Dale Griffin
Kenneth Banks
Kurtis Gregg
Sarah Shedler
Brian Walker
20200218
Southeast Florida and Florida Keys Antibiotic Resistance Study
Tabular Digital Data
U.S. Geological Survey Data Release
doi:10.5066/P98KQWDN
Reston, VA
U.S. Geological Survey
https://doi.org/10.5066/P98KQWDN
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 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.
20180611
20190311
ground condition
Not planned
-79.9
-82.5
26.5
24.3
ISO 19115 Topic Category
environment
biota
health
USGS Thesaurus
field monitoring stations
contamination and pollution
microbiology
genetic diversity
None
sewage outfalls
environmental health (human and ecosystem)
coral reef sediment
antibiotic resistance
Geographic Names Information System
Florida Keys
Miami-Dade County
Broward County
Oregon GEO Stratum Keywords
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)
Dale W. Griffin
Kenneth Banks
Kurtis Gregg
Sarah Shedler
Brian K. Walker
20200311
Antibiotic Resistance in Marine Microbial Communities Proximal to a Florida Sewage Outfall System
Antibiotics
9(3):118
https://doi.org/10.3390/antibiotics9030118
Shawn C. Fisher
Timothy J. Reilly
Daniel K. Jones
William M. Benzel
Dale W. Griffin
Keith A. Loftin
Luke R. Iwanowicz
Jonathan A. Cohl
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
https://doi.org/10.3133/ofr20151188B
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 carefµlly 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.
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.
20180601
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.
20180706
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.
20180709
WetSeason_PCR_data_sheet.csv
Table containing attribute information associated with the dataset. Presence/absence qPCR data are provided in comma separated values format.
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.
U.S. Geological Survey
Sample identifier
Sample type
Type of sample (sediment, water, or coral mucus) collected at each sampling location.
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
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
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
tetL
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
tetM
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
tetO
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
tetW
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
ampC
Presence/absence of cephalosporin (ampicillin, penicillin, etc.) resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
vanA
Presence/absence of Vancomyucin resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
ermB
Presence/absence of Erythromycin resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
mecA
Presence/absence of Methicillin resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
blaSHV
Presence/absence of Cephalosporin (ampicillin, penicillin, etc.) resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
blaPSE
Presence/absence of Cephalosporin (ampicillin, penicillin, etc.) resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
floR
Presence/absence of Chloramphenenicol resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
aadA2
Presence/absence of Streptomycin resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
tetG
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
tetQ
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
DrySeason_PCR_data_sheet.csv
Table containing attribute information associated with the dataset. Presence/absence qPCR data are provided in comma separated values format.
U.S. Geological Survey
Sample type
Type of sample (sediment or water) collected at each sampling location.
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
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
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
tetL
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
tetM
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
tetO
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
tetW
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
ampC
Presence/absence of Cephalosporin (ampicillin, penicillin, etc.) resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
vanA
Presence/absence of Vancomyucin resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
ermB
Presence/absence of Erythromycin resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
mecA
Presence/absence of Methicillin resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
blaSHV
Presence/absence of Cephalosporin (ampicillin, penicillin, etc.) resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
blaPSE
Presence/absence of Cephalosporin (ampicillin, penicillin, etc.) resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
floR
Presence/absence of Chloramphenenicol resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
aadA2
Presence/absence of Streptomycin resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
tetG
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
tetQ
Presence/absence of Tetracycline resistance genetic target
U.S. Geological Survey
{Null Value / Empty Field Entry}
Not detected
U.S. Geological Survey
(+/+)
Present in two of two PCR reactions
U.S. Geological Survey
Notes
Sample notes
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.
U.S. Geological Survey
Collection Date (month/day/year)
Date samples were collected
FLDEP
Sample dates in month/day/year format
Site
Sample site location
FLDEP
Site location description
Sample/Site ID
Sample site identification
FLDEP
Site identifier
Depth
Sample site depth, in feet
FLDEP
Site depth
Water Temp. (F)
Sample site water temperature, in Fahrenheit
FLDEP
Collection site water temperature
Weather
Sample site weather
FLDEP
Site descriptions of weather conditions include: seas in feet, atmospheric condition, and wind speed in knots or miles per hour.
Notes
Sample site
FLDEP
Other metadata
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 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.
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.
comma-delimited text
None
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
None
20200330
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