PERSISTENCE OF FOODBORNE PATHOGENS IN MICROGREENS GROWN WITH CONTAMINATED SEEDS AND NONTRADITIONAL WATER SOURCES

Abstract

Over the past few decades, various changes in weather conditions have intensified the possibilities of water scarcity, posing a significant threat to global food production. These concerns have prompted researchers and growers in the agricultural sector to explore alternative irrigation strategies. Among these, the reuse of nontraditional water sources such as reclaimed and roof-harvested rainwater has garnered increasing interest. However, concerns regarding their chemical and microbial safety, as well as their potential impact on crop quality and food safety remain. Irrigation water alone has been implicated as a source of contamination in many foodborne outbreaks but upon examination of the farm to fork continuum, several points for entry of pathogens can be identified, such as contaminated seeds. Several voluntary recalls by fresh produce growers have been attributed to seeds contaminated with foodborne pathogens, indicating the need for seed treatments and thorough inspections of receiving documents. The overarching goal of this dissertation was to evaluate the safety, microbial ecology, and nutritional implications of using alternative irrigation sources and seed contamination in controlled environmental agriculture, using microgreens as a model system. Potential research interests and gaps were identified using a scientometric analysis of 3,072 peer-reviewed publications from 1990 to 2022. The Web of Science database was used to characterize global trends in water reuse research. Results revealed a growing international focus on reclaimed and harvested rainwater, with significant gaps identified at the nexus of water quality, food safety, and crop nutrition. Subsequently, the transfer and persistence of three major foodborne pathogens of concern such as Salmonella enterica, Escherichia coli O157:H7, and Listeria monocytogenes in four Brassicaceae microgreens irrigated with pathogen-inoculated municipal and rainwater was assessed. Pathogen survival was quantified over a 14-day growth period. Although reductions in recovery were observed over time, all pathogens persisted in both plant and soil samples, through the entirety of the harvest period. Notably, rainwater irrigation resulted in lower pathogen loads at low inoculum levels, indicating a reduced likelihood of pathogen persistence under these conditions. In parallel, metabolomic investigations revealed species-dependent variations in glucosinolate profiles influenced by irrigation water source, demonstrating a link between water composition and plant nutritional quality. To explore seeds as a possible route of contamination, the survival dynamics of the same pathogens introduced at both low and high inoculum levels using contaminated microgreen seeds was investigated. Pathogen populations peaked at day 7 and declined by day 14, with no significant differences in survival trends across microgreen types. These results emphasize the critical role of seed hygiene in minimizing pre-harvest contamination. Shotgun metagenomics was also used to assess microbial community dynamics with the intention of exploring the role of native microbiomes in pathogen persistence. Significant shifts were observed in microbial community structure and diversity across microgreen types and timepoints. Pseudomonas emerged as the dominant genus across all samples, while pathogen inoculation altered both alpha and beta diversity metrics. Overall, this dissertation contributes to a deeper understanding of the complex dynamics between contamination sources, pathogen survival trends, microbial ecology, and crop metabolite profiles in microgreens. By integrating a multi-pronged combination of classical microbiological detection methods, metagenomics and metabolomics, this research supports the development of sustainable and safe irrigation practices for resilient food systems under potentially changing weather conditions.