Dale W. Griffin
William M. Benzel
Shawn C. Fisher
Michael J. Focazio
Luke R. Iwanowicz
Daniel K. Jones
Keith A. Loftin
Timothy J. Reilly
20190425
Digital Polymerase Chain Reaction (dPCR) Data from the Sediment-Bound Contaminant Resiliency and Response Strategy Pilot Study, Northeastern United States, 2015
Tabular Digital Data
U.S. Geological Survey Data Release
doi:10.5066/F7XS5SH2
Reston, VA
U.S. Geological Survey
https://doi.org/10.5066/F7XS5SH2
Timothy J. Reilly
Daniel K. Jones
Michael J. Focazio
Kimberly C. Aquino
Chelsea L. Carbo
Erika E. Kaufhold
Elizabeth K. Zinecker
William M. Benzel
Shawn C. Fisher
Dale W. Griffin
Luke R. Iwanowicz
Keith A. Loftin
William B. Schill
20150101
Strategy to evaluate Persistent Contaminant Hazards Resulting from Sea-Level Rise and Storm-Derived Disturbances: Study Design and Methodology for Station Prioritization
Publication (Other)
Reston, VA
U.S. Geological Survey
https://pubs.usgs.gov/of/2015/1188/A/ofr20151188a.pdf
Due to the recognized proliferation and spread of antibiotic resistance genes by anthropogenic use of antibiotics for human, agriculture and aquaculture purposes, antibiotic resistance genes have been defined as an emerging contaminant (Laxminarayan and others, 2013; Rodriguez-Rojas and others, 2013; Niu and others, 2016). The presence and spread of these genes in non-clinical and non-agricultural environments has created the need for background investigations to enhance our understanding of the magnitude and risks associated with this emerging field (Allen and others, 2010). The current global economic costs of antibiotic resistant microorganisms is about 5.8 trillion USD, which is approximately equivalent to the combined GDP of Germany and the United Kingdom (Taylor and others, 2014). In this study we screened soil and sediment samples for the presence of 15 antibiotic resistance gene targets and 5 species of Vibrio (a marker of marine inundation) to determine natural background concentrations. These data provide a foundation to address background prevalence of these genetic targets in the northeastern United States (U.S.) to address regional influences (sources of pollutants) and to contrast future influences due to sea-level rise and large scale storms.
The purpose of these datasets was to define which samples contained antibiotic resistance genes (screened antibiotic resistance gene targets) and Vibrio species, the number of detectable targets per sample and the quantity of those respective gene targets per gram of soil. These data were determined from samples collected in the northeastern U.S. in support of Sediment-bound Contaminant Resiliency and Response (SCoRR) study.
20150803
20151112
ground condition
Not planned
-79.303957
-66.983372
44.972041
33.352132
USGS Metadata Identifier
USGS:356648ef-627a-40c0-8e13-d71276879f5b
ISO 19115 Topic Category
environment
biota
health
USGS Thesaurus
field sampling
field monitoring stations
contamination and pollution
environmental health (human)
microbiology
genetic diversity
soil resources
unconsolidated deposits
Geographic Names Information System
Connecticut
District of Columbia
Delaware
Massachusetts
Maryland
Maine
New Hampshire
New Jersey
New York
Pennsylvania
Rhode Island
South Carolina
Virginia
Oregon GEO Stratum Keywords
Intertidal
Estuarine
Soil
Surface
Sediment
Oregon GEO temporal Keywords
Modern
none
Public domain data from the U.S. Government are freely redistributable with proper metadata and source attribution. The U.S. Geological Survey requests to be acknowledged as originator of these data in future products or derivative research.
Dale W Griffin
U.S. Geological Survey, Southeast Region
Environmental and Public Health Microbiologist
mailing address
600 4Th Street South
St. Petersburg
FL
33701
USA
727-502-8075
727-502-8182
dgriffin@usgs.gov
Environment as of Metadata Creation: Microsoft Windows 7 Version 6.1 (Build 7601) Service Pack 1; Esri ArcGIS 10.3.1 (Build 4959) Service Pack N/A (Build N/A)
Griffin, D.W., Benzel, W.M., Fisher, S.C., Focazio, M.J., Iwanowicz, L.R., Loftin, K.A., Reilly, T.J., Jones, D.K.
2019
The presence of antibiotic resistance genes in coastal soil and sediment samples from the eastern seaboard of the USA
publication
Environmental Monitoring and Assessment
v.191, Issue 2, p.1573-2959
https://doi.org/10.1007/s10661-019-7426-z
Laxminarayan, R., Duse, A., Wattal, C., Zaidi, A.K.M., Wertheim, H.F.L., Sumpradit, N., Vlieghe, E., Hara, G.L., Gould, I.M., Goossens, H., Greko, C., So, A.D., Bigdeli, M., Tomson, G., Woodhouse, W., Ombaka, E., Peralta, A.Q., Qamar, F.N., Mir, F., Kariuki, S., Bhutta, Z.A., Coates, A., Bergstrom, R., Wright, G.D., Brown, E.D., Cars, O.
2013
Antibiotic resistance-the need for global solutions
report
Lancet Infectious Diseases
v.13, no. 12, p.1057-1098
Rodriguez-Rojas, A., Rodriguez-Beltran, J., Couce, A., Blazquez, J.
2013
Antibiotics and antibiotic resistance: A bitter fight against evolution
report
International Journal of Medical Microbiology
v.303, Issues 6-7, p.293-297
Niu, Z-G., Zhang, K., Zhang, Y.
2016
Occurrence and distribution of antibiotic resistance genes in the coastal area of the Bohai Bay, China
report
Marine Pollution Bulletin
v.107, Issue 1, p.245–250
https://doi.org/10.1016/j.marpolbul.2016.03.064
Allen, H.K., Donato, J., Wang, H.H., Cloud-Hansen, K.A., Davies, J., Handelsman, J.
2010
Call of the wild: antibiotic resistance genes in natural environments
report
Nature Reviews Microbiology
v.8, p.251-259
Taylor, J., Hafner, M., Yerushalmi, E., Smith, R., Bellasio, J., Vardavas, R., Bienkowska-Gibbs, T., Rubin, J.
2014
Estimating the economic cost of antimicrobial resistance: Model and Results
report
Santa Monica, CA
RAND Corporation
http://www.rand.org/pubs/research_reports/RR911.html
Knapp C.W., Dolfing J., Ehlert P.A.I., Graham D.W.
2010
Evidence of Increasing Antibiotic Resistance Gene Abundances in Archived Soils since 1940
Environmental Science & Technology
v.44, Issue 2, p.580-587
Bockelmann U., Dorries H.H., Ayuso-Gabella M.N., de Marcay M.S., Tandoi V., Levantesi C., Masciopinto C., Van Houtte E., Szewzyk U., Wintgens T., Grohmann E.
2009
Quantitative PCR Monitoring of Antibiotic Resistance Genes and Bacterial Pathogens in Three European Artificial Groundwater Recharge Systems
Applied and Environmental Microbiology
v.75, no.1, p.154-163
Singh P., Mustapha A.
2013
Multiplex TaqMan (R) detection of pathogenic and multi-drug resistant Salmonella
International Journal of Food Microbiology
v.166, Issue 2, p.213-218
Panicker G., Bej A.K.
2005
Real-time PCR detection of Vibrio vulnificus in oysters: Comparison of oligonucleotide primers and probes targeting vvhA
Applied and Environmental Microbiology
v.71, no.10, p.5702-5709
Plaon S., Longyant S., Sithigorngul P., Chaivisuthangkura P.
2015
Rapid and Sensitive Detection of Vibrio alginolyticus by Loop-Mediated Isothermal Amplification Combined with a Lateral Flow Dipstick Targeted to the rpoX Gene
Journal of Aquatic Animal Health
v.27, Issue 3, p.156-163
Pollock F.J., Morris P.J., Willis B.L., Bourne D.G.
2010
Detection and quantification of the coral pathogen Vibrio coralliilyticus by real-time PCR with TaqMan fluorescent probes
Applied and Environmental Microbiology
v.76, no.15, p.5282-5286
Lyon W.J.
2001
TaqMan PCR for detection of Vibrio cholerae O1, O139, non-O1, and non-O139 in pure cultures, raw oysters, and synthetic seawater
Applied and Environmental Microbiology
v.67, no.10, p.4685-4693
Rizvi A.V., Panicker G., Myers M.L., Bej A.K.
2006
Detection of pandemic Vibrio parahaemolyticus O3 : K6 serovar in Gulf of Mexico water and shellfish using real-time PCR with Taqman (R) fluorescent probes
Fems Microbiology Letters
v.262, Issue 2, p.185-192
No formal attribute accuracy tests were conducted.
No formal logical accuracy tests were conducted.
Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details.
A formal accuracy assessment of the horizontal positional information in the dataset has not been conducted.
A formal accuracy assessment of the vertical positional information in the dataset has either not been conducted, or is not applicable.
The SCoRR standard operating procedure (SOP) (https://pubs.usgs.gov/of/2015/1188/B/ofr20151188b.pdf) details the sample-collection methods used in this data release. The SOP provides step-by-step instructions for site preparation, sample collection and processing, quality assurance, and shipping of soil and surficial and bed sediment.
20151217
DNA extraction was performed by first calibrating the Mettler scale with a 50 gram certified weight and documented on the Mettler QA/QC sheet. Using sterile-techniques, approximately 0.25 g of soil from each sample weighted out and transferred to a PowerSoil bead beating tube. Sample weight was logged in the project electronic laboratory notebook (ELN). The MoBio PowerSoil kit protocol was used to elute DNA to a volume of 150 ul using Qiagens AE buffer recipe (10mM Tris-HCL, 0. 5mM EDTA, pH 9.0, filter sterilized and autoclaved). Eluted DNA was stored at -70 degrees C until use.
20160705
Digital PCR was run for all presence/absence qPCR positive samples using a QuantStudio 3D Digital PCR System and the following master mix recipe and amplification profile. Data was normalized and reported as gene copies per gram of soil.
Master mix recipe (volumes per reaction): 2x digital master mix – 7.25ul, primer/probe mix – 1 ul, H2O – 4.25 ul, template - 2 ul.
Amplification profile: 96 degrees C for 10 min – 1X, 60 degrees C for 2min and 98 degrees C for 0.5 min – 39X, 60 degrees C for 2min – 1X and hold at 10 degrees C.
20160705
Added keywords section with USGS persistent identifier as theme keyword.
20201013
U.S. Geological Survey
VeeAnn A. Cross
Marine Geologist
Mailing and Physical
384 Woods Hole Road
Woods Hole
MA
02543-1598
508-548-8700 x2251
508-457-2310
vatnipp@usgs.gov
dPCRdata_SCoRR2015.csv
Table containing attribute information associated with the dataset. Digital polymerase chain reaction (dPCR) data are provided in comma separated values format.
U.S. Geological Survey
Sample
Sample bottle identifier
U.S. Geological Survey
Sample bottle identifier
SCoRR_ID
Sediment-bound Contaminant Resiliency and Response (SCoRR) site identifier
U.S. Geological Survey
SCoRR site identifier
NA
SCoRR ID not applicable.
U.S. Geological Survey
Sample_Date
Date sample was collected
U.S. Geological Survey
20150803
20151112
Date (YYYYMMDD)
NA
Sample date not applicable.
U.S. Geological Survey
Sample_Mode
Samples collected under Resiliency (baseline) or Response (event) Mode
U.S. Geological Survey
NA
Sampling mode not applicable.
U.S. Geological Survey
resiliency
Samples collected under Resiliency (baseline) mode
U.S. Geological Survey
response
Samples collected under Response (event) mode
U.S. Geological Survey
tetB
Tetracycline resistance genetic target
U.S. Geological Survey
313.2
2305.5
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
tetL
Tetracycline resistance genetic target
U.S. Geological Survey
3023.3
10122.5
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
tetM
Tetracycline resistance genetic target
U.S. Geological Survey
1518.2
4990320
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
tetO
Tetracycline resistance genetic target
U.S. Geological Survey
308.9
15636945
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
tetW
Tetracycline resistance genetic target
U.S. Geological Survey
278.4
458707.5
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
ampC
Cephalosporin (ampicillin, pcn, etc.) resistance genetic target
U.S. Geological Survey
4393.8
5387475
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
vanA
Vancomyucin resistance genetic target
U.S. Geological Survey
41116.2
41116.2
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
ermB
Erythromycin resistance genetic target
U.S. Geological Survey
269.7
9428614
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
mecA
Methicillin resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
blaSHV
Cephalosporin (ampicillin, pcn, etc.) resistance genetic target
U.S. Geological Survey
295.8
9572175
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
blaPSE
Cephalosporin (ampicillin, pcn, etc.) resistance genetic target
U.S. Geological Survey
295.8
195119.3
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
floR
Chloramphenenicol resistance genetic target
U.S. Geological Survey
2818.8
126063
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
aadA2
Streptomycin resistance genetic target
U.S. Geological Survey
261
169815.3
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
tetG
Tetracycline resistance genetic target
U.S. Geological Survey
561.2
193562
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
tetQ
Tetracycline resistance genetic target
U.S. Geological Survey
304.5
169989.3
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
Vibrio_cholerae
Bacterial pathogen and marine inundation marker for Vibrio cholerae
U.S. Geological Survey
8151.9
8151.9
Number of copies of genetic target per gram of soil
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
NA
Not screened
U.S. Geological Survey
V_parahaemolyticus
Bacterial pathogen and marine inundation marker for V. parahaemolyticus
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
NA
Not screened
U.S. Geological Survey
V_vulnificus
Bacterial pathogen and marine inundation marker for V. vulnificus
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
NA
Not screened
U.S. Geological Survey
V_alginolyticus
Bacterial pathogen and marine inundation marker for V. alginolyticus
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
NA
Not screened
U.S. Geological Survey
V_coralliilyticus
Bacterial pathogen and marine inundation marker for V. coralliilyticus
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not analyzed as the presence/absence PCR reactions were both negative
U.S. Geological Survey
NA
Not screened
U.S. Geological Survey
Note
Sample notes
U.S. Geological Survey
Samples identified with complete inhibition of the assay as stated for each. IPC normal reaction was set at an Rn (normalized reporter value) of 0.1 with a CT (threshold cycle) of 29 plus or minus 1. Target reactions were judged positive if they breached Rn of 0.1 with an exponential type signal.
{Null Value / Empty Field Entry}
No notes recorded
U.S. Geological Survey
The entity and attribute information provided here describes the tabular data associated with the dataset. Please review the detailed descriptions that are provided (the individual attribute descriptions) for information on the values that appear as fields/table entries of the dataset.
The entity and attribute information was generated by the individual and/or agency identified as the originator of the dataset. Please review the rest of the metadata record for additional details and information.
U.S. Geological Survey
Physical and Mailing
600 4th Street South
St. Petersburg
FL
33701
USA
727-502-8000
dgriffin@usgs.gov
Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
CSV (Comma Separated Values)
none
https://coastal.er.usgs.gov/data-release/doi-F7XS5SH2/data/dPCRdata_SCoRR2015.zip
None
20201013
Dale W Griffin
U.S. Geological Survey, Southeast Region
Environmental and Public Health Microbiologist
mailing address
600 4Th Street South
St. Petersburg
FL
33701
USA
727-502-8075
727-502-8182
dgriffin@usgs.gov
Content Standard for Digital Geospatial Metadata
FGDC-STD-001-1998