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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Research Project #438257

Research Project: Precision Bacteriophage Identification Through Machine Learning for Mitigating Persistent Colonization of Shiga Toxin...

Location: Meat Safety and Quality

Project Number: 3040-42000-020-006-I
Project Type: Interagency Reimbursable Agreement

Start Date: Jan 1, 2021
End Date: Dec 31, 2024

Beef feedlots are a known reservoir for 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 colonization rectal anal junction (RAJ) in inoculated cattle.

1. Develop a phage library by sequencing E. coli O157 strains and identifying the different phages in our feed yard. Plate-based activity assays will be used to characterize their efficacy against a panel of E. coli O157 strains, including key E. coli O157 clades known to be persistent at the USMARC feed yard. 2. Predict and select phages with distinct activity profiles and test these in combination with feedlot E. coli O157 isolates in liquid culture assays looking for those that prevent bacterial outgrowth. Test activity of optimum phage combinations with E. coli O157 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 E. coli strains know to persist in the USMARC feed yard.