Glossary of Antimicrobial Resistance

If you are just starting to learn about antimicrobials and resistance, first off welcome to the club, we are so happy to have more microbe obsessives! Second, we guessed you might have been encountering some words or concepts that you haven’t heard before. So, we’ve put together this visual glossary for you to explore. Search the table below for a word or unfamiliar phrase and you’ll find a definition AND videos or other websites where you can learn more about that concept. 

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Antibiotic use in food animals and its effect on antimicrobial resistance spread and human health

Most people alive today have never known a world without antibiotics. Antibiotics became widely used to treat bacterial infections in the 1930s and ‘40s, and were quickly labeled a “miracle drug”. But, as the widespread use of antibiotics evolved, so did the discovery of antibiotic-resistant bacteria. And we have now entered an era where antibiotic resistance is considered one of the biggest worldwide public health challenges of our time. Continue reading “Antibiotic use in food animals and its effect on antimicrobial resistance spread and human health”

Composting can reduce antimicrobial resistance in manure

A brief summary of the manuscript, Dissipation of Antimicrobial Resistance Determinants in Composted and Stockpiled Beef Cattle Manure by Xu et al. (2016)

Key Points:

  • Composting manure can reduce pathogen presence and antimicrobial residues in manure.
  • Composting efficacy in reducing antimicrobial residues in manure is associated with elevated temperatures within the composting process.
  • Stockpiling manure marginally reduce pathogen presence and antimicrobial residues in manure when compared to composting.

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Antimicrobial Resistance Resource Library

Antimicrobial-resistant (AMR) infections are a serious threat to global public health. Each year AMR accounts for roughly 700,000 deaths worldwide. While AMR-related research is ongoing, conveying research-based knowledge about AMR mechanisms, risks, and opportunities to improve outcomes to the general public, agricultural producers, food safety experts, educators, and consumers is imperative.

The iAMResponsible Project team, a nationwide extension effort for addressing AMR, has developed a shared resource library to curate and translate the latest news and research findings on AMR for a non-technical audience. This library is designed to provide educators and advisors with access to resources that will assist you in your discussion of antimicrobial resistance.  Please feel free to share and re-purpose educational products in this library with local audiences. Continue reading “Antimicrobial Resistance Resource Library”

Fate of Antimicrobials during Dairy Manure Management and Processing

The effect of anaerobic digestion (AD) and composting manure management strategies on antimicrobial resistance (AMR) was explored at the farm and bench-scale. At the farm-scale, a collaborative project investigated the fate of antibiotics and antimicrobial resistance genes (ARGs) during manure handling, treatment, and storage at 11 dairy farms. Results showed that antimicrobials were not consistently removed during manure treatment, with most samples below detection limit, yet, others showing concentrations up to 34,000 ng/g DW in the AD effluent, for example. Antimicrobials also did not degrade significantly during field-scale composting. The farm-scale results illuminated limitations of tracking antimicrobials in complex manure treatment systems with varying manure treatment practices, retention times, and heterogeneous manure substrates. At the bench-scale, triplicate reactors with tetracycline (TC) and sulfadimethoxine (SDM) additions of 1 and 10 mg/L were digested with dairy manure and inoculum for 44-days. The AD process degraded 85% of antimicrobials at the bench-scale. There was a 99% reduction of SDM during AD. The AD reactors with TC additions showed more variability in degradation products. The ARG analysis showed that TetM gene copies decreased during AD and correlated with declines in TC, however, reductions in SDM did not correlate with decreases in Sul1 gene copies. Overall, our results showed that dairy farm antibiotics usage varies significantly from farm to farm, with occasional short-term spikes in usage in response to the treatment of illness/infection outbreaks, and therefore, tracking these spikes through complex manure handling systems proved challenging. The settling, separation, and differing retention times of solids throughout manure handling processes also made whole-farm analyses challenging, as recovery rates in the extraction process for testing antimicrobials in the laboratory varied with solid-based and liquid-based manure samples.


Stephanie Langsing, University of Maryland,

Schueler, Jenna (University of Maryland); Crossette, Emily (University of Michigan); Naas, Kayla (University of Buffalo); Hurst, Jerod (University of Buffalo); Oliver, Jason (Cornell University); Raskin, Lutgarde (University of Michigan); Wigginton, Krista (University of Michigan); Gooch, Curt, (Cornell University); Aga Diana (University of Buffalo)

The authors are solely responsible for the content of these proceedings. The technical information does not necessarily reflect the official position of the sponsoring agencies or institutions represented by planning committee members, and inclusion and distribution herein does not constitute an endorsement of views expressed by the same. Printed materials included herein are not refereed publications. Citations should appear as follows. EXAMPLE: Authors. 2019. Title of presentation. Waste to Worth. Minneapolis, MN. April 22-26, 2019. URL of this page. Accessed on: today’s date.

Manure Land Application Strategies to Mitigate Antibiotics and Antibiotic Resistance Genes in the Agricultural Environment

When it comes to the land application of livestock manure, a major environmental concern is the loss of manure-borne nutrients to surface runoff. Management practices and regulations focus on how nutrients travel in runoff as functions of the timing and method of land application as well as proximity to water sources. When manure is applied to soil, manure constituents other than nutrients are also introduced to soil, such as heavy metals, antibiotics, and antibiotic resistance genes. Knowledge about the behaviors of these manure constituents in the environment as a function of manure application strategies is limited.

In this article we will discuss the effects of various land application strategies on the fate and transport of manure borne antibiotics and antibiotic resistance genes in soil and runoff. This will be broken down into three sections: manure storage; land application methods; and vegetative barrier. Although our studies were conducted using swine manure slurry, it is expected that that the general conclusion would also apply to other types of manure. Prior to a detailed description of our findings, we will first present some background information about manure-borne antibiotics and antibiotic resistance genes.

Why Care About Antibiotics?

Antibiotics are often used in concentrated animal feeding operations (CAFOs) to prevent and treat diseases in livestock animals, increasing the density at which livestock can be kept. A substantial portion of these antibiotics can move thorough the digestive system of livestock, and end up in livestock urine and feces. These antibiotics can persist in the livestock manure and go on to alter the microbiome of soil and water. Bacteria exposed to these antibiotics may gain resistance to the antibiotics. This can be a major public health concern, because even the antibiotic resistant bacteria are harmless they may spread the resistance genes to pathogens. This, in turn, could impact human and animal health, as the antibiotics which we rely upon to treat infection will no longer be effective on treating resistant pathogens.

graphic showing antibiotic movement from adminstration to cropland to runoff

Manure Storage

Prior to land application, manure is usually stored in livestock waste management structures. In one study, the effects of anaerobic storage of manure on the fate of antibiotics and antibiotic resistance genes in manure were investigated. In this study, the levels of chlortetracycline and tylosin in manure slurry were monitored. The two antibiotics in swine manure degraded substantially over time under the anaerobic condition. The antibiotic resistance genes corresponding to chlortetracycline was also reduced substantially during manure storage.  In contrast, the resistance genes corresponding to tylosin did not decrease significantly.

Application Method

land application with manure tankerManure and manure slurry may be applied to fields using application methods such as broadcast, injection, and incorporation. These land application methods have varying effects on the spread of antibiotics and antibiotic resistance genes in croplands. A study was conducted to investigate how these land application methods may affect the concentrations of antibiotics and antibiotic resistance genes in runoff and soil following the land application of swine slurry. Results show that land application methods had no statistically significant effect on the aqueous concentrations of antibiotics in the runoff.  However, among the three land application methods tested, broadcast resulted in the highest total mass load of antibiotics in runoff from the three simulated rainfall events. Similarly, broadcast resulted in higher concentrations of antibiotic resistance genes in runoff than did injection and incorporation. In manure amended soils, the effects of land application on the concentration of antibiotics were compound specific. No clear trend was observed in the antibiotic resistance gene levels in soil.

Vegetative Barrier

grasses in a vegetative bufferVegetative barriers are strips of densely growing perennial plants seeded downslope on cropland adjacent to surface water. Vegetative barriers can stabilize the soil in local areas and reduce dissolved and sediment bound compounds in runoff, such as nutrients and particulates. The barriers are often used as an erosion control measure and some states regulate the use of vegetative barriers next to bodies of water and in areas with high slopes. One study tested whether vegetative barriers are effective in reducing antibiotics and antibiotic resistance genes. Results show that stripes of switchgrass (panicum virgatum L.) can effectively reduce antibiotic tylosin and its corresponding resistance gene erm(B) in runoff. Hence, vegetative barriers can be used as a low-cost option to reduce the spread of antibiotic and antibiotic resistance gene through runoff.


The control of manure-borne antibiotics and antibiotic resistance genes in the environment is complicated. Different antibiotic compounds have different properties, such as vulnerability to photo degradation and tendency to adsorb to soil particles. Hence, it is hard to use one land application strategy to effectively manage multiple antibiotics in both runoff and soil. Hence, knowing the dominant antibiotic compounds in the manure can be important. Similarly, different antibiotic resistance genes may be hosted in different bacterial species. These bacteria differ in their metabolisms and consequently respond differently to various land application strategies. Like the case for antibiotics, it is difficult to develop one land application strategy that would be effective to all classes of antibiotic resistance genes in manure. So, in addition to land application strategies, attention should also be given to develop manure storage strategies to reduce antibiotics and antibiotic resistance genes prior to land application.

For more information about this article, contact Xu Li.