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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Research Project #439620

Research Project: Precision Bacteriophage Identification Through Machine Learning for Mitigating Persistent Colonization of Escherichia Coli O157:H7 in Cattle

Location: Meat Safety and Quality

Project Number: 3040-42000-020-007-A
Project Type: Cooperative Agreement

Start Date: Jan 1, 2021
End Date: Sep 30, 2023

Beef feedlots are a known reservoir for Shiga Toxin producing Escherichia coli O157:H7 (STEC O157:H7), with an increase in prevalence associated with an increase in contamination of meat during slaughter. Twenty-five years of sampling in this specific USDA feedlot, which is closed to cattle not born on the research facility, has demonstrated specific STEC O157:H7 strains are consistently present. We hypothesize that in order to reduce persistent STEC O157:H7 propagation, there is a need to halt this cycle of repeated colonization by STEC O157:H7 populations and so reduce the baseline reservoir of the pathogen. We propose a custom, machine-learning selected, set of location specific bacteriophages administered at the known site of STEC O157:H7 colonization, the rectal anal junction (RAJ), in inoculated cattle.

1. Develop a phage library by sequencing STEC O157:H7 strains and identifying the different phages in our feed yard. A plate-based activity assays will be used to characterize their efficacy against a panel of STEC O157:H7 strains, including key STEC O157:H7 clades known to be persistent at the USMARC feed yard. 2. Predict and select phages with distinct activity profiles and test these in combination on feedlot STEC O157:H7 isolates in liquid culture assays looking for those that prevent bacterial outgrowth. Test activity of optimum phage combinations with STEC O157:H7 attached to bovine epithelial cells/2-D organoids as well as when cultured in bovine rectal mucus. 3. Use facilities at NADC to test the efficacy of the phage cocktail in calves inoculated with STEC O157:H7 strains know to persist in the USMARC feed yard.