Isolates listed by unique identifiers and levels of resistance to various antibiotics. This dataset is associated with the following publication: Hoelle, J., J.R. Johnson, B. Johnston, B. Kinkle, L. Boczek, H. Ryu, and S. Hayes. Survey of US wastewater for carbapenem-resistant Enterobacteriaceae. JOURNAL OF WATER AND HEALTH. IWA Publishing, London, UK, 17(2): 219-226, (2019).

,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.,

ARG, intI1, fecal indicator bacteria PCR data. This dataset is associated with the following publication: Keely, S., N. Brinkman, E. Wheaton, M. Jahne, S. Siefring, M. Varma, R. Hill, S. Leibowitz, R. Martin, J. Garland, and R. Haugland. Geospatial Patterns of Antimicrobial Resistance Genes in the US EPA National Rivers and Streams Assessment Survey. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 56(21): 14960–14971, (2022).

ARG, intI1, fecal indicator bacteria PCR data. This dataset is associated with the following publication: Keely, S., N. Brinkman, E. Wheaton, M. Jahne, S. Siefring, M. Varma, R. Hill, S. Leibowitz, R. Martin, J. Garland, and R. Haugland. Geospatial Patterns of Antimicrobial Resistance Genes in the US EPA National Rivers and Streams Assessment Survey. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 56(21): 14960–14971, (2022).

Estimated mean log10 concentration of genetic markers for CQQ_056, CPQ_064, HF183/BacR287, and HumM2 genetic markers in nine sewage and two surface water samples. This dataset is associated with the following publication: Stachler, E., C. Kelty, M. Sivaganesan, X. Li, K. Bibby, and O. Shanks. Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 51(16): 9146-9154, (2017).

Estimated mean log10 concentration of genetic markers for CQQ_056, CPQ_064, HF183/BacR287, and HumM2 genetic markers in nine sewage and two surface water samples. This dataset is associated with the following publication: Stachler, E., C. Kelty, M. Sivaganesan, X. Li, K. Bibby, and O. Shanks. Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 51(16): 9146-9154, (2017).

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.

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.

This dataset contains results for treated wastewater samples collected at food processing facilities across the United States to characterize the potential contaminant profile of this type of wastewater. The associated report (Hubbard and others, 2021) can be found at https://doi.org/10.1021/acs.est.XXXXXXX. Samples were analyzed by USGS laboratories using 10 target organic (576 unique analytes), 13 inorganic (32 unique analytes), and 18 microbial (15 bacterial groups) methods. Concentration results and site descriptions are presented within.