Southeast Florida and Florida Keys Antibiotic Resistance Study

Frequently anticipated questions:

• What does this data set describe?
  1. How might this data set be cited?
  2. What geographic area does the data set cover?
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
  5. What is the general form of this data set?
  6. How does the data set represent geographic features?
  7. How does the data set describe geographic features?
• Who produced the data set?
  1. Who are the originators of the data set?
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
• Why was the data set created?
• How was the data set created?
  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
  3. What similar or related data should the user be aware of?
• How reliable are the data; what problems remain in the data set?
  1. How well have the observations been checked?
  2. How accurate are the geographic locations?
  3. How accurate are the heights or depths?
  4. Where are the gaps in the data? What is missing?
  5. How consistent are the relationships among the data, including topology?
• How can someone get a copy of the data set?
  1. Are there legal restrictions on access or use of the data?
  2. Who distributes the data?
  3. What's the catalog number I need to order this data set?
  4. What legal disclaimers am I supposed to read?
  5. How can I download or order the data?
• Who wrote the metadata?

What does this data set describe?

1. How might this data set be cited?
   Griffin, Dale, Banks, Kenneth, Gregg, Kurtis, Shedler, Sarah, and Walker, Brian, 20200218, Southeast Florida and Florida Keys Antibiotic Resistance Study: U.S. Geological Survey Data Release doi:10.5066/P98KQWDN, U.S. Geological Survey, Reston, VA.

   Online Links:

   • https://doi.org/10.5066/P98KQWDN

2. What geographic area does the data set cover?

   West_Bounding_Coordinate: -79.9
   East_Bounding_Coordinate: -82.5
   North_Bounding_Coordinate: 26.5
   South_Bounding_Coordinate: 24.3
   

3. What does it look like?
4. Does the data set describe conditions during a particular time period?

   Beginning_Date: 11-Jun-2018

   Ending_Date: 11-Mar-2019

   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?

   WetSeason_PCR_data_sheet.csv

   Table containing attribute information associated with the dataset. Presence/absence qPCR data are provided in comma separated values format. (Source: U.S. Geological Survey)

   Tube #

   Laboratory-assigned tube number. Keys 1-24 contain samples collected from the Florida Keys and Broward 1-38 includes those acquired from Broward County. (Source: U.S. Geological Survey) Sample identifier

   Sample type

   Type of sample (sediment, water, or coral mucus) collected at each sampling location. (Source: U.S. Geological Survey) Samples obtained from Coffins Patch, a shallow coral reef located within the Florida Keys National Marine Sanctuary, were collected prior to and after diseased corals were treated with amoxicillin. Theses coral specimens had Ò -pretreatmentÓ or Ò- post treatmentÓ appended to their sample type. For example, sediment - post treatment, mucus - pretreatment, etc.

   Sample site

   Sample site location (Source: U.S. Geological Survey) A total of 80 samples were collected from mµltiple sites by FDEP, Broward County and NOAA staff. Sample sites included: Broward North WWTP, Broward North WWTP Outfall, Haµlover (Miami-Dade North) Outfall, Hollywood Outfall, Hollywood WWTP, and Miami-Dade North WWTP. Florida Keys sample sites 1 and 2 were located on Coffins Patch Reef.

   tetB

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   tetL

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   tetM

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   tetO

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   tetW

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   ampC

   Presence/absence of cephalosporin (ampicillin, penicillin, etc.) resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   vanA

   Presence/absence of Vancomyucin resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   ermB

   Presence/absence of Erythromycin resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   mecA

   Presence/absence of Methicillin resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   blaSHV

   Presence/absence of Cephalosporin (ampicillin, penicillin, etc.) resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   blaPSE

   Presence/absence of Cephalosporin (ampicillin, penicillin, etc.) resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   floR

   Presence/absence of Chloramphenenicol resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   aadA2

   Presence/absence of Streptomycin resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   tetG

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   tetQ

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   DrySeason_PCR_data_sheet.csv

   Table containing attribute information associated with the dataset. Presence/absence qPCR data are provided in comma separated values format. (Source: U.S. Geological Survey)

   Sample type

   Type of sample (sediment or water) collected at each sampling location. (Source: U.S. Geological Survey) Water samples were obtained from either the water column or the wastewater treatment plant tap water effluent.

   Sample site

   Sample site location (Source: U.S. Geological Survey) Sample sites included: Broward North WWTP, Broward North WWTP Outfall, Haµlover Outfall (Miami-Dade North), Hollywood Outfall, Hollywood WWTP, and Miami-Dade North WWTP.

   tetB

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   tetL

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   tetM

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   tetO

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   tetW

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   ampC

   Presence/absence of Cephalosporin (ampicillin, penicillin, etc.) resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   vanA

   Presence/absence of Vancomyucin resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   ermB

   Presence/absence of Erythromycin resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   mecA

   Presence/absence of Methicillin resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   blaSHV

   Presence/absence of Cephalosporin (ampicillin, penicillin, etc.) resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   blaPSE

   Presence/absence of Cephalosporin (ampicillin, penicillin, etc.) resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   floR

   Presence/absence of Chloramphenenicol resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   aadA2

   Presence/absence of Streptomycin resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   tetG

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected

   tetQ

   Presence/absence of Tetracycline resistance genetic target (Source: U.S. Geological Survey)

   Value	Definition
   {Null Value / Empty Field Entry}	Not detected
   (+/+)	Present in two of two PCR reactions

   Notes

   Sample notes (Source: U.S. Geological Survey) sed## = sediment sample, distance from outfall pipe in meters. (+/+) = two positive PCR reactions. IPC normal reaction was set at a Rn (normalized reporter) value of 0.1 with a CT (threshold cycle) of 28 plus or minus 1. Target reactions were judged positive if they breached the Rn of 0.1 with an exponential type signal in both reactions. {Null Value / Empty Field Entry} means no notes were recorded.

   FLDEPSampleCollectionLog_DrySeason.csv, FLDEPSample CollectionLog_WetSeason.csv

   Table containing attribute information associated with the dataset. Presence/absence qPCR data are provided in comma separated values format. (Source: U.S. Geological Survey)

   Collection Date (month/day/year)

   Date samples were collected (Source: FLDEP) Sample dates in month/day/year format

   Site

   Sample site location (Source: FLDEP) Site location description

   Sample/Site ID

   Sample site identification (Source: FLDEP) Site identifier

   Depth

   Sample site depth, in feet (Source: FLDEP) Site depth

   Water Temp. (F)

   Sample site water temperature, in Fahrenheit (Source: FLDEP) Collection site water temperature

   Weather

   Sample site weather (Source: FLDEP) Site descriptions of weather conditions include: seas in feet, atmospheric condition, and wind speed in knots or miles per hour.

   Notes

   Sample site (Source: FLDEP) Other metadata

   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 were 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 Griffin
   • Kenneth Banks
   • Kurtis Gregg
   • Sarah Shedler
   • Brian Walker
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 objective of this project was to determine the prevalence of 15 antibiotic resistant genes (tetB, tetG, tetL, tetM, tetO, tetQ, tetW, ampC, vanA, ermB, mecA, blaSHV, blaPSE, floR, and aadA2) in bacterial popµlations in impacted (close to and alongside outfall pipes and within the wastewater stream) and control (along transects extending away from the outfalls) sediment samples around the Hollywood, FL wastewater treatment plantÕs ocean outfall. A total of 38 wet season and 42 dry season samples were collected by the Florida Department of Environmental Protection, Broward County and National Oceanic and Atmospheric Administration (NOAA) research teams and shipped to and analyzed by scientists at the U.S. Geological Survey (USGS) St. Petersburg Environmental and Public Health Microbiology Laboratory.

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: 01-Jun-2018 (process 1 of 4)

   Sediment, coral mucus and water samples acquired from Southeast Florida between 2018 and 2019 were analyzed for 15 different antibiotic resistant gene targets via PCR presence/absence assays. The SCoRR standard operating procedure (SOP) (Fisher and others, 2015) details a related study using similar collection methods to those utilized for this project with the exception of the coral mucus samples, which were collected by aspiration, using a sterile 60 cubic centimeter plastic syringe. The SOP provides step-by-step instructions for site preparation, sample processing, quality assurance, and shipping of soil and surficial bed sediment.

   Date: 06-Jul-2018 (process 2 of 4)

   DNA extraction was performed by first calibrating the Mettler scale with a 50-gram (g) certified weight and then documenting that value on the Mettler QA/QC sheet. Using sterile-techniques, approximately 0.25 g of sediment or 200 microliters (µl) of water from each sample was weighted out or pipetted and transferred to a MoBio PowerSoil bead beating tube. Sample weight or volume was logged in the project electronic laboratory notebook (ELN). The MoBio PowerSoil kit protocol was used to elute DNA to a volume of 100 µl using Qiagens AE buffer recipe (10 millimolar (mM) Tris-HCL, 0.5 mM EDTA, pH 9.0, filter sterilized and autoclaved). Eluted DNA was stored at -70 degrees Celsius (¡C) until use.

   Date: 09-Jul-2018 (process 3 of 4)

   The following recipes and plate(s) layouts were used to set up quantitative polymerase chain reaction (qPCR) reactions. All reactions were run in duplicate and positives were those reactions where amplification was noted in both reactions that reached a normalized reporter signal (Rn) value of 0.1 (with an exponential trend). All duplicate positives were screened with digital PCR. Master Mix recipes (volumes per reaction) are as follows: Single probe reactions Ð 20 µl reactions - row 1 Internal Positive Control (IPC): 2x TaqMan Fast Universal Master Mix (10 µl); Template (2 µl); Primer/probe (10 micrometers (µm)/5 µm working stock) (1 µl each); 10x Exo Internal Positive Control (2 µl); 50x EXo IPC DNA (0.4 µl); PCR grade water (4.6 µl). IPC control reactions - row 8: 2x TaqMan Fast Universal Master Mix (10 µl); Template (2 µl); 10x Exo Internal Positive Control (2 µl); 50x EXo IPC DNA (0.4 µl); PCR grade water (5.6 µl). Mµltiplex (two primer and probe sets) Ð rows 2 through 7: 2x TaqMan Fast Universal Master Mix (10 µl); Template (2 µl); primer/probe (10 µm/5 µm working stock) (1 µl each); PCR grade water (6.0 µl). PCR amplification profile Master details are as follows: Pre PCR read Ð 60 ¡C for 0.5 minutes (min); Holding stage Ð 50 ¡C for 2 min then 95 ¡C for 5 min; Cycling stage Ð 45 cycles of 95 ¡C for 0.25 min then 60 ¡C for 1 min; Post PCR read Ð 60 ¡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 Ð columns 9 and 10) and IPC negative control (2 µl of IPC block Ð columns 11 and 12). Ninety-six well PCR plate 2 layout - row 1-7 = tetG/tetQ for all the samples and the same layout of controls in row 8 as described for plate 1. Two dyes, FAM and VIC, were used to monitor amplification in the real-time PCR reaction assays. FAM-labeled probes are tetB, tetL, tetO, ampC, ermB, blaSHV, floR, and tetG. VIC-labeled probes are the IPC, TetM, TetW, vanA, mecA, blaPSE, aadA2, 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, Dale W., Banks, Kenneth, Gregg, Kurtis, Shedler, Sarah, and Walker, Brian K., 20200311, Antibiotic Resistance in Marine Microbial Communities Proximal to a Florida Sewage Outfall System: Antibiotics 9(3):118.

   Online Links:

   • https://doi.org/10.3390/antibiotics9030118

   Fisher, Shawn C., Reilly, Timothy J., Jones, Daniel K., Benzel, William M., Griffin, Dale W., Loftin, Keith A., Iwanowicz, Luke R., and Cohl, Jonathan A., 20151217, Standard operating procedure for collection of soil and sediment samples for the Sediment-bound Contaminant Resiliency and Response (SCoRR) strategy pilot study: U.S. Geological Survey Open-File Report 2015-1188b.

   Online Links:

   • https://doi.org/10.3133/ofr20151188B

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 carefµlly 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?
   • Availability in digital form:

     Data format:	comma-delimited text (version None)
     Network links:	https://coastal.er.usgs.gov/data-release/doi-P98KQWDN/data/WetSeason_PCR_data_sheet.zip https://coastal.er.usgs.gov/data-release/doi-P98KQWDN/data/DrySeason_PCR_data_sheet.zip https://coastal.er.usgs.gov/data-release/doi-P98KQWDN/data/FLDEPSampleCollectionLog_WetSeason.zip https://coastal.er.usgs.gov/data-release/doi-P98KQWDN/data/FLDEPSampleCollectionLog_DrySeason.zip

   • Cost to order the data: None

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)