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).

,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 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.

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.

This data set includes information on collections of surface water and fecal samples from wild gulls (Larus spp.) at two locations on the Kenai Peninsula, Alaska, USA. Samples were screened for Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) and tested for resistance to multiple antibiotics.

This data set includes information on collections of surface water and fecal samples from wild gulls (Larus spp.) at two locations on the Kenai Peninsula, Alaska, USA. Samples were screened for Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) and tested for resistance to multiple antibiotics.

This data set describes results for two laboratory experiments to validate a quantitative PCR assay for the assessment of antimicrobial resistance genes in surface waters. Data are also provided for the application of the assay surface water samples collected from three national parks in Alaska.

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.