Characterization of Escherichia coli Isolates from Agricultural Water on Kansas and Missouri Fresh Produce Farms by Whole-Genome Sequencing

Abstract

Contaminated agricultural water has been a source of pathogenic Escherichia coli in recent produce-related outbreaks. The purpose of this study was to characterize E.coli isolates from agricultural water sources by usingwhole-genome sequencing (WGS) to better understandcontamination routes. Groundwater and surface watersamples were collected quarterly from five farms inMissouri and Kansas over a 1-year period. Samples weretested for generic E. coli by using U.S. EnvironmentalProtection Agency Method 1603, and presumptive E. colicolonies were isolated. In total, 570 isolates were analyzedby PCR, with 191 of these isolates confirmed as E. coli.WGS was completed using an Illumina MiSeq system. Thede novo genome assemblies were obtained with Shovillpipeline version 0.9. The NCBI Pathogen Detection systemwas used to identify antimicrobial resistance (AMR)genes. The prevalence of E. coli was higher during springand summer than winter. A diverse serotype pool wasobserved where more than 53% of isolates could be linkedto a bovine source as the potential animal host. An AMRanalysis showed that 100% of isolates carried at least two antimicrobial resistance genes. Recognizing the diversity of E. coli may help guide agricultural water assessments as proposed in the new agricultural water rule Food Safety Modernization Act Produce Safety Rule.