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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Dietary Impact on Antibiotic Resistance in Feedlot Manure

Report on research conducted at the University of Nebraska, originally printed in the 2021 Nebraska Beef Cattle Report.


There is a growing public concern regarding antibiotic resistance and the use of antibiotics, including in livestock management. Understanding the ecology of antibiotic resistance among microbes, identifying resistance gene reservoirs, and implementing antibiotic resistance mitigation practices in livestock production is critical to protecting animal and human health while meeting increasing food demands. This research is one of several studies seeking to assess risk for livestock-to-human transfer of antibiotic resistance and to identify mechanisms for reducing that risk where possible. This study evaluated the impact of forage concentration and supplemental essential oil in beef cattle finishing diets on antibiotic resistance in freshly excreted and consolidated beef feedlot manure. Results indicate that antibiotic resistance in manure was not impacted by either of the two dietary treatments considered. Continue reading “Dietary Impact on Antibiotic Resistance in Feedlot Manure”

Antibiotic Resistance in Manure-Amended Agricultural Soils

Report on research conducted at the University of Nebraska, originally printed in the 2021 Nebraska Beef Cattle Report.


Manure application to agricultural land benefits soil health and agronomic yields. However, as antibiotic resistance becomes a more serious threat to public health, there is concern that antibiotic resistance originating from livestock manure could impact human health through contamination of the environment or food. This study sought to quantify this risk by monitoring concentrations of antibiotic-resistant bacteria and genes in fallow soil during the period of October through April, representing fall manure application through spring planting. Resistance to three common antibiotics – tylosin, azithromycin, and tetracycline – was monitored following application of fresh, stockpiled, or composted beef feedlot manure, or inorganic fertilizer. Overall, concentrations of all monitored resistant bacteria were below the detection limit for enumeration. Results indicate that while all the manure treatments increased at least one measure of antibiotic resistance during the sampling period, by the final sampling day antibiotic resistance prevalence and concentrations in manured plots were not significantly different from soil receiving no fertilizer treatments  Continue reading “Antibiotic Resistance in Manure-Amended Agricultural Soils”

Antimicrobial Resistant Bacteria in Surface Water Bodies

Antimicrobial resistance is a challenge that many face today in the agricultural field. As antibiotics and supplements are given to farm animals and their manure applied to crops and pasture, microbes are demonstrating resistance to antibiotics in agricultural settings. These bacteria have also been found residing in surface water bodies after being influenced by agriculture or animal production. These highly resistant bacteria have caused problems for human health with exposure to these bacteria.

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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”

Environmental Antibiotic Resistance Bacteria and Genes: A Link to Public Health?


The emergence of antibiotic resistant bacterial genes in previously susceptible pathogens has become a major challenge in treatment of infectious diseases in the 21st century. I will describe how environmental antibiotic resistance genes and resistant bacteria affect and interact with human health issues and the connection between human, animal and environmental health using the One Health model.

diagram of One Health

Figure 1. Antibiotic resistant genes and antibiotic resistant bacteria are shared by animals, humans and the environment.


What did we do?

The 2013 CDC publication estimates ~2 million people develop antibiotic-resistant infections with ~ 23,000 dying as a direct result of these infections. The rapid development of antibiotic resistant bacteria (ARB) and the identification of many new antibiotic resistant genes (ARG) over the last few decades is a recent event following the large-scale production and use of antibiotics in clinical/veterinary medicine, agriculture, aquaculture and horticulture over the past 70 years. The majority of today’s antibiotics are produced by soil Streptomyces spp. These microbes have genes which are able to protect their host from the action of these naturally produced antibiotics. These protection proteins often have similar action to “classical ARGs” or are genetically related to ARGs found in pathogens. Environmental bacteria are thought to be one ancestral source for many of the clinically relevant antibiotic resistant genes ass ociated with pathogens infecting humans and animals today. Another example is the qnrA gene which is associated with plasmid-linked fluoroquinolone resistance that originated in the aquatic bacterium Shewanell algae. Gene cluster conferring glycopeptide resistance in enterococci, which create vancomycin resistant enterococci (VRE), have been identified in many Gram-positive bacteria including common soil bacteria, some of which are plant pathogens. These same soil bacteria are also resistant to daptomycin, a relative newly developed antibiotic, which currently has restrictive use in clinical medicine. Recently it has been determined that municipal wastewater treatment does not remove antibiotics, ARGs and may be enriched for ARBs which contaminate the water environment. Indicating that human civilization, unknowingly is contaminating the environment, and contributes to the development of new ARB/ARGs.

In recent years, carbapenemase-producing Enterobacteriaceae (CPE) have increased throughout the USA and the world. Carbapenemase producing Klebsiella pneumoniae (KPC) have been associated with USA hospital outbreaks while other CREs carrying the New Delhi metallo-beta-lactamase (NDM-1) producing Enterobacteriaceae have generally been imported and still rarely cause disease in the USA. The NDM-1 containing Enterobacteriaceae have been found in sewage and drinking water and the environment in India, sewage in China and more recently in Brazilian waters. Where these resistant genes have come from is not clear. However, our recent work suggests that we can isolated environmental bacteria that can grow in the presence of meropenem and by qPCR we can get positive reactions for some CRE genes in environmental as well as sewage samples. All together suggests that their may be environmental sources for carbapenemase resistances.

What have we learned?

Data is accumulating to indicate that antibiotic resistant genes from the environment play an important role not only as reservoirs for antibiotic resistance genes found because of human/animal contamination but also independently providing new antibiotic resistant genes which can then be spread to humans and animals and create serious problems as is currently occurring with CRE.

Future Plans

Verify the potential sources of CRE genes within the environment including identification of the bacteria which are current resistant to carbapenems and what their mechanism of resistance is.


Marilyn C. Roberts, Professor, Department of Environmental & Occupational Health Sciences, School of Public Health, University of Washington, Seattle WA 98195-7234

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