Project Summary

Harnessing the Ecological Dynamics of Naturally Occurring Bacteriophage in the Feedlot Environment to Control Multidrug-Resistant Salmonella in Slaughter-Ready Beef Cattle  

Principle Investigator(s):
Keri Norman1, Ashley Arnold2, Kerri Gehring2, Jason Gill2,3, John Richeson4, Harvey Morgan Scott5, Jason Smith6, Matthew Taylor2
1Department of Veterinary Integrative Biosciences, Texas A&M University
2Department of Animal Science, Texas A&M University
3Center for Phage Technology, Texas A&M University
4Texas A&M AgriLife Research, Texas A&M University System
5Department of Veterinary Pathobiology, Texas A&M University
6Texas A&M AgriLife Research, Department of Animal Science, Texas A&M University
Completion Date:
June 2022



  • Salmonella serovars vary significantly by collection month, sample type, and feedlot pen through longitudinal sampling of beef cattle and the feedlot environment.
  • Applying naturally occurring bacteriophages using dust abatement sprinkler systems and using backpack sprayers to apply targeted bacteriophages are easy-to-implement environmental methodologies.
  • Environmental mitigation strategies may be effective methods to target Salmonella of public health importance by reducing Salmonella in the feedyard environment and subsequently in the cattle feces and lymph nodes.


Despite the reduction of contaminated beef cuts through the post-harvest control of Salmonella carcass contamination, Salmonella in ground beef products has remained an issue. This suggests the current post-harvest Salmonella mitigation techniques are not adequate to address Salmonella harbored in bovine lymph nodes which are commonly incorporated into ground beef products. While the use of vaccinations and direct-fed microbials are options, there remains a lack of pre-harvest alternatives. Environmental interventions such as dust abatement sprinklers for bacteriophage applications could reduce Salmonella in the feedlot and subsequently the cattle and their lymph nodes. To develop effective environmental intervention strategies, longitudinal research investigating Salmonella dynamics between the feedlot environment and beef cattle needs to be understood. Applying naturally occurring environmental bacteriophage through dust abatement sprinklers and targeted bacteriophage stocks with backpack sprayers may reduce overall Salmonella prevalence and shift Salmonella serovars in the feedlot environment and cattle host towards favorable pan-susceptible populations.

The first year of the study was conducted at the West Texas A&M University (WTAMU) Research Feedlot. An observational study was conducted that included longitudinal sampling of cattle feces and the environment to study Salmonella and associated bacteriophage population dynamics. Pen-level sample collection of freshly voided feces, environmental pen (manure pack), environmental pen dry matter, feed, and water occurred from May to December 2019. Subiliac lymph nodes were collected from carcasses following harvest and dressing procedures and were processed and analyzed per the USDA-FSIS Microbiology Laboratory Guidebook. Fecal and environmental samples were cultured for Salmonella using standard selective and enrichment methods. Phenotypically characteristic Salmonella colonies were selected and subjected to matrix-assisted laser desorption ionization– time of flight mass spectrometry (MALDI-TOF) for confirmation of Salmonella. Salmonella isolates were sequenced on the Illumina MiSeq platform using 2x250 paired-end reads and Salmonella serovars and antimicrobial resistance genes were determined from raw sequencing reads. Thirty samples were randomly selected to determine the presence of naturally occurring bacteriophages in the feedlot pen environment. A Salmonella cocktail including serovars Anatum, Cerro, Kentucky, Lubbock, Montevideo, and Newport was used to enrich for Salmonella infecting bacteriophages. Bacteriophages were harvested and subjected to sequencing on an Illumina MiSeq and the sequencing data was analyzed to determine the identity of the bacteriophages.   

The experimental trial began at the WTAMU Research Feedlot. A total of 216 cattle were source and weight blocked into 18 pens. The cattle spent 36 days at the WTAMU feedlot to establish and determine the Salmonella population dynamics. A subset of 162 cattle was transported to the Texas A&M AgriLife Research/USDA-ARS Research Feedlot for the 30-day experimental field trial. The experimental field trial was a 2x2 factorial design that included targeted bacteriophage application and a diluted environmental pen sample as treatments. The cattle had a 7-day acclimation period in their new environment prior to initial sampling and treatments. Cattle fecal and hide samples and environmental pen samples were collected on Days 7, 14, 21, and 28 of the study. Environmental phage treatments developed from selected pen environment from the WTAMU Feedlot were applied via the dust abatement sprinkler system to 9 pens at a flow rate of about 57 gallons per minute on Days 8-25 (excluding Days 12, 13, 19, and 20) at the Bushland experimental feedyard. A selected phage stock of SW2 and Melville was applied via portable backpack sprayer at a flow rate of 1L/min on days 8 and 22. Sampling of the cattle and pens continued monthly until the cattle went to slaughter and subiliac lymph nodes were harvested. Samples were cultured for Salmonella using standard selective and enrichment methods and confirmed. WGS and analysis of sequencing data was conducted using previously described methods.

It was determined through longitudinal sampling of the cattle and the feedlot environment that most Salmonella serovars varied by collection month, sample type, and feedlot pen; however, serovars did not vary by feedlot row, block, or dietary treatment. This information suggests that interventions can be developed to target specific Salmonella serovars. Applying naturally occurring bacteriophages from the feedlot environment and using backpack sprayers to apply targeted bacteriophages was an easy and cost-effective environmental treatment. Preliminary data from the experimental trial shows strong pen-level effects regarding Salmonella prevalence and serovar dynamics.

Salmonella serovars vary by collection month, sample type, and feedlot pen through longitudinal sampling of beef cattle and the feedlot environment. Not all Salmonella serovars are of public health concern. Environmental treatments can be used to reduce Salmonella or target Salmonella of public health concern. Applying naturally occurring bacteriophages using dust abatement sprinkler systems provides an easy and cost-effective treatment for changing the Salmonella population dynamics. Additionally, targeted bacteriophage treatments can be used to reduce Salmonella serovars of public health importance in the feedlot environment. Further analysis is needed to see how both the environmental treatment and targeted bacteriophage treatment are associated with these pen-level effects.