Exometabolomic-enabled discovery of compounds associated with Escherichia coli O157:H7 population dynamics in the lettuce phyllosphere

BACKGROUND: Contamination of fresh produce with human pathogens remains a serious public health and economic concern due to the absence of effective kill steps in the farm-to-fork chain. Escherichia coli O157:H7 has been implicated in multiple illness outbreaks linked to lettuce. RESULTS: We examined the exometabolomic profile of 31 lettuce genotypes and identified variations in the chemical composition of both the leaf surface and the leaf apoplast, supporting variable bacterial growth. Furthermore, inoculation with E. coli O157:H7 induced changes in the overall chemistry of these leaf niches, allowing the identification of many niche-specific differentially accumulated metabolites (DAMs). Intersection analysis revealed little overlap of DAMs among the genotypes, suggesting that multiple metabolites, or a combination of metabolites, may contribute to bacterial persistence in phyllosphere niches. This information guided the design of metabolite cocktails to supplement bacterial inoculations of leaves. Overall, we observed that inhibitory and promoting cocktails significantly shifted the bacterial population titer to lower and higher, respectively, when compared to the control without metabolite supplementation. These shifts were more pronounced in some lettuce genotypes than others. CONCLUSIONS: These findings provide new insights into how the phyllosphere chemistry influences the survival of E. coli O157:H7, offering potential targets to mitigate food safety concerns through genetic and metabolic engineering.