How Should We Be Determining Background and Baseline Antibiotic Resistance Levels in Agroecosystem Research?

Rothrock, Michael J.; Keen, Patricia L.; Cook, Kyle DeMeo; Durso, Lisa M.; Franklin, Alison M.; Dungan, Robert S.

doi:10.2134/jeq2015.06.0327

Cited by 40 publications

(35 citation statements)

References 116 publications

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“…When monitoring for AMR it is critical to recognize that, just as antibiotics are largely natural or naturally-derived compounds, there is a ubiquitous background level of antibiotic resistance for certain ARGs (Rothrock et al, 2016). Microbes have evolved the ability to both produce antibiotics (e.g., to ward off competitors), as well as the ability to resist antibiotics (Davies, 2006;Martinez, 2008;Forsberg et al, 2012;Culyba et al, 2015;Westhoff et al, 2017).…”

Section: Detection Methods For Antibiotic Resistance Monitoring Targetsmentioning

confidence: 99%

Antimicrobal Resistance: Fecal Sanitation Strategies for Combatting a Global Public Health Threat

Ashbolt¹,

Pruden²,

Miller³

et al. 2019

Water and Sanitation for the 21st Century: Health and Microbiological Aspects of Excreta and Wastewater Management (Global Wate

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Section: Detection Methods For Antibiotic Resistance Monitoring Targetsmentioning

confidence: 99%

Antimicrobal Resistance: Fecal Sanitation Strategies for Combatting a Global Public Health Threat

Ashbolt¹,

Pruden²,

Miller³

et al. 2019

Water and Sanitation for the 21st Century: Health and Microbiological Aspects of Excreta and Wastewater Management (Global Wate

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“…Because ARGs are naturally occurring, accounting for background sources of antibiotic resistance is critical (Rothrock et al, 2016). There are three common approaches to address background resistance: historical comparisons, pristine environments as controls, and antibiotic-free or organic agricultural systems as controls.…”

Section: Background and Controlsmentioning

confidence: 99%

Molecular Methods for Assessment of Antibiotic Resistance in Agricultural Ecosystems: Prospects and Challenges

et al. 2016

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Agricultural ecosystems are of special interest for monitoring the potential for antibiotic resistance to spread through the environment and contribute to human exposure. Molecular methods, which target DNA, RNA, and other molecular components of bacterial cells, present certain advantages for characterizing and quantifying markers of antibiotic resistance and their horizontal gene transfer. These include rapid, unambiguous detection of targets; consistent results; and avoidance of culture bias. However, molecular methods are also subject to limitations that are not always clearly addressed or taken into consideration in the interpretation of scientific data. In particular, DNA-based methods do not directly assess viability or presence within an intact bacterial host, but such information may be inferred based on appropriate experimental design or in concert with complementary methods. The purpose of this review is to provide an overview of existing molecular methods for tracking antibiotic resistance in agricultural ecosystems, to define their strengths and weaknesses, and to recommend a path forward for future applications of molecular methods and standardized reporting in the literature. This will guide research along the farm-to-fork continuum and support comparability of the growing number of studies in the literature in a manner that informs management decisions and policy development.

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“…While research in isolated and pristine environments indicates that antibiotic resistance is an ancient phenomenon (Bhullar et al, 2012), the use of anthropogenic antibiotics also influences the presence of antibiotic compounds, ARB, and ARGs in an environment. Consequently, Rothrock et al (2016b) emphasize that the determination of background and baseline levels of antibiotic resistance is crucial for an accurate assessment of the impacts of anthropogenic inputs in agroecosystems. Universally accepted definitions of background and baseline levels are not found in the literature; therefore, for this review article, background is defined as the concentration in an environment not influenced by local human activity, and baseline as the numerical average and/or range of antibiotic drugs, ARB, and/or ARGs levels present at the beginning of a study (Rothrock et al, 2016b).…”

Section: How Should We Be Determining Background and Baseline Antibiomentioning

confidence: 99%

“…Consequently, Rothrock et al (2016b) emphasize that the determination of background and baseline levels of antibiotic resistance is crucial for an accurate assessment of the impacts of anthropogenic inputs in agroecosystems. Universally accepted definitions of background and baseline levels are not found in the literature; therefore, for this review article, background is defined as the concentration in an environment not influenced by local human activity, and baseline as the numerical average and/or range of antibiotic drugs, ARB, and/or ARGs levels present at the beginning of a study (Rothrock et al, 2016b). Without knowledge of background and/or baseline levels at the beginning of a study, it is difficult to draw conclusions regarding the impact of human activities in applied animal production systems (Durso and Cook, 2014).…”

Section: How Should We Be Determining Background and Baseline Antibiomentioning

confidence: 99%

“…While attempts have been made to prioritize which antibiotic drugs from human and animal medicine should be examined in antibiotic resistance research (Boxall et al, 2003;FDA, 2003;WHO, 2011), determining which drugs that may enter agroecosystems pose the greatest risk to human, animal, and/ or ecological health is difficult. Therefore, with the purpose of aiding scientists working in agroecosystem research, an antibiotic resistance decision-making tool (AR-DMT) was created to assist in selection of the most important and relevant antibiotics to evaluate given particular research goals/criteria, as well as to guide the experimental design process (Rothrock et al, 2016b). Antibiotics are rated using three main criteria: (i) use within agroecosystems, (ii) ranking within major scientific databases and surveillance programs, and (iii) target bacteria or ARB for treatment.…”

Section: How Should We Be Determining Background and Baseline Antibiomentioning

confidence: 99%

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Antibiotics in Agroecosystems: Introduction to the Special Section

et al. 2016

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The presence of antibiotic drug residues, antibiotic resistant bacteria, and antibiotic resistance genes in agroecosystems has become a significant area of research in recent years and is a growing public health concern. While antibiotics are used in both human medicine and agricultural practices, the majority of their use occurs in animal production where historically they have been used for growth promotion, in addition to the prevention and treatment of disease. The widespread use of antibiotics and the application of animal wastes to agricultural lands play major roles in the introduction of antibiotic‐related contamination into the environment. Overt toxicity in organisms directly exposed to antibiotics in agroecosystems is typically not a major concern because environmental concentrations are generally lower than therapeutic doses. However, the impacts of introducing antibiotic contaminants into the environment are unknown, and concerns have been raised about the health of humans, animals, and ecosystems. Despite increased research focused on the occurrence and fate of antibiotics and antibiotic resistance over the past decade, standard methods and practices for analyzing environmental samples are limited and future research needs are becoming evident. To highlight and address these issues in detail, this special collection of papers was developed with a framework of five core review papers that address the (i) overall state of science of antibiotics and antibiotic resistance in agroecosystems using a causal model, (ii) chemical analysis of antibiotics found in the environment, (iii) need for background and baseline data for studies of antibiotic resistance in agroecosystems with a decision‐making tool to assist in designing research studies, as well as (iv) culture‐ and (v) molecular‐based methods for analyzing antibiotic resistance in the environment. With a focus on the core review papers, this introduction summarizes the current state of science for analyzing antibiotics and antibiotic resistance in agroecosystems, discusses current knowledge gaps, and develops future research priorities. This introduction also contains a glossary of terms used in the core reivew papers of this special section. The purpose of the glossary is to provide a common terminology that clearly characterizes the concepts shared throughout the narratives of each review paper. Core Ideas Antibiotic resistant bacteria are an emerging threat to human, animal, and ecological health. Agroecosystems often contain elevated levels of antibiotics and antibiotic resistance. The impact of antibiotics at low concentrations in the environment is not fully known. Research is needed to understand the spread of antibiotic resistance within and beyond agroecosystems. Standardized approaches will help bring a consensus among scientific community datasets.

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How Should We Be Determining Background and Baseline Antibiotic Resistance Levels in Agroecosystem Research?

Cited by 40 publications

References 116 publications

Antimicrobal Resistance: Fecal Sanitation Strategies for Combatting a Global Public Health Threat

Antimicrobal Resistance: Fecal Sanitation Strategies for Combatting a Global Public Health Threat

Molecular Methods for Assessment of Antibiotic Resistance in Agricultural Ecosystems: Prospects and Challenges

Antibiotics in Agroecosystems: Introduction to the Special Section

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