The genomics of soil-persistant E. coli
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Escherichia coli’s remarkable ability to thrive both in the gut and in soil confounds many assumptions made about the bacterium’s ecological niche specialisation, and a growing body of research has challenged the long-held assertion that E. coli can only survive transiently outside of the gut. In order to probe the genetic mechanisms that allow for such long-term adaptation and assess any potential human-health risks associated with soil- adapted E. coli, whole-genome sequencing was performed on a collection long-term soil- adapted E. coli isolates. The isolates were collected from maritime temperate soils that had been protected from fecal contamination for periods of at least 9 to 13 years. The isolates were found to display a range of growth and motility capabilities. The genomes of the isolates were used to assess phylogenetic relationships; the strains were found to represent each of the E. coli phylogroups, with phylogroup B1 be the most represented. Potentially-clonal pairs were identified and some isolates were removed to de-duplicate the dataset. Phylogenetic analysis also suggested that the rates of evolution may be constrained in some clades. The strains were compared to a wider collection of E. coli isolates and found to be dispersed throughout the phylogeny, rather than clustering with each other; a small number of strains showed little similarity to their nearest phylogenetic neighbour, indicating that the soil can harbour strains not observed elsewhere. Assessing the virulence and antimicrobial resistance profiles of these isolates revealed that the majority of strains appear to be benign, but a small number exhibit gene profiles typically associated with successful pathogens. Lastly, pan-genome analysis was used in conjunction with genome-wide association approaches to attempt to identify marker genes or regions responsible for soil persistence; no such marker was identified. The genomic diversity of this strain collection suggests that soil survival is not a trait limited to a single lineage. Soil-persistent isolates are phenotypically, phylogenetically, and potentially pathogenically diverse. Further understanding of these isolates will potentially lead to improved water quality diagnostics and a more complete knowledge of stress adaptation and virulence in E. coli.
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