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Survival of E. coli O104:H4 Strain C227/11Φcu in a Soil Microenvironment is Associated with a Broad Time-Dependent Τranscriptional Activity of Metabolic Genes

ABSTRACT: Plant-associated outbreaks with enterohemorrhagic E. coli (EHEC) increased worldwide during the last decades. Agricultural soil is an important contamination source for edible plants. Thus, the survival of pathogenic E. coli in agricultural soil samples was analyzed in previous studies. Thereby, the influence of environmental factors and biotic factors was investigated. In the current study, genetic factors that influence the survival of enterohemorrhagic/enteroaggregative E. coli (EHEC/EAEC) O104:H4 strain C227/11Φcu in agricultural soil microenvironments was investigated. The strain was incubated in alluvial loam (AL) for up to 4 weeks and total RNA was prepared from samples taken immediately after inoculation (time point 0), after 1 week and after 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes. The two lists of differentially expressed genes were then subject to gene set enrichment of Gene ontology terms. After 1 week of incubation 36 gene sets were significantly enriched while only 38 gene sets were found to be enriched for the genes that were differentially expressed after 4 weeks. Especially stress response genes and genes of the primary metabolism such as carbohydrate and amino acid metabolism were concerned for both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment

ORGANISM(S): Escherichia coli

PROVIDER: GSE222589 | GEO | 2023/11/29

REPOSITORIES: GEO

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