Evaluation of niche adaptation features by genome data mining approach of Escherichia coli urinary and gastrointestinal strains
- Published
- Accepted
- Subject Areas
- Bioinformatics, Microbiology
- Keywords
- Escherichia coli, pangenome analysis, niche adaptation, urinary tract infections
- Copyright
- © 2019 Paim et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. Evaluation of niche adaptation features by genome data mining approach of Escherichia coli urinary and gastrointestinal strains. PeerJ Preprints 7:e27720v1 https://doi.org/10.7287/peerj.preprints.27720v1
Abstract
Background. Urinary Tract Infections (UTIs) are among most common infections in humans. The vast majority are caused by Escherichia coli, occasionally responsible for severe clinical manifestations. Although the species frequently adheres and colonizes the bladder mucosa, its reservoir is the host gastrointestinal tract. Therefore, the study was designed to evaluate genomic features for niche adaptation of urinary and gastrointestinal strains of E. coli by data mining approach.
Results. In the E. coli strains, the repertoire of genes was higher than those found in previous studies, and the majority of genes associated to primary metabolism did not depend of bacteria niche, with exception of cell cycle-division, cell motility and secondary metabolite metabolism. Urinary tract isolates of E. coli had great density of virulence and resistance genes carried by prophages.
Conclusion. The urinary and gastrointestinal strains of E. coli evaluated in the study presented an open pan-genome, with groups of functional annotation genes associated to specific niches. In addition, gastrointestinal isolates of E. coli were demonstrated as important reservoir of resistance genes.
Author Comment
This is a preprint submission to PeerJ Preprints.