationary), five physiological shocks (high salt, low pH, low iron, anaerobic and human urine), and three antibiotic shocks (ciprofloxacin, cefotaxime and fosfomycin). We observed 3463 genes, representing 68% of the genome, were expressed in at least one condition. Differential expression analysis identified expression signatures specific for each condition as well as a common signature in response to antibiotic exposure. Transcription start sites were mapped using differential RNA-seq. A striking finding was the identification of >200 novel noncoding RNA (ncRNA) candidates, several of which were confirmed by Northern blotting and their abundance correlated well with the RNA-seq dataset. Interestingly, the transcriptomic response to ciprofloxacin was similar to that of low iron shock, prompting us to further investigate the ncRNA-mRNA interactions in these two conditions using UV cross-linking, ligation and sequencing of hybrids (CLASH). A total of 780 ncRNA-mRNA interactions were identified, 57 of which were from ncRNA and mRNA that were differentially expressed. Further work is currently underway to examine the function of these ncRNA, their mechanism of interaction with target genes, and their association with responses to fluoroquinolone exposure and low iron shock. Overall, this study has defined a transcription blueprint of ST131 that contributes to its adaptation to infection-relevant stresses.