Presence/absence Quantitative Polymerase Chain Reaction (qPCR) Data from the Sediment-Bound Contaminant Resiliency and Response Strategy Pilot Study, Northeastern United States, 2015

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Frequently anticipated questions:

What does this data set describe?

Title:
Presence/absence Quantitative Polymerase Chain Reaction (qPCR) Data from the Sediment-Bound Contaminant Resiliency and Response Strategy Pilot Study, Northeastern United States, 2015
Abstract:
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 researchers 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.
  1. How might this data set be cited?
    Griffin, Dale W., Benzel, William M., Fisher, Shawn C., Focazio, Michael J., Iwanowicz, Luke R., Jones, Daniel K., Loftin, Keith A., and Reilly, Timothy J., 20190425, Presence/absence Quantitative Polymerase Chain Reaction (qPCR) Data from the Sediment-Bound Contaminant Resiliency and Response Strategy Pilot Study, Northeastern United States, 2015: U.S. Geological Survey Data Release doi:10.5066/F7XS5SH2, U.S. Geological Survey, Reston, VA.

    Online Links:

    This is part of the following larger work.

    Reilly, Timothy J., Jones, Daniel K., Focazio, Michael J., Aquino, Kimberly C., Carbo, Chelsea L., Kaufhold, Erika E., Zinecker, Elizabeth K., Benzel, William M., Fisher, Shawn C., Griffin, Dale W., Iwanowicz, Luke R., Loftin, Keith A., and Schill, William B., 20150101, Strategy to evaluate Persistent Contaminant Hazards Resulting from Sea-Level Rise and Storm-Derived Disturbances: Study Design and Methodology for Station Prioritization: U.S. Geological Survey, Reston, VA.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -79.303957
    East_Bounding_Coordinate: -66.983372
    North_Bounding_Coordinate: 44.972041
    South_Bounding_Coordinate: 33.352132
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 03-Aug-2015
    Ending_Date: 12-Nov-2015
    Currentness_Reference:
    ground condition
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: Tabular Digital Data
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
    2. What coordinate system is used to represent geographic features?
  7. How does the data set describe geographic features?
    qPCRdata_SCoRR2015.csv
    Table containing attribute information associated with the dataset. Presence/absence quantitative polymerase chain reaction (qPCR) data are provided in comma separated values format. (Source: U.S. Geological Survey)
    Sample
    Sample bottle identifier (Source: U.S. Geological Survey) Sample bottle identifier
    SCoRR_ID
    Sediment-bound Contaminant Resiliency and Response (SCoRR) site identifier (Source: U.S. Geological Survey)
    ValueDefinition
    NASCoRR ID not applicable.
    SCoRR site identifier
    Sample_Date
    Date sample was collected (Source: U.S. Geological Survey)
    ValueDefinition
    NASample date not applicable.
    Range of values
    Minimum:20150803
    Maximum:20151112
    Units:Date (YYYYMMDD)
    Sample_Mode
    Samples collected under Resiliency (baseline) or Response (event) Mode (Source: U.S. Geological Survey)
    ValueDefinition
    NASampling mode not applicable.
    resiliencySamples collected under Resiliency (baseline) mode
    responseSamples collected under Response (event) mode
    tetB
    Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    tetL
    Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    tetM
    Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    tetO
    Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    tetW
    Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    ampC
    Presence/absence of Cephalosporin (ampicillin, pcn, etc.) resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    vanA
    Presence/absence of Vancomyucin resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    ermB
    Presence/absence of Erythromycin resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    mecA
    Presence/absence of Methicillin resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    blaSHV
    Presence/absence of Cephalosporin (ampicillin, pcn, etc.) resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    blaPSE
    Presence/absence of Cephalosporin (ampicillin, pcn, etc.) resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    floR
    Presence/absence of Chloramphenenicol resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    aadA2
    Presence/absence of Streptomycin resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    tetG
    Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    tetQ
    Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    +Present in two of two PCR reactions
    Vibrio_cholerae
    Presence/absence of Vibrio cholerae (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    +Present in two of two PCR reactions
    NANot screened
    V_parahaemolyticus
    Presence/absence of V. parahaemolyticus (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    NANot screened
    V_vulnificus
    Presence/absence of V. vulnificus (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    (+)Present in one of two PCR reactions
    NANot screened
    V_alginolyticus
    Presence/absence of V. alginolyticus (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    NANot screened
    V_coralliilyticus
    Presence/absence of V. coralliilyticus (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}Not detected
    NANot screened
    Note
    Sample notes (Source: U.S. Geological Survey)
    ValueDefinition
    {Null Value / Empty Field Entry}No notes recorded
    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.
    Entity_and_Attribute_Overview:
    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.
    Entity_and_Attribute_Detail_Citation:
    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.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Dale W. Griffin
    • William M. Benzel
    • Shawn C. Fisher
    • Michael J. Focazio
    • Luke R. Iwanowicz
    • Daniel K. Jones
    • Keith A. Loftin
    • Timothy J. Reilly
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    Dale W Griffin
    U.S. Geological Survey, Southeast Region
    Environmental and Public Health Microbiologist
    600 4Th Street South
    St. Petersburg, FL
    USA

    727-502-8075 (voice)
    727-502-8182 (FAX)
    dgriffin@usgs.gov

Why was the data set created?

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.

How was the data set created?

  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
    Date: 17-Dec-2015 (process 1 of 4)
    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.
    Date: 05-Jul-2016 (process 2 of 4)
    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 (10 mM Tris-HCL, 0.5 mM EDTA, pH 9.0, filter sterilized and autoclaved). Eluted DNA was stored at -70 degrees C until use.
    Date: 05-Jul-2016 (process 3 of 4)
    The following recipes and plate(s) layouts were used to set up qPCR reactions. All reactions were run in duplicate and positives were those reactions where amplification was noted in both reactions that reached an Rn of 0.1 (with an exponential trend). Reactions that only produced amplification in one of the two reactions were noted in parenthesis in the data spreadsheet. All duplicate positives were screened with digital PCR. Master Mix recipes (volumes per reaction) are as follows: Single probe reactions – 20 ul rxns - row 1 IPC control: 2x TaqMan Fast Universal Master Mix (10 ul); Template (2 ul); Primer/probe (10 um/5 um working stock) (1 ul each); 10x Exo Internal Positive Control (2 ul); 50x EXo IPC DNA (0.4 ul); PCR grade H2O (4.6 ul). IPC control rxns - row 8: 2x TaqMan Fast Universal Master Mix (10 ul); Template (2 ul); 10x Exo Internal Positive Control (2 ul); 50x EXo IPC DNA (0.4 ul); PCR grade H2O (5.6 ul). Multiplex (two primer and probe sets) – rows 2 through 7: 2x TaqMan Fast Universal Master Mix (10 ul); Template (2 ul); primer/probe (10 um/5 um working stock) (1ul each); PCR grade H2O (6.0 ul). PCR amplification profile Master details are as follows: Pre PCR read – 60 degrees C for 0.5min; Holding stage – 50 degrees C for 2min then 95 degrees C for 5min; Cycling stage – 45 cycles of 95 degrees C for 0.25min then 60 degrees C for 1min; Post PCR read – 60 degrees C for 0.5 min. Ninety-six well PCR plate 1 layout - row 1 = tetB/IPC, row 2 = tetL/M, row 3 = tetO/W, row 4 = ampC/vanA, row 5 = ermB/mecA, row 6 = blaSHV/blaPSE, row 7 = floR/aadA2, row 8 = controls (pcr grade water for template – columns 9 and 10) and IPC negative control (2ul of IPC block – columns 11 and 12). Ninety-six well PCR plate 2 layout - row 1 = V.vulnificus/IPC, row 2 = V.cholerae/V.parahaemolyticus, row 3 = V.alginolyticus/V.coralliilyticus, row 4 = tetG/tetQ and the same layout of controls in row 8 as described for plate 1. Two dyes used, FAM and VIC. FAM labeled probes are tetB, tetL, tetO, ampC, ermB, blaSHV, floR, V. vulnificus, V. cholera, V. alginolyticus and tetG. VIC labeled probes are the IPC, TetM, TetW, vanA, mecA, blaPSE, aadA2, V. parahaemolyticus, V. coralliilyticus and tetQ.
    Date: 13-Oct-2020 (process 4 of 4)
    Added keywords section with USGS persistent identifier as theme keyword. Person who carried out this activity:
    U.S. Geological Survey
    Attn: VeeAnn A. Cross
    Marine Geologist
    384 Woods Hole Road
    Woods Hole, MA

    508-548-8700 x2251 (voice)
    508-457-2310 (FAX)
    vatnipp@usgs.gov
  3. What similar or related data should the user be aware of?
    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: Environmental Monitoring and Assessment v.191, Issue 2, p.1573-2959.

    Online Links:

    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: 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: 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: Marine Pollution Bulletin v.107, Issue 1, p.245–250.

    Online Links:

    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: 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: RAND Corporation, Santa Monica, CA.

    Online Links:

    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.

    W.J., Lyon, 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.

How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?
    No formal attribute accuracy tests were conducted.
  2. How accurate are the geographic locations?
    A formal accuracy assessment of the horizontal positional information in the dataset has not been conducted.
  3. How accurate are the heights or depths?
    A formal accuracy assessment of the vertical positional information in the dataset has either not been conducted, or is not applicable.
  4. Where are the gaps in the data? What is missing?
    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.
  5. How consistent are the relationships among the observations, including topology?
    No formal logical accuracy tests were conducted.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
Access_Constraints: none
Use_Constraints:
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.
  1. Who distributes the data set? (Distributor 1 of 1)
    U.S. Geological Survey
    600 4th Street South
    St. Petersburg, FL
    USA

    727-502-8000 (voice)
    dgriffin@usgs.gov
  2. What's the catalog number I need to order this data set?
  3. What legal disclaimers am I supposed to read?
    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.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 13-Oct-2020
Metadata author:
Dale W Griffin
U.S. Geological Survey, Southeast Region
Environmental and Public Health Microbiologist
600 4Th Street South
St. Petersburg, FL
USA

727-502-8075 (voice)
727-502-8182 (FAX)
dgriffin@usgs.gov
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)
This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/qPCRdata_SCoRR2015_metadata.faq.html>
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