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

Prevalence, Quantity and Antibiotic Resistance Profiles of Salmonella enterica Late in the Feeding Period and at Slaughter in Response to Antibiotic use Early in the Cattle Feeding Period - Part 2

The objective of this study was to determine the effects of tulathromycin and ceftiofur treatment on the prevalence, quantity, and antimicrobial resistance of Salmonella in feedlot cattle immediately following treatment, through the feeding period, and at slaughter.

Identifying Alternatives to Antibiotics

The objectives of the study were to 1) isolate microbial species from the rumen using different media compositions and incubation methods to develop a library of rumen microbial isolates and 2) screen the isolates for microbial species that could inhibit the growth of Streptocococcus bovis, Fusobacterium necrophorum, Arcanobacterium pyogenes, and Pasteurella multocida.

The Use of a Yeast Fermentation Product or an Essential Oil as an Alternative to Tylosin in the Diets of Finishing Cattle

As efforts to reduce antimicrobial use in beef production continue, alternatives to Tylosin must be explored. The addition of Saccharomyces cerevisiae fermentation products (SCFP) and essential oils to finishing diets are two potential alternatives—both of which act by altering the rumen microbial communities and plausibly reduce the incidence of liver abscesses.

Quantitative Evaluation of the Antimicrobial Food Safety Risks Associated with the use of Tylosin for Reduction of Liver Abscesses in Fed Cattle

Concerns have been raised that in-feed use of antimicrobials for livestock production may increase antimicrobial resistance (AMR) in the environment and meat products entering the human food supply. This study evaluated the impact of in-feed use of a specific antimicrobial: tylosin. The objective of this study was to collect data regarding the occurrence of antimicrobial-resistant (AMR) bacteria in cattle feces and on cattle pen surfaces as part of a risk assessment to determine if AMR bacterial populations were significantly altered by in-feed use of tylosin..

Prevalence, Quantity and Antibiotic Resistance Profiles of Salmonella enterica at Slaughter in Response to Antibiotic use Early in the Cattle Feeding Period

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

Method Development to Enable Surveillance of Rare Resistance Phenotypes of Public-Health Concern

Multi-drug resistant bacteria, more precisely bacteria producing extended-spectrum β-lactamases and carbapenemases are causing a serious public health concern. The development of method for the isolation, detection and characterization of the genes encoding for these resistances in the environment, such as bovine fecal samples, are important for the surveillance of the distribution and prevalence of the different gene families and the different variants within these resistance gene families. The objectives of this study were to develop a more sensitive isolation method for carbapenemase-producing bacteria from bovine fecal samples, as well as a molecular method to detect and identify ESBL and carbapenemase genes (blaCTX-M, blaCMY, blaTEM, blaNDM, blaKPC, and blaOXA-48) from fecal samples..

Effects of Cattle Feeding Location and use of Tylosin on Expression of Antimicrobial Resistance (AMR) and Liver Abscesses

Significant pressure has been placed on livestock producers to reduce and/or eliminate their use of antibiotics, such as Tylosin. However, in order to effectively identify alternative strategies, more information related to the microbiological impact of Tylosin supplementation is needed. The purpose of this study was to provide information related to the impact of Tylosin supplementation on microorganisms recovered from pen-floor fecal samples, liver abscess, and subiliac lymph nodes of commercial feedlot cattle.

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.