Transcriptomic response of Escherichia coli O157:H7 on Romaine lettuce from harvest to storage during the pre-processing interval

Commercially harvested lettuce generally undergoes short- or long-haul transportation from the growing region to facilities near the destination markets for fresh-cut processing. The interval of time between harvest and processing varies by location of the processing facility. To determine how duration of the pre-processing interval (1 versus 8 d) may affect food safety risk, we investigated how pre-harvest and post-harvest, pre-processing conditions affected the gene expression patterns of lettuce-associated Escherichia coli O157:H7, using the reference strain EDL933 and a recent, recurring lettuce outbreak strain 2705C. Transcriptomic shifts were detected in E. coli O157:H7 responding to the lettuce phyllosphere pre-harvest, and subsequently under one or eight days of storage conditions post-harvest (4 °C, 99 % RH, without or with an interval of reduced atmospheric pressure). Pre-harvest, up-regulation of genes linked to stress was common to both strains; including oxidative, osmotic and acid stress, the starvation response, cold shock and antimicrobial stress. Both strains appeared to form biofilms, but differential gene expression patterns between the two strains suggested that they utilized distinct strategies to adapt to the lettuce phyllosphere and switch to a biofilm state. While initial EDL933 responses predominantly encompassed up-regulation of motility, chemotaxis and quorum sensing genes, 2705C more markedly up-regulated genes needed for irreversible attachment, and involved more genes related to oxidative and antimicrobial stress. The elevated expression of osmotic stress, cold shock and antimicrobial stress genes in both strains were sustained or increased throughout the post-harvest interval. On the other hand, down-regulation of several genes involved in starvation, oxidative and acid stress, and attachment was detected in the outbreak strain 2705C from pre- to post-harvest conditions, while expression levels in EDL933 remained mostly unchanged. In both strains, the expression of yhcN, involved in oxidative and acid stress, bhsA, involved in biofilm formation, and mdtG and marB, involved in efflux of antimicrobial compounds, were further augmented in post-harvest storage. Except for the stationary phase gene mgtS in EDL933, the few genes that were differentially regulated in E. coli O157:H7 associated with lettuce subjected to a prolonged 8-d pre-processing delay, compared to a short 1-d interval, were down-regulated. While some genes were downregulated, no transcriptomic response specific to prolonged storage or fluctuations in atmospheric pressure (simulating forward pre-processing delays) was detected. Overall, these results suggest that E. coli O157:H7 adaptation to the harsh, nutrient-depleted pre-harvest lettuce surface involved stress adaptations that primed the bacteria for post-harvest conditions in storage, in a strain-dependent manner. The suite of genes induced in the pre-harvest phyllosphere and sustained in post-harvest lettuce could pre-adapt this pathogen to conditions during post-harvest handling such as sanitizer exposure. Findings provide insights on strain differences in the genetic mechanisms adopted by E. coli O157:H7 associating with lettuce pre- and post-harvest, which could translate to variable food safety risk.