Transcription profiling of E. coli K-12 and O157:H7 during exposure to acetic, lactic, and hydrochloric acid at pH 5.5

The foodborne pathogen Escherichia coli O157:H7 is commonly exposed to organic acid in processed and preserved foods, allowing adaptation and the development of tolerance to pH levels otherwise lethal. Since little is known about the molecular basis of adaptation of E. coli to organic acids, we studied K-12 MG1655 and O157:H7 Sakai during exposure to acetic-, lactic-, and hydrochloric acid at pH 5.5. The conditions required to maximimally induce the ATR of the pathotypes to all acidulants was experimentally determined. This involved incubation at pH 5.5 for 3 h (K-12) and for 2 h (O157:H7), and generated acid adapted cultures more resistant to acid challenge at pH 3.5 than bacteria that had been grown at neutral pH prior to acid-shock. To determine the transcriptomic response of K-12 and O157:H7 to each of the three acids, RNA was extracted from samples of cultures at the time of incubation corresponding to maximal induction of the ATR and from the corresponding overnight culture to serve as a control. The Affy package of the Bioconductor software was used to process raw CEL files using the robust multiarray average algorithm (RMA) for normalization, background correction, and expression value calculation. Expression levels obtained from four independent biological replicates of every condition were compared using the Limma package of the Bioconductor software. Elements with expression levels ? twofold higher or lower than the reference at a statistical significance (P-value adjustment with Benjamini and Hochberg with an adjusted P value ? 0.01, Average Expression (A value) ? 2, Log-odds (B value)  ? 0) were selected. This is the first transcriptomic study to demonstrate and characterise the stationary phase acidulant and pathotype specific ATR of E. coli. A core set of genes were also found to be universally expressed by both pathotypes regardless of acidulant type.  

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