Metagenomic analysis of fecal microbiome in Escherichia coli O157:H7-shedding and non-shedding animals from a single dairy farm

Authors: SALAHEEN, SERAJUS - US Department Of Agriculture (USDA); KIM, SEON-WOO - University Of Maryland; KARNS, JEFFREY - US Department Of Agriculture (USDA); HOVINGH, ERNEST - Pennsylvania State University; Haley, Bradd; Van Kessel, Jo Ann

Submitted to: Food Control
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/15/2019
Publication Date: 3/19/2019
Citation: Salaheen, S., Kim, S., Karns, J.S., Hovingh, E., Haley, B.J., Van Kessel, J.S. 2019. Metagenomic analysis of fecal microbiome in Escherichia coli O157:H7-shedding and non-shedding animals from a single dairy farm. Food Control. 102:76-80. https://doi.org/10.1016/j.foodcont.2019.03.022.
DOI: https://doi.org/10.1016/j.foodcont.2019.03.022

Interpretive Summary: Shiga toxin-producing Escherichia coli O157:H7 is a major bacterial pathogen estimated to cause 63,000 foodborne illnesses, 2000 hospitalizations, and 10 deaths in the U.S. each year. Cattle serve as natural reservoirs of this zoonotic pathogen that can be transferred to humans through direct animal contact, through consumption of contaminated foods, and through contamination of the environment. Although a lot of work has been done in this area, we need to understand more about the factors that influence carriage of Escherichia coli O157:H7 in dairy animals. So in this study we compared the microbial community composition of the feces from E. coli O157:H7-shedding and non-shedding cows using metagenomic sequence analysis (analyzed the total bacterial DNA extracted from the feces). Findings from this study indicated that, there may be subtle differences associated with E. coli O157:H7 carriage in the bovine fecal microbial community structures. Differential relative abundance of several bacterial genera (groups) and virulence genes (associated with causing disease) were identified in the fecal samples from the two groups. Continued research on the dynamics of E. coli O157:H7 carriage and shedding in cattle may help identify interventions that will hinder the spread of this pathogen on farms. This research will eventually help reduce human exposure to these pathogens.

Technical Abstract: Escherichia coli O157:H7 (O157:H7) is a major zoonotic pathogen responsible for severe and often fatal infections in humans. Cattle are the primary reservoir of O157:H7, although other animal species are also known carriers. Fecal shedding of this pathogen can potentially lead to contamination of pre-pasteurized milk, meat, water, produce, wildlife, and the environment. Understanding the relationships between O157:H7-carriage and the structure of the ruminant intestinal microbiome may inform development of mitigation strategies. To assess the compositional differences in the fecal microbiota of O157:H7-shedding and non-shedding cows, 14 fecal samples from lactating cows in the same dairy herd were analyzed using shotgun metagenomic sequencing. Results indicated that there may be subtle differences in lactating cow fecal metagenomes associated with O157:H7 shedding. Lower relative abundance of Firmicutes and several unique bacterial genera were identified in the fecal metagenomes of O157:H7-shedding cows. Differential relative abundance in twenty-four operational taxonomic units, mostly belonging to Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, were observed in the fecal samples from the two groups. Community-wide differences in virulence factor (VF) profiles were not observed using ordination space-based analysis. However, six VF-related genes that were previously detected in O157:H7 were identified in the fecal metagenomes of O157:H7-shedding cows and were not detected in the fecal metagenomes of non-O157-shedding cows. The differential taxa and VF-related gene profiles provided significant insights into fecal microbiomes of O157:H7-shedding dairy cattle.