2018 ASHS Annual Conference

In the past 20 years, FDA has been involved in over 48 outbreaks associated with sprouts. These events resulted in 179 hospitalizations and 3 deaths. Most outbreaks were attributed to alfalfa sprouts, although clove, mung bean and sprouted chia were also implicated. Salmonella was the most common pathogen identified, followed by E. coli and then Listeria monocytogenes. There has been substantial interest from commercial sprout growers to apply metagenomic methods to the description of the entire sprout production process to get an improved understanding of critical control points to ensure safe sprout production. To that end, shotgun metagenomics was used to study source water and water from each of the four days of growth in a typical alfalfa sprout production system to better understand the complete microbial ecology that sprouts are exposed to.
Viral, fungal, bacterial and protist taxa were described for each day.
Dominant bacterial species included: Klebsiella, Pseudomonas, Acinetobacter, Enterobacter, Curvibacter, Delftia, Flavobacterium, Escherichia and Pantoea. From the first day of growing to the last, there was an increase in the relative abundance of Curvibacter and Delftia. Escherichia was more prominent on days two and three and then appeared to be moderately suppressed by day four. Dominant protist taxa shifted from a majority on the first day of Pseudoperonospora to a balance of Endolimax and Pseudoperonospora by day four. Dominant fungal taxa included Enterocytozoon, Clavaria and Ongeneales. Dominant viral taxa observed were Lactococcus, Erwinia and Enterobacter phages.
A huge amount of data has now been amassed to better understand the agro-ecology of a single sprouts operation. Challenges remain however, in terms of understanding how well these data may represent a wider array of sprout production, and also with regard to how to use these data to improve safe stewardship of this crop.