Seasonality, shelf life and storage atmosphere are main drivers of the microbiome and E. coli O157:H7 colonization of post-harvest lettuce cultivated in a major production area in California

Authors: LEONARD, SUSAN - Food And Drug Administration(FDA); Simko, Ivan; MAMMEL, MARK - Food And Drug Administration(FDA); RICHTER, TAYLOR - Food And Drug Administration(FDA); Brandl, Maria

Submitted to: Environmental Microbiome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2021
Publication Date: 12/20/2021
Citation: Leonard, S., Simko, I., Mammel, M., Richter, T., Brandl, M. 2021. Seasonality, shelf life and storage atmosphere are main drivers of the microbiome and E. coli O157:H7 colonization of post-harvest lettuce cultivated in a major production area in California. Environmental Microbiome. 16. Article 25. https://doi.org/10.1186/s40793-021-00393-y.
DOI: https://doi.org/10.1186/s40793-021-00393-y

Interpretive Summary: Lettuce has caused recurrent outbreaks of Shiga toxin-producing E. coli (STEC) infections, the seasonality of which remains unresolved. These infections have occurred largely from processed lettuce, which undergoes substantial physiological changes during storage. We investigated the effect of shelf life on the microbiome and STEC O157:H7 (EcO157) colonization of cut lettuce of two cultivars harvested in the spring and fall in California, and stored as washed cut product in modified atmosphere packaging (MAP) at cold and warm temperatures. Under cold storage, EcO157 survived significantly better on cultivar Triple Threat (TT) with poor shelf life than on cultivar Darkland (DA) with good shelf life, as well as on lettuce harvested in the fall than in the spring. EcO157 multiplied rapidly on MAP lettuce stored under temperature abuse conditions of 24°C, independently of cultivar and harvest season. Both, season and lettuce shelf life were significant factors in the microbiome structure of MAP lettuce at 6°C but not at 24°C. Bacterial species in the 6°C lettuce microbial community were identified that differentiated lettuce microbiomes by shelf life, EcO157 survival, and harvest season. Our findings shed light on the known seasonality of STEC outbreaks linked to lettuce by demonstrating that fall-harvested lettuce enhances EcO157 survival at 6°C and harbors a different microbiome than in the spring before and during storage at cold and warm temperature.

Technical Abstract: Lettuce has caused recurrent outbreaks of Shiga toxin-producing E. coli (STEC) infections, the seasonality of which remains unresolved. These infections have occurred largely from processed lettuce, which undergoes substantial physiological changes during storage. We investigated the effect of shelf life on the microbiome and STEC O157:H7 (EcO157) colonization of cut lettuce of two cultivars harvested from conventional and experimental fields in the spring and fall in California, and stored in modified atmosphere packaging at cold and warm temperatures. EcO157 declined significantly less on the cold-stored cultivar Triple Threat (TT) with poor shelf life than on cultivar Darkland (DA) with good shelf life, while multiplying rapidly at 24°C independently of cultivar. Metagenomic sequencing of the lettuce microbiome revealed that the pre-storage core bacterial community was small but expanded considerably to be dominated by Erwiniaceae and Pseudomonadaceae while not including any Enterobacteriaceae at 6°C. At 24°C, Pseudomonadaceae formed only 8% of the core community, whereas Erwiniaceae and Enterobacteriaceae had 60% relative abundance. LEfSe indicated that a high proportion of Pseudomonadaceae on DA and Erwiniaceae on TT differentiated their 6°C microbiomes. Recursive partitioning identified fall harvest followed by lettuce deterioration and species richness as factors associated with highest EcO157 survival at 6°C, and package CO2 content and field type with highest multiplication at 24°C. Fall and spring microbiome structures differed significantly pre-storage and at both storage temperatures. The pre-storage noncore microbiome was much larger in spring (79%) than in fall (35%). High representation of Pantoea agglomerans was a significant predictor of fall microbiomes, lettuce deterioration, and enhanced EcO157 survival at 6°C. Fall samples supporting the least EcO157 decline included both cultivars. These results strongly support a role for season and lettuce deterioration in EcO157 survival in cold-stored fresh-cut lettuce and its microbiome. Our findings shed light on the known seasonality of STEC outbreaks linked to lettuce by demonstrating that fall-harvested lettuce enhances EcO157 survival at 6°C and harbors a different microbiome than in the spring before and during storage at cold and warm temperature.