Metagenomic survey of pre-harvest agricultural water using long read sequencing

Leafy greens are responsible for nearly half of the produce-related Shiga toxin-producing Escherichia coli (STEC) outbreaks in the United States, implicating agricultural water as a potential source. Current FDA detection protocols require extensive analysis time. Development of methods for rapid detection of STECs in the field are imperative to maintain food safety. We aimed to use Oxford Nanopore rapid sequencing kits for an in-field determination of agricultural water microbiome and possible detection and characterization of STECs strain(s) in these samples.