This work investigated efficacies of commonly used healthcare and personal care disinfectants, including glutaraldehyde, chlorhexidine, ethanol, povidone-iodine, benzalkonium chloride, phenol, free chlorine, hydrogen peroxide (H2O2), and 254 nm UV light, in degrading (as measured by qPCR analyses of ∼1000 bp amplicon loss) and deactivating (as measured by transforming activity loss) bacterial antibiotic resistance genes (ARGs) during inactivation of antibiotic-resistant bacteria (ARB) on inanimate surfaces or in aqueous suspension. Intracellular ARGs (iARGs) blt, mecA, and ampC, within vegetative cells of Bacillus subtilis, Staphylococcus aureus, and Pseudomonas aeruginosa, respectively, were treated on PTFE and/or stainless-steel surfaces or in aqueous phosphate buffer (PB; H2O2 only), to simulate potential healthcare and personal care cleaning applications under representative disinfectant exposure conditions. No chemical disinfectant yielded more than limited (≤1.9log10) iARG degradation/deactivation under the conditions investigated, even when ARB cells were extensively inactivated (at levels from 3.1log10 to ≥6log10). In contrast, UV irradiation yielded up to ∼2.8-3.2log10 iARG degradation/deactivation at corresponding ARB inactivation levels up to ∼4log10 in the case of the blt gene within B. subtilis cells on PTFE surfaces, though levels of iARG degradation/deactivation and ARB inactivation were generally lower than expected based on prior aqueous-phase results, likely due to light-shielding effects at the typical ∼108-109 CFU/mL cell inoculum densities used for surface disinfection tests. During exposure to H2O2 in PB, iARG deactivation and ARB inactivation reached up to 1.7log10 and >3.5log10, respectively, while iARG degradation was minimal (≤0.2log10); this appears to be driven by DNA-strand fragmentation (as observed by pulsed-field gel electrophoresis analysis) likely resulting from reaction with endogenous HO• (or Fe(IV)) generated via intracellular iron-catalyzed H2O2 decomposition. While all investigated disinfectants were able to effectively inactivate ARB cells themselves, these results demonstrate that most are ineffective in simultaneously degrading and deactivating iARGs, highlighting the potential benefits of employing disinfectants such as 254 nm UV light, that selectively target bacterial DNA, to improve mitigation of antibiotic resistance dissemination.

BACKGROUND:As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases. RESULTS:Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). CONCLUSIONS:This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.

We analyzed whole genome sequences of 308 Escherichia coli isolates from a marine ecosystem to determine the prevalence and relationships of heavy metal resistance genes (HMRGs) and antibiotic resistance genes (ARGs), as well as the presence of plasmid sequences. We screened all genomes for presence of 18 functional HMRGs conferring resistance to arsenic, cadmium, copper, or cadmium/mercury. In subset analyses, we examined geographic variations of HMRG carriage patterns in 224 isolates from water sources, and sought genetic linkages between HMRGs and ARGs in 25 genomes of isolates resistant to antibiotics. We found high carriage rates of HMRGs in all genomes, with 100% carrying at least one copy of 11 out of 18 HMRGs. A total of 173 (56%) of the isolates carried both HMRGs and plasmid sequences. In the 25 genomes of antibiotic-resistant isolates, 80% (n = 20) carried HMRGs, ARGs, and plasmid sequences, while 40% (n = 10) had linked HMRGs and ARGs on their assembled genomes. We found no evidence of geographic variation in HMRG frequency, nor any association between locational proximity to Superfund sites and co-carriage of HMRGs and ARGs. Our study findings indicate that HMRGs are common among E. coli in marine ecosystems, suggesting widespread heavy metal presence in water sources of a region with history of environmental pollution. Further research is needed to determine the role HMRGs play in driving antimicrobial resistance in human pathogens through genetic linkage and the value their detection in environmental bacterial genomes may offer as an indicator of environmental heavy metal pollution.

Staphylococcus aureus is a widespread and common opportunistic bacterium that can colonise or infect humans as well as a wide range of animals. There are a few studies of both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolated from monkeys, apes, and lemurs, indicating a presence of a number of poorly or unknown lineages of the pathogen. In order to obtain insight into staphylococcal diversity, we sequenced strains from wild and captive individuals of three macaque species (Macaca mulatta, M. assamensis, and M. sylvanus) using Nanopore and Illumina technologies. These strains were previously identified by microarray as poorly or unknown strains. Isolates of novel lineages ST4168, ST7687, ST7688, ST7689, ST7690, ST7691, ST7692, ST7693, ST7694, ST7695, ST7745, ST7746, ST7747, ST7748, ST7749, ST7750, ST7751, ST7752, ST7753, and ST7754 were sequenced and characterised for the first time. In addition, isolates belonging to ST2990, a lineage also observed in humans, and ST3268, a MRSA strain already known from macaques, were also included into the study. Mobile genetic elements, genomic islands, and carriage of prophages were analysed. There was no evidence for novel host-specific virulence factors. However, a conspicuously high rate of carriage of a pathogenicity island harbouring edinB and etD2/etE as well as a higher number of repeat units within the gene sasG (encoding an adhesion factor) than in human isolates were observed. None of the strains harboured the genes encoding Panton–Valentine leukocidin. In conclusion, wildlife including macaques may harbour an unappreciated diversity of S. aureus lineages that may be of clinical relevance for humans, livestock, or for wildlife conservation, given the declining state of many wildlife populations.

This study investigated antibiotic resistance gene (ARG) degradation kinetics in wastewaters during bench- and full-scale treatment with UV light and chlorine─with the latter maintained as free available chlorine (FAC) in low-ammonia wastewater and converted into monochloramine (NH2Cl) in high-ammonia wastewater. Twenty-three 142-1509 bp segments (i.e., amplicons) of seven ARGs (blt, mecA, vanA, tet(A), ampC, blaNDM, blaKPC) and the 16S rRNA gene from antibiotic resistant bacteria (ARB) strains Bacillus subtilis, Staphylococcus aureus, Enterococcus faecium, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae were monitored as disinfection targets by qPCR. Rate constants for ARG and 16S rRNA gene amplicon degradation by UV, FAC, and NH2Cl were measured in phosphate buffer and used to expand and validate several recently developed approaches to predict DNA segment degradation rate constants based solely on their nucleotide contents, which were then applied to model ARG degradation during bench-scale treatment in buffer and wastewater matrixes. Kinetics of extracellular and intracellular ARG degradation by UV and FAC were well predicted up to ∼1-2-log10 elimination, although with decreasing accuracy at higher levels for intracellular genes, while NH2Cl yielded minimal degradation under all conditions (agreeing with predictions). ARB inactivation kinetics varied substantially across strains, with intracellular gene degradation lagging cell inactivation in each case. ARG degradation levels observed during full-scale disinfection at two wastewater treatment facilities were consistent with bench-scale measurements and predictions, where UV provided ∼1-log10 ARG degradation, and chlorination of high-ammonia wastewater (dominated by NH2Cl) yielded minimal ARG degradation.

The main objective of this study was to characterize the tet(X) genes, which encode a monooxygenase that catalyzes the degradation of tetracycline antibiotics, carried by the resistant strains FP105 and FP233-J200, using whole-genome sequencing analysis. The isolates were recovered from fin lesion and kidney samples of diseased rainbow trout Oncorhynchus mykiss, during two Flavobacteriosis outbreaks occurring in freshwater farms located in Southern Chile. The strains were identified as Epilithonimonas spp. by using biochemical tests and by genome comparison analysis using the PATRIC bioinformatics platform and exhibited a minimum inhibitory concentration (MIC) of oxytetracycline of 128 µg/mL. The tet(X) genes were located on small contigs of the FP105 and FP233-J200 genomes. The sequences obtained for the tet(X) genes and their genetic environment were compared with the genomes available in the GenBank database of strains of the Chryseobacterium clade belonging to the Flavobacterium family, isolated from fish and carrying the tet(X) gene. The Tet(X) proteins synthesized by the Chilean Epilithonimonas strains showed a high amino acid similarity (range from 84% to 100%), with the available sequences found in strains belonging to the genus Chryseobacterium and Flavobacterium isolated from fish. An identical neighborhood of tet(X) genes from both Chilean strains was observed. The genetic environment of tet(X) observed in the two strains of Epilithonimonas studied was characterized by the upstream location of a sequence encoding a hypothetical protein and a downstream located alpha/beta hydrolase-encoding gene, similar to the observed in some of the tet(X) genes carried by Chryseobacterium and Flavobacterium strains isolated from fish, but the produced proteins exhibited a low amino acid identity (25–27%) when compared to these synthesized by the Chilean strains. This study reports for the first time the carriage of the tet(X) gene by the Epilithonimonas genus and their detection in fish pathogenic bacteria isolated from farmed salmonids in Chile, thus limiting the use of therapies based on oxytetracycline, the antimicrobial most widely used in Chilean freshwater salmonid farming. This results suggest that pathogenic strains of the Chryseobacterium clade occurring in Chilean salmonid farms may serve as important reservoirs of tet(X) genes.

OBJECTIVES:WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. METHODS:The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. RESULTS:Genotype-phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype-phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. CONCLUSIONS:WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.

Normal 0 false false false MicrosoftInternetExplorer4 Bacteria such as extra-intestinal pathogenic E. coli (ExPEC) and methicillin-resistant S. aureus (MRSA) are important opportunistic pathogens. They might belong to pandemic, epidemic and/or sporadic clones. Some of the clones are associated with humans, others are associated with wild and/or domestic animals. Some clones are shared by both and may be found contaminating the environment. In these studies, we examined the spread of ExPEC from feces of Southern Resident Killer Whale (SRKW; Orcinus orca ) that are associated with human diseases. We also examine MRSA isolates in wild rhesus macaques ( Macaca mulatta ), their environment and from humans. This One Health Approach aims to better understand the sources/reservoirs and possible transmissions of potential pathogens between animals, humans and their shared environment. /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;}

Nowadays, antimicrobial agents are among the most frequently used therapeutics in human and veterinary medicine. Resistance to antimicrobial agents can be subdivided into two basic types of resistance, intrinsic resistance and acquired resistance. Resistance to ß-lactam antibiotics is mainly due to inactivation by ß-lactamases and decreased ability to bind to penicillin-binding proteins (PBPs) in both gram-positive and gram-negative bacteria, but may also be based on decreased uptake of ß-lactams due to permeability barriers or increased efflux via multidrug transporter systems. Different types of multidrug transporters mediating resistance to tetracycline in addition to resistance to a number of structurally unrelated compounds are described, for instance, in Escherichia coli, Salmonella, and P. aeruginosa. Plasmids, genomic islands, transposons, gene cassettes, and integrons are spread vertically during the division of the host cell, but can also be transferred horizontally between bacteria of the same or different species and genera via transduction, conjugation and mobilization, or transformation. The development of antimicrobial resistance—by either mutations, generation of new resistance genes, or acquisition of resistance genes already present in other bacteria—is a complex process that involves different mechanisms. Due to the usage of all types of antimicrobial substances for selection of resistant bacteria, prudent use of the antimicrobial agents is strongly recommended in both human and veterinary medicine, as well as in food animal production, to retain the efficacy of antimicrobial agents for the control of bacterial infections in animals.

Environmental MicrobiologyVolume 20, Issue 7 p. 2322-2333 Tribute Farewell Stan Stanley Falkow: 1934–2018 F. C. Cabello, F. C. Cabello felipe_cabello@nymc.edu Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USASearch for more papers by this authorS. N. Cohen, S. N. Cohen sncohen@stanford.edu Department of Genetics, Stanford University, Stanford, CA, USASearch for more papers by this authorR. Curtiss III, R. Curtiss III rcurtiss@ufl.edu Departments of Infectious Diseases and Immunology and Comparative, Diagnostic and Population Medicine, University of Florida, Gainesville, FL, USASearch for more papers by this authorG. Dougan, G. Dougan gd312@medschl.cam.ac.uk Microbial Pathogenesis Group, Welcome Sanger Institute, Hinxton, UKSearch for more papers by this authorJ. van Embden, J. van Embden jan@ictnet.nl Division of Infectious Diseases, National Institute of Public Health and the Environment, Bilthoven, The NetherlandsSearch for more papers by this authorB. B. Finlay, B. B. Finlay bfinlay@mail.ubc.ca Michael Smith Laboratories, University of British Columbia, Vancouver, BC, CanadaSearch for more papers by this authorF. Heffron, F. Heffron fredheffron@gmail.com Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USASearch for more papers by this authorD. Helinski, D. Helinski dhelinski@ucsd.edu Biological Sciences, University of California San Diego, La Jolla, CA, USASearch for more papers by this authorR. Hull, R. Hull rhull@bcm.edu Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USASearch for more papers by this authorS. Hull, S. Hull sheilahull66@gmail.com Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USASearch for more papers by this authorR. Isberg, R. Isberg ralph.isberg@tufts.edu Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USASearch for more papers by this authorD. J. Kopecko, D. J. Kopecko kopecko@netscape.net CombiVax, LLC, Silver Spring, MD, USASearch for more papers by this authorS. Levy, S. Levy stuart.levy@tufts.edu Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USASearch for more papers by this authorJ. Mekalanos, J. Mekalanos john_mekalanos@hms.harvard.edu Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USASearch for more papers by this authorJ. M. Ortiz, J. M. Ortiz jose.ortiz@unican.es Departamento de Biologia Molecular, Universidad de Cantabria, Santander, SpainSearch for more papers by this authorR. Rappuoli, R. Rappuoli rino.r.rappuoli@gsk.com GlaxoSmithKline Vaccines, Siena, ItalySearch for more papers by this authorM. C. Roberts, M. C. Roberts marilynr@u.washington.edu Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USASearch for more papers by this authorM. So, M. So somaggie@email.arizona.edu Department of Immunobiology, University of Arizona, Tucson, AZ, USASearch for more papers by this authorK. N. Timmis, K. N. Timmis k.timmis@tu-braunschweig.de Institute of Microbiology, Technical University of Braunschweig, Braunschweig, GermanySearch for more papers by this author F. C. Cabello, F. C. Cabello felipe_cabello@nymc.edu Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USASearch for more papers by this authorS. N. Cohen, S. N. Cohen sncohen@stanford.edu Department of Genetics, Stanford University, Stanford, CA, USASearch for more papers by this authorR. Curtiss III, R. Curtiss III rcurtiss@ufl.edu Departments of Infectious Diseases and Immunology and Comparative, Diagnostic and Population Medicine, University of Florida, Gainesville, FL, USASearch for more papers by this authorG. Dougan, G. Dougan gd312@medschl.cam.ac.uk Microbial Pathogenesis Group, Welcome Sanger Institute, Hinxton, UKSearch for more papers by this authorJ. van Embden, J. van Embden jan@ictnet.nl Division of Infectious Diseases, National Institute of Public Health and the Environment, Bilthoven, The NetherlandsSearch for more papers by this authorB. B. Finlay, B. B. Finlay bfinlay@mail.ubc.ca Michael Smith Laboratories, University of British Columbia, Vancouver, BC, CanadaSearch for more papers by this authorF. Heffron, F. Heffron fredheffron@gmail.com Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USASearch for more papers by this authorD. Helinski, D. Helinski dhelinski@ucsd.edu Biological Sciences, University of California San Diego, La Jolla, CA, USASearch for more papers by this authorR. Hull, R. Hull rhull@bcm.edu Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USASearch for more papers by this authorS. Hull, S. Hull sheilahull66@gmail.com Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USASearch for more papers by this authorR. Isberg, R. Isberg ralph.isberg@tufts.edu Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USASearch for more papers by this authorD. J. Kopecko, D. J. Kopecko kopecko@netscape.net CombiVax, LLC, Silver Spring, MD, USASearch for more papers by this authorS. Levy, S. Levy stuart.levy@tufts.edu Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USASearch for more papers by this authorJ. Mekalanos, J. Mekalanos john_mekalanos@hms.harvard.edu Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USASearch for more papers by this authorJ. M. Ortiz, J. M. Ortiz jose.ortiz@unican.es Departamento de Biologia Molecular, Universidad de Cantabria, Santander, SpainSearch for more papers by this authorR. Rappuoli, R. Rappuoli rino.r.rappuoli@gsk.com GlaxoSmithKline Vaccines, Siena, ItalySearch for more papers by this authorM. C. Roberts, M. C. Roberts marilynr@u.washington.edu Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USASearch for more papers by this authorM. So, M. So somaggie@email.arizona.edu Department of Immunobiology, University of Arizona, Tucson, AZ, USASearch for more papers by this authorK. N. Timmis, K. N. Timmis k.timmis@tu-braunschweig.de Institute of Microbiology, Technical University of Braunschweig, Braunschweig, GermanySearch for more papers by this author First published: 26 August 2018 https://doi.org/10.1111/1462-2920.14308 Stanley Falkow was a giant among microbiologists, a pioneer of microbial pathogenesis research, a wonderful mentor, father of an enormous family of world leading microbiology scholars, a gifted and dedicated teacher, and a warm, friendly, generous, relaxed, articulate and humorous communicator. He will be sorely missed. Below are some fond personal memories of times and experiences of colleagues from the early days of Stan's amazing career. 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During the past decades resistance to virtually all antimicrobial agents has been observed in bacteria of animal origin. This chapter describes in detail the mechanisms so far encountered for the various classes of antimicrobial agents. The main mechanisms include enzymatic inactivation by either disintegration or chemical modification of antimicrobial agents, reduced intracellular accumulation by either decreased influx or increased efflux of antimicrobial agents, and modifications at the cellular target sites (i.e., mutational changes, chemical modification, protection, or even replacement of the target sites). Often several mechanisms interact to enhance bacterial resistance to antimicrobial agents. This is a completely revised version of the corresponding chapter in the book Antimicrobial Resistance in Bacteria of Animal Origin published in 2006. New sections have been added for oxazolidinones, polypeptides, mupirocin, ansamycins, fosfomycin, fusidic acid, and streptomycins, and the chapters for the remaining classes of antimicrobial agents have been completely updated to cover the advances in knowledge gained since 2006.

Antibiotic use has steadily increased since its introduction in the 1940s. This has led to millions of metric tons of antibiotics produced and used worldwide with contamination of both natural and man-made environments, as well as domestic and wild animals, man, and plants. This contamination has influenced the increase in antibiotic resistance over time. It is now recognized that a global "One Health" approach is needed to understand how antibiotic-resistant bacteria and resistance genes spread among and between animals, humans, and the environment. In this chapter, I will discuss specific examples of how environmental bacteria have played roles in the development of specific antibiotic resistance genes as well as their roles as reservoirs for these genes which have impacted the health of humans and animals globally.

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) cultureand (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. Antibiotics in Agroecosystems: Introduction to the Special Section