Chemical and microbiological results, quality assurance and quality control, site location, and method information for surface water, bed sediment, and wastewater effluent collected from 34 stream locations across Iowa (United States). Environmental samples were analyzed for a suite of 29 antibiotics, plated on selective media for 15 types of bacteria growth, and DNA was extracted from culture growth and used in downstream polymerase chain reaction (PCR) assays for the detection of 24 antibiotic resistance genes. Environmental field data were collected in-situ for water temperature (°C), specific conductivity (µs/cm), dissolved oxygen (mg/L), pH (standard units), and turbidity (FNU) using a multiparameter sonde and recorded in the National Water Information System (NWIS) (Table S2). Stream discharge (ft3/s) and gage height (ft) values were estimated using available rating curves from adjacent USGS stream gages when available and relative flow was categorized by comparing discharge on the day of sample collection to discharge over the previous three to five years. Samples were analyzed at U.S. Geological Survey laboratories: bacteria enumeration and growth and antibiotic resistance genes at the Michigan Bacteriological Research Laboratory and antibiotic concentrations at the Organic Geochemistry Research Laboratory.

,Groundwater was collected by dead-end ultrafiltration and small-volume grab sampling from 138 wells in southwest Wisconsin across Grant, Iowa, and Lafayette Counties. Samples were collected to assess occurrence of antibiotic resistance genes in private wells and investigate their association with microbial source tracking markers. For ultrafiltration samples, microbes were backflushed, desiccated beef extract was added to the eluate, and samples were concentrated by polyethylene glycol precipitation; concentrate was frozen at -80 degrees Celcius (C). Small-volume grab samples were concentrated on 0.45-micron mixed cellulose ester filters, filters were eluted, and eluate was frozen at -80 degrees C following addition of beef extract. Nucleic acids were extracted from both sample types using a QIAcube and QIAamp DNA mini kit with viral lysis buffer (AVL) and carrier RNA (Qiagen). Nucleic acids were extracted from 280 microliter (µL) of sample concentrate and eluted into 140 µL AE Buffer (Qiagen). Nucleic acids were analyzed in duplicate using quantitative polymerase chain reaction (qPCR) on a Roche LightCycler 480 II using hydrolysis probes. Inhibition was assessed for every sample using Sketa DNA as inhibition control and mitigated by dilution with AE buffer as necessary. No-template negative controls were performed for all analysis steps: secondary concentration, nucleic acid extraction, and qPCR. For each assay with amplification in negative controls, the cycle of quantification (Cq) in unknown samples must be below the censoring threshold to be accepted as positive. Censoring thresholds were calculated as the mean Cq of negative controls - 3 standard deviations; censoring thresholds for each assay and sample type are reported in a separate file (Censoring thresholds.csv). Positive controls (bovine herpes virus vaccine) for extraction were included with each analysis batch and evaluated qualitatively. Positive controls were run in duplicate reactions for all targets and had to be within 0.5 cycles of the expected Cq. Data are expressed as genomic copies per liter of groundwater sampled. Dataset consists of 1 spreadsheet file (qPCR data results.csv). Variables in this file are described in the included data dictionary.,

Chemical and biological results, quality assurance and quality control, and method information from groundwater, surface water, and litter samples, collected from nine locations in Iowa and one in Wisconsin in 2016. Thirteen groundwater, nine surface water, four poultry litter, and four QA/QC samples were collected. Samples were analyzed at U.S. Geological Survey laboratories; bacteria, pathogens, and antibiotic resistance genes at the Michigan Bacteriological Research Laboratory, F+ specific coliphage at the St. Petersburg Coastal and Marine Science Center, hormones and antibiotics at the Organic Geochemistry Research Laboratory, nutrients at the National Water Quality Laboratory, total estrogenicity at Fish Health Laboratory.

Chemical and biological results, quality assurance and quality control, and method information from groundwater, surface water, and litter samples, collected from nine locations in Iowa and one in Wisconsin in 2016. Thirteen groundwater, nine surface water, four poultry litter, and four QA/QC samples were collected. Samples were analyzed at U.S. Geological Survey laboratories; bacteria, pathogens, and antibiotic resistance genes at the Michigan Bacteriological Research Laboratory, F+ specific coliphage at the St. Petersburg Coastal and Marine Science Center, hormones and antibiotics at the Organic Geochemistry Research Laboratory, nutrients at the National Water Quality Laboratory, total estrogenicity at Fish Health Laboratory.

Surface water samples (n = 33) were collected in fall of 2023 at stream sites in Scott County Iowa, USA and were analyzed for microbial source tracking markers by quantitative polymerase chain reaction at the Laboratory for Infectious Disease and the Environment (LIDE). Microbial source tracking markers identify fecal sources of contamination by detecting microbes that are specific to certain animals. Cooperators include Partners of Scott County Watersheds, Prairie Rivers of Iowa, and U.S. Department of Agriculture-Agricultural Research Service.

Surface water samples (n = 33) were collected in fall of 2023 at stream sites in Scott County Iowa, USA and were analyzed for microbial source tracking markers by quantitative polymerase chain reaction at the Laboratory for Infectious Disease and the Environment (LIDE). Microbial source tracking markers identify fecal sources of contamination by detecting microbes that are specific to certain animals. Cooperators include Partners of Scott County Watersheds, Prairie Rivers of Iowa, and U.S. Department of Agriculture-Agricultural Research Service.

Dataset for a year long watershed study in southwestern Ohio to analyze antimicrobial resistant bacteria (E. coli, Enterococcus, and Salmonella) in surface waters and wastewater treatment plant effluent.

,Nebraska Prairie Study for Agricultural Antibiotic Resistance in Lincoln, Nebraska The inherent spatial heterogeneity and complexity of antibiotic resistant bacteria and antibiotic resistance (AR) genes in manureaffected soils makes it difficult to sort out resistance that can be attributed to human antibiotic use from resistance that occurs naturally in the soil. This study characterizes native Nebraska prairie soils that have not been affected by human or food-animal waste products to provide data on background levels of resistance in southeastern Nebraskan soils. Soil samples were collected from 20 sites enumerated on tetracycline and cefotaxime media; screened for tetracycline-, sulfonamide-, b-lactamase–, and macrolide-resistance genes; and characterized for soil physical and chemical parameters. All prairies contained tetracyclineand cefotaxime-resistant bacteria, and 48% of isolates collected were resistant to two or more antibiotics. Most (98%) of the soil samples and all 20 prairies had at least one tetracycline gene. Most frequently detected were tet(D), tet(A) tet(O), tet(L), and tet(B). Sulfonamide genes, which are considered a marker of human or animal activity, were detected in 91% of the samples, despite the lack of human inputs at these sites. No correlations were found between either phenotypic or genotypic resistance and soil physical or chemical parameters. Heterogeneity was observed in AR within and between prairies. Therefore, multiple samples are necessary to overcome heterogeneity and to accurately assess AR. Conclusions regarding AR depend on the gene target measured. To determine the impacts of food-animal antibiotic use on resistance, it is essential that background and/or baseline levels be considered, and where appropriate subtracted out, when evaluating AR in agroecosystems.,

In this study, the abundance and distribution of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), as well as the concentrations of antibiotics present in a mixed-use watershed in Athens, GA, USA were examined, in order to enhance understanding of the existing state of AR in the freshwater environment. The current study has shown that antibiotic-related contaminants are prevalent in the freshwater environment, including commensal and pathogenic bacteria that are resistant to antibiotics used for human and veterinary purposes, medically important antibiotics, as well as the genes associated with resistance to these antibiotics. This dataset is not publicly accessible because: Data belong to coauthor at USDA ARS. It can be accessed through the following means: The data presented in this study are available on request from the corresponding author, Jonathan Frye at USDA. Format: Statistical analysis of data from surface water samples, see the journal article's Supplementary Materials for additional information: https://www.mdpi.com/article/10.3390/antibiotics12111586/s1. This dataset is associated with the following publication: Cho, S., L. Hiott, Q. Read, J. Damashek, J. Westrich, M. Edwards, R. Seim, D. Glinski, J. Bateman McDonald, E. Ottesen, E. Lipp, M. Henderson, C. Jackson, and J. Frye. Distribution of Antibiotic Resistance in a Mixed-Use Watershed and the Impact of Wastewater Treatment Plants on Antibiotic Resistance in Surface Water. The Journal of Antibiotics. Springer Nature, New York, NY, USA, 12(11): 1586, (2023).

The prevalence of antibiotic resistance genes in microbial communities from sewage wastewater streams and from offshore marine sediments in the vicinity of sewage wastewater outfalls in Southeast Florida was investigated from June 2018 to March 2019. Sediment and wastewater samples were analyzed for 15 different antibiotic resistant gene targets via polymerase chain reaction (PCR) presence/absence assays in Southeast Florida coral reef environments. Data collected from five sites (Broward North Wastewater Treatment Plant (WWTP), Broward North WWTP Outfall, Haµlover (Miami-Dade North) Outfall, Hollywood Outfall, Hollywood WWTP, and Miami-Dade North WWTP) illustrated widespread prevalence of antibiotic resistance genes in these microbial communities with the highest concentrations occurring in the sewage wastewater stream and in close proximity to the outfall pipe and outfall. Data indicated seasonal (wet versus dry season) trends and potential public and ecosystem health risks. Additionally, a reef in the Florida Keys was evaluated during the wet season using the same tools and approach prior to and after diseased corals were treated with amoxicillin. Resistance to amoxicillin was only observed in the post-treatment sample set.