Antimicrobial Resistance Research

Fact Sheets

Antibiotic Resistance: A Human Health Perspective

Antimicrobial resistance is a global challenge that will require dedicated approaches from both animal and human health communities. Working with Dr. Steve Solomon, formerly of the Centers for Disease Control and Prevention, this fact sheet overviews the human health community’s approach to preventing antibiotic resistance, which is based on two priority areas: 1) improving the use of antibiotics—the practice of antibiotic stewardship— by ensuring that antibiotics are prescribed in the most appropriate way and only when truly necessary, and 2) preventing the spread of antibiotic-resistant bacteria particularly within and between healthcare institutions, but also within communities among people who haven’t been in the hospital.

Journal Articles

Use of Metagenomic Shotgun Sequencing Technology to Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain

This checkoff-funded study, published in the peer-reviewed Journal of Applied Microbiology, is one in a series of research projects that aim to evaluate the ecology of microbial communities using state-of-the-art tools to evaluate samples collected at the animal-human and animal-environment interface. The study is the first-of-its-kind to show quantitative changes in foodborne pathogens/indicators within their microbiome using a “shotgun metagenomics” approach.

Full text available at:

Appl. Environ. Microbiol. April 2016 vol. 82 no. 8 2433-2443

This peer-reviewed journal article was based on the following checkoff-funded Project Summary:

Use of Metagenomic High-throughput Sequencing Technology and Robust Bioinformatics to Assess the Microbiome of Cattle

Resistome Diversity in Cattle and the Environment Decreases During Beef Production

This checkoff-funded study, published in eLife, represents the largest study published to date examining the ecology of antimicrobial resistance (AMR) in the beef production system using shotgun metagenomics. This study is unique because it follows the same groups of cattle from feedlot entry through the harvest process to market-ready beef products.

Full text available at:

eLife 2016;5:e13195

This peer-reviewed journal article was based on the following checkoff-funded Project Summary:

Use of Metagenomic High-throughput Sequencing Technology and Robust Bioinformatics to Assess the Microbiome of Cattle

Project Summaries

Antibiotic Resistance by Source

The objective of this study was to determine the baseline prevalence of antimicrobial resistance in multiple environments.

Use of Shotgun Metagenomic NGS Combined with a Previously Developed Bioinformatics Pipeline vs. Traditional Culture/Screening Diagnostics to Evaluate Ecology of AMR and Diagnose Salmonella spp. in Cattle Feces before and after Ceftiiofur Metaphylaxis

The goal of this study was to assess the impact of metaphylaxis treatment of feeder cattle with Draxxin (tulathromycin) on microbial ecology (i.e., the effect of treatment on fecal genomics) and the resistome (collection of all antimicrobial resistance genes). Further, the study was conducted to develop and validate a metagenomics pipeline for Salmonella enterica detection, and compare results to aerobic culture.

Effects of Chlortetracycline and Ceftiofur Treatment on Prevalence, Quantity, and Antimicrobial Resistance of Salmonella in Feedlot Cattle

The objective of this study was to determine the effects of chlortetracycline and ceftiofur treatment on the prevalence, quantity and antimicrobial resistance of Salmonella in feedlot cattle.

Exploiting Antibiotic Resistance Mechanisms to Combat Antibiotic Resistance

The objective of this study was to determine the feasibility of using a modified antibiotic to “trick” bacteria into expressing antibiotic resistance traits when they are not needed by inducing a significant fitness disadvantage for the antibiotic-resistant bacteria so that they are rapidly reduced in numbers without harming normal microbial flora.

Determination of Factors Affecting Frequency of Conjugative Transfer of Antimicrobial Resistance and Virulence

The objectives of this study were to examine the association between multiple drug resistance (MDR) and virulence in both MDR and pansusceptible E. coli and MDR and pansusceptible Salmonella from different sectors of the beef industry; to determine if the compartment proximity of donor and recipient bacteria affected the conjugation frequency; and to evaluate the effect of pH and organic acids on conjugation frequency.

Antibiotic Resistant Bacteria Carried by Flies in Cattle Farms versus Nonfarm Environments

The objectives of this study were to determine the incidence of antibiotic-resistant bacteria in various flies and to compare the incidences of antibiotic-resistant bacteria in flies from cattle versus non-cattle environments.

Evaluation of and Factors that Influence the Site and Extent of Salmonella in Extra-Intestinal Tissue of Cattle

The objectives of this study were to evaluate the role of stress hormones in the extent of Salmonella replication within extra-intestinal tissues of cattle (in particular, PLN), to perform whole genome sequencing (WGS) on Salmonella isolates recovered from cattle samples (feces, hides and PLN), to explore common attributes that could confer a fitness advantage, and to perform WGS on a selection of non-type-specific E. coli isolates recovered from cattle feces that display a phenotype consistent with extended-spectrum beta-lactamase (ESBL) producing E. coli which are resistant to many cephalosporins.

Identifying Bacteriophages Capable of Inactivating Multi-Drug Resistant (MDR) Salmonella Newport as a Pre-Harvest Antimicrobial Intervention

The objectives of this research were to: i) sample beef feedyards for the identification of Salmonella Newport-specific bacteriophage, and; ii) characterize phage for the ability to infect and lyse S. Newport or other serovars of Salmonella

Screening for Antibiotic-Resistance Genes and Class 1 Integrons in Commensal Bacteria in Agricultural and Other Environments and their Potential Transfer to Pathogenic Bacteria

The purpose of this study was to assess the distribution of antibiotic-resistance genes and Class 1 integrons in farm and non-farm environments, and the transferability of Class 1 integrons to pathogenic bacteria.