U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2015–1013

Prepared in cooperation with the Great Lakes Restoration Initiative

Occurrence and Distribution of Fecal Indicator Bacteria and 

Gene Markers of Pathogenic Bacteria in Great Lakes 

Tributaries, March–October 2011
Cover: Bad River, Wisconsin (photo by Eric Dantoin, U.S. Geological Survey).
Occurrence and Distribution of Fecal 

Indicator Bacteria and Gene Markers 

of Pathogenic Bacteria in Great Lakes 

Tributaries, March–October 2011

By Angela K. Brennan, Heather E. Johnson, Alex R. Totten, and Joseph W. Duris

Prepared in cooperation with the Great Lakes Restoration Initiative

Open-File Report 2015–1013

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2015

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Suggested citation:

Brennan, A.K., Johnson, H.E., Totten, A.R., and Duris, J.W., 2015, Occurrence and distribution of fecal indicator bacteria and gene markers of pathogenic bacteria in Great Lakes tributaries, March–October 2011: U.S. Geological Survey 

Open-File Report 2015–1013, 29 p., http://dx.doi.org/10.3133/ofr20151013.

ISSN 2331-1258 (online)
iii

Contents

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................1

Purpose and Scope ..............................................................................................................................2

Description of Study Area ...................................................................................................................2

Sampling and Analytical Methods..............................................................................................................2

Site Selection.........................................................................................................................................2

Sample Collection.................................................................................................................................2

Microbiological Analyses ...................................................................................................................6

Bacteria Enumeration, Enrichment, and Preservation..........................................................6

DNA Extraction.............................................................................................................................6

Polymerase Chain Reaction Assays for Pathogen Detection ..............................................6

Results of Microbiological Analyses..........................................................................................................6

Occurrence and Distribution of Fecal Indicator Bacteria .............................................................6

Occurrence and Distribution of Bacterial Pathogen Gene Markers ...........................................8

Quality-Control Results ...............................................................................................................................10

Summary........................................................................................................................................................10

Acknowledgements.....................................................................................................................................11

References Cited..........................................................................................................................................11

Appendixes ................................................................................................................................................13

Figures

1. Graph showing land cover surrounding tributary sites sampled as part of the 

Great Lakes Restoration Initiative (GLRI) pathogens study...................................................3

2. Map showing Great Lakes Restoration Initiative (GLRI) USGS tributary sampling 

locations and number of samples collected for pathogens study, 2011 .............................4

3. Graph showing frequency of samples testing positive for pathogen gene markers ........8

4. Graph showing percentage of pathogen gene markers in relation to water quality 

criteria.....................................................................................................................................................9

Tables

1. Great Lakes Restoration Initiative (GLRI) pathogens study sampling locations, 2011......5

2. Growth media, target organisms, and incubation temperature requirements for the 

Great Lakes Restoration Initiative (GLRI) pathogens study...................................................7

3. Selected pathogen gene targets and virulence traits of the organism...............................7

4. Summary of the frequency of pathogen gene detections in a single sample....................8

5. Percentage of samples that tested positive for pathogenic gene markers during 

high-flow and normal-flow conditions ......................................................................................9

6. Relative standard deviation of field replicates for quantitative microbial methods 

in the Great Lakes Restoration Initiative (GLRI) pathogens study......................................10

7. Frequency of agreement between field replicates for qualitative microbial 

methods in the Great Lakes Restoration Initiative (GLRI) pathogens study .....................10
iv

Multiply By To obtain

Length

mile (mi) 1.609 kilometer (km)

Area

square mile (mi2

) 2.590 square kilometer (km2) 

Volume

milliliter (mL) 1,000 microliter (μL)

Temperature in degrees Celsius (°C) may be converted to degrees 

Fahrenheit (°F) as follows: °F=(1.8×°C)+32

Horizontal coordinate information is referenced to North American 

Datum of 1983 (NAD 83).

Concentrations of fecal indicator bacteria are given in colonyforming units per 100 milliliters (CFU/100 mL).

Conversion Factors
v

Abbreviations used in report

CDC Centers for Disease Control and Prevention

CFU colony-forming unit

DNA Deoxyribonucleic acid

E. coli Escherichia coli

EWI equal-width-increment

FIB Fecal indicator bacteria

GLRI Great Lakes Restoration Initiative

MI-BaRL USGS Michigan Bacteriological Research Laboratory

MI-WSC USGS Michigan Water Science Center

PBS phosphate buffered saline

PCR polymerase chain reaction

QC quality control

RSD relative standard deviation

STEC Shiga-toxin producing Escherichia coli

EPA U.S. Environmental Protection Agency

USGS U.S. Geological Survey

WQC water quality criteria

Occurrence and Distribution of Fecal Indicator Bacteria 

and Gene Markers of Pathogenic Bacteria in Great Lakes 

Tributaries, March–October 2011

By Angela K. Brennan, Heather E. Johnson, Alex R. Totten, and Joseph W. Duris

Abstract

From March through October 2011, the U.S. Geological 

Survey (USGS), conducted a study to determine the frequency 

of occurrence of pathogen gene markers and densities of fecal 

indicator bacteria (FIB) in 22 tributaries to the Great Lakes. 

This project was funded as part of the Great Lakes Restoration Initiative (GLRI) and included sampling at 22 locations 

throughout 6 states that border the Great Lakes. 

A total of 177 environmental samples were collected at 

USGS streamgaging stations during both normal-flow and 

high-flow conditions and were analyzed by the Michigan Bacteriological Research Laboratory at the USGS Water Science 

Center in Lansing, Michigan. 

Water samples were analyzed for the presence of FIB 

concentrations (FIB; fecal coliform bacteria, Escherichia 

coli [E. coli], and enterococci) by using membrane filtration 

and serial dilution methods. The resulting enrichments from 

standard culturing of the samples were then analyzed by using 

polymerase chain reaction (PCR) to determine the occurrence 

of pathogen gene markers for Shigella species, Campylobacter 

jejuni and coli, Salmonella species, and pathogenic E. coli, 

including Shiga toxin-producing E. coli (STEC). 

Introduction

In 2009, the Great Lakes Restoration Initiative (GLRI) 

was started as an interagency initiative to protect and restore 

the Great Lakes. This report describes data collected in 2011 

as part of the U.S. Geological Survey (USGS) GLRI effort led 

by the Michigan Water Science Center (MI-WSC), in conjunction with USGS Water Science Centers in Indiana, Minnesota, 

Ohio, New York, and Wisconsin, and complements the ongoing USGS GLRI Great Lakes Nutrient and Sediment Loadings 

study (GLRI Loadings study) being conducted at the same 

sampling locations. 

The microbiological monitoring network for this study 

consisted of 22 sampling locations, representing multiple 

land-use types, drainage areas, and soil characteristics typical 

of the Great Lakes region. Samples were collected to better 

understand the occurrence and distribution of fecal indicator 

bacteria (FIB) and selected bacterial pathogens that are commonly associated with waterborne illnesses.

Within the broad FIB groups (Escherichia coli [E. coli], 

fecal coliforms, and enterococci), there are specific strains of 

bacteria that are pathogenic (infection causing) to humans. 

The bacterial pathogen gene markers evaluated in this study 

included genes from the genera Shigella, Campylobacter 

(jejuni and coli) and Salmonella. In addition, several genes 

were also evaluated from a class of pathogenic E. coli known 

as Shiga toxin-producing E. coli (STEC), which includes E. 

coli O157:H7. 

Fecally derived bacterial pathogens have long been 

known to be a health threat to humans, and exposure to these 

pathogens can result in illness and occasionally even death 

(Centers for Disease Control and Prevention [CDC], 2012b). 

STEC, including E. coli O157:H7, can cause illness ranging 

from mild intestinal disease to severe kidney complications 

and death in animals and humans (CDC, 2012d). Shigella’s 

pathogenicity functions similarly to that of STEC; however, 

Shigella mainly affects humans. Campylobacter is one of the 

most common causes of diarrheal illness in the United States, 

and symptoms include cramping, abdominal pain, and fever 

(CDC, 2012a). Salmonella infection can cause diarrhea, fever, 

and abdominal cramps, and severe cases can even lead to 

death (CDC, 2012c).

Current methods for evaluating recreational and drinking 

water safety typically rely on the enumeration of FIB (U.S. 

Environmental Protection Agency [EPA], 2012). FIB are 

used to indicate the potential for illness associated with fecal 

contamination (EPA, 2012). Primary contact refers to watercontact activities where immersion and ingestion are likely, 

such as swimming, water skiing, and diving. Even though 

most tributaries are not used for “primary contact” recreational 
2 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries

water activities, many of these major tributaries enter the 

Great Lakes at or near a beach which is designated as a recreation area. Most tributaries are used for partial, or secondary, 

contact recreation, indicating water activities where there is 

the potential of submergence, such as boating and fishing. 

FIB concentrations and the occurrence of bacterial pathogens 

associated with these bodies of water are important, not only 

to partial contact recreational users in rivers but ultimately to 

primary contact recreational users at Great Lakes beaches. The 

partial body contact recreation standard (Dufour and Ballantine, 1986) was used for data interpretation for this report 

because the EPA 2012 guidance does not include a numerical 

standard for partial body contact in recreational waters.

Purpose and Scope

This report presents data obtained during a Great Lakeswide study conducted in 2011 by the USGS as part of the 

GLRI. The purpose of this study was to determine the occurrence and distribution of FIB and pathogenic gene markers 

within 22 major tributaries to the Great Lakes. Normal-flow 

and high-flow samples were analyzed for FIB and for pathogens Shigella, Campylobacter (jejuni and coli), Salmonella, 

and STEC, which included E. coli O157:H7. The relations of 

FIB concentrations and bacterial pathogen gene occurrence to 

recreational water quality criteria were also assessed. 

Description of Study Area

Approximately 132,208 miles of tributaries (EPA and 

USGS, 2012), with a drainage area of almost 295,000 square 

miles (Great Lakes Information Network, 2013), drain into the 

Great Lakes from six states (Indiana, Michigan, Minnesota, 

New York, Ohio, Wisconsin) and Canada. The 22 monitoring 

locations are grouped on the basis of predominant land cover 

surrounding the major tributaries in this study (fig. 1) (USGS, 

2011) and were distributed geographically throughout the 

Great Lakes region of the United States (fig. 2).

Sampling and Analytical Methods

Site Selection

All sampling locations were at USGS streamgaging 

stations. Twenty-two sampling locations (fig. 2, table 1) were 

selected (out of 59 GLRI Loadings study sites) to create a geographically distributed study and to address the variability in 

land cover throughout the Great Lakes region. Sampling locations, as well as timing of sample collection, were designed to 

complement the GLRI Loadings study (USGS, 2014). In addition to those sites selected from the GLRI Loadings study, the 

Paw Paw River at Riverside, MI, was included as a sampling 

location for this study because the site was routinely visited as 

part of another USGS MI-WSC project.

Sample Collection

Hydrologic conditions were determined on the basis of 

mean daily discharge1 at each USGS streamgage on the date of 

collection, calculated from date of first record to current. Conditions were evaluated such that if daily discharge2

 was greater 

than or equal to the 75th percentile, the corresponding sample 

was considered a high-flow sample; otherwise, the sample 

was considered a normal-flow sample. Owing to a short 

period of record, the Grand River at Grand Rapids station was 

used to estimate hydrologic conditions for the Grand River 

at Eastmanville station. Water samples were collected during 

normal-flow conditions from March through October 2011 in 

an effort to target the recreational water season. Samples were 

also collected during high-flow conditions (storm events), 

but sampling frequency varied among sites in response to the 

frequency of storm events and availability of staff (table 1). 

The sampling frequency depended on the sampling 

schedule of the GLRI Loadings study. Some sites were 

sampled more often than others, including those sites targeted 

for analysis of certain chemical constituents (such as wastewater indicator compounds) in addition to FIB and pathogenic 

gene markers.

Normal-flow and high-flow sampling events typically 

coincided with GLRI Loadings study sampling. All samples 

were collected by USGS personnel using either equal-widthincrement (EWI) or multiple vertical sampling techniques 

designed to account for the variable distribution of constituents across the stream channel and throughout the water 

column (USGS, 2006). EWI samples were typically collected 

off bridges by using a crane apparatus with an attached DH-95 

depth integrating sampler, or from boats. There were instances 

when wading measurements were made, but typically only 

during normal-flow conditions.

For each sample, a 1-liter sterile high density polyethylene (HDPE) sample bottle was filled to the shoulder to allow 

some head space for sample mixing. Once collected, water 

samples were placed on ice in a cooler (away from ultraviolet 

light) and shipped overnight to the MI-BaRL (Michigan Bacteriological Research Laboratory) at the MI-WSC in Lansing, 

Michigan. Upon receipt of the shipments, sample information 

and streamflow condition were logged in to the laboratory 

database system, and samples were placed into the refrigerator 

at 4–7 degrees Celsius (°C) until processing and analysis (typically the same day).

A total of 177 water samples were collected, including 

field quality-control (QC) samples. There were 59 normalflow samples and 54 high-flow samples used for data analysis. 

Quality-control samples included 21 field blank samples, 21 

source solution blank samples, and 22 field replicate samples. 

1

The arithmetic mean of discharges for all instances of a particular calendar 

day on record or for a specific set of years.

 2The arithmetic mean discharge for a single day.
Sampling and Analytical Methods 3

0 

50 40 30 20 10 

Land cover within sampling-location drainage area, in percent. River Rouge, MI

Clinton River, MI

St. Joseph River, MI

St. Louis River, MN

River Raisin, MI

Ontonagon River, MI

Au Sable River, MI

Genessee River, NY

Oswego River, NY

St. Regis River, NY

Cuyahoga River, OH

Maumee River, OH

Portage River, OH

Fox River, WI

Saginaw River, MI

Grand River, MI

Burns Ditch, IN

Milwaukee River, WI

Manitowoc River, WI

Bad River, WI

Menominee River, WI

100 

90 80 70 60 

Land cover types

EXPLANATION

Tributary sampling location

Shrubland/Water/BarrenWetlands

Agricultural (Includes Herbaceous  upland, planted/cultivated)

ForestDeveloped

Figure 1. Land cover surrounding tributary sites sampled as part of the Great Lakes Restoration Initiative (GLRI) pathogens study (data from 2006 National 

Land Cover Data [USGS, 2011]).
4 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries St. Louis River at Scanlon, MN (ST) Bad River nr Odanah, WI (BD)Ontonagon River nr Rockland, MI (ON) Menominee River nr McAllister, WI (MM) Fox River at Oil Tank Depot at Green Bay, WI (FX) Manitowoc River at Manitowoc, WI (MN) Milwaukee River at Milwaukee, WI (MW) Burns Ditch at Portage, IN (BN) St. Joseph River at Niles, MI (SJ) Au Sable River nr Au Sable, MI (AU) Saginaw River at Saginaw, MI (SG) Clinton River at Moravian Drive at Mt. Clemens, MI (CL) River Rouge at Detroit, MI (RR) River Raisin nr Monroe, MI (RS) Maumee River at Waterville, OH (MA) Portage River at

Woodville, OH (PO)

Cuyahoga River atIndependence, OH (CY)

Genessee River atFord St. Bridge, Rochester, NY (GS)

Oswego River atLock 7, Oswego, NY (OS)

St. Regis River atBrasher Center, NY (SR)

Grand River nrEastmanville, MI (GR)

Paw Paw River atRiverside, MI (PP)

75° 80° 85° 90°

45°40°

0 50 100 150 200 250MILES0 50 100 150 200 250KILOMETERS

Base from ESRI, GEBCO, NOAA, National Geographic, DeLorme, HERE, Geonames.org, and other contributors

Hydrology modified from U.S. Geological Survey, ERF1_2 - -

Enhanced River Reach File 2.0, 2002

EXPLANATION

USGS GLRI pathogen samplinglocation with field IDStream

W I S C O N S I N

I N D I A N A

O H I O

N E W Y O R K

M I C H I G A N

M I C H I G A N

M I N N E S O T A

I L L I N O I S P E N N S Y L V A N I A

Figure 2. Great Lakes Restoration Initiative (GLRI) USGS tributary sampling locations and number of samples collected for pathogens study, 2011.
Sampling and Analytical Methods 5

Field blanks, source solution blanks, and field replicate samples were collected according to the methods described in the 

USGS National Field Manual, with inorganic-grade reagent 

water being used as the sample medium (USGS, 2006). 

Twelve samples were excluded from the data analysis because 

the samples exceeded the holding time (48 hours) established 

by the MI-BaRL for FIB culturing for nonregulatory purposes. 

There were also three instances where the bacteria plates 

were uncountable (coded as “unc”), owing to smearing or a 

heavy amount of particulates on the filter. A total of 165 water 

samples were included in the final analysis.

Table 1. Great Lakes Restoration Initiative (GLRI) pathogens study sampling locations, 2011.

[nr, near]

USGS site name

USGS site 

identification 

number

Field 

ID

Number of samples 

collected during 

normal flow

Number of samples 

collected during 

high flow

Indiana

Burns Ditch at Portage 04095090 BN 3 4

Michigan

Au Sable River nr Au Sable 04137500 AU 5 1

Clinton River at Moravian Drive at Mt. Clemens 04165500 CL 0 2

Grand River nr Eastmanville 04119400 GR 0 5

Ontonagon River nr Rockland 04040000 ON 8 1

Paw Paw River at Riverside 04102500 PP 2 5

River Rouge at Detroit 04166500 RR 1 2

River Raisin nr Monroe 04176500 RS 2 0

Saginaw River at Saginaw 04157000 SG 5 3

St. Joseph River at Niles 04101500 SJ 3 4

Minnesota

St. Louis River at Scanlon 04024000 ST 7 2

New York

Genessee River at Ford St. Bridge at Rochester 04231600 GS 3 3

Oswego River at Lock 7 at Oswego 04249000 OS 4 4

St. Regis River at Brasher Center 04269000 SR 5 5

Ohio

Cuyahoga River at Independence 04208000 CY 1 4

Maumee River at Waterville 04193500 MA 2 1

Portage River at Woodville 04195500 PO 0 3

Wisconsin

Bad River nr Odanah 04027000 BD 3 1

Fox River at Oil Tank Depot at Green Bay 040851385 FX 1 1

Menominee River nr McAllister 04067500 MM 2 0

Manitowoc River at Manitowoc 04085427 MN 1 1

Milwaukee River at Milwaukee 04087170 MW 1 1
6 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries

Microbiological Analyses 

Bacteria Enumeration, Enrichment, and 

Preservation

Water samples were analyzed for the presence of FIB and 

FIB concentrations by using standard membrane filtration and 

serial dilution methods (Myers and others, 2014). Fecal coliform bacteria were analyzed according to standard methods 

of the American Public Health Association and others (1998), 

E. coli bacteria were analyzed according to EPA method 1603 

(EPA, 2009a), and enterococci bacteria were analyzed according to EPA method 1600 (EPA, 2009b). Media were prepared 

according to manufacturer’s instructions.

A volume of 50 milliliters (mL) of sample water was 

filtered through a 0.45-micrometer-pore-size nylon-membrane 

filter (Advantec, USA) by means of aseptic techniques. The 

enriched filter was then placed on a selective growth medium 

for enumeration and enrichment of target bacterial pathogen 

groups and incubated at the optimal temperature (table 2).

The filters with E. coli, enterococci, and fecal coliform 

bacteria growth were transferred to a vial containing 1 mL of 

phosphate buffered saline solution (PBS), preserved with 20 

percent glycerol, and frozen at −70 °C until further analysis; 

these samples are referred to as “glycerol stocks.” The filters 

with Campylobacter and Salmonella growth were aseptically 

removed from the Gram Negative and Bolton Broth enrichments, and the remaining culture was centrifuged to form 

a pellet. The supernatant was decanted, and the pellet was 

resuspended in 1 mL of PBS solution and preserved with 20 

percent glycerol and frozen at −70 °C until deoxyribonucleic 

acid (DNA) extraction.

DNA Extraction

Glycerol stocks were thawed at room temperature and 

DNA was extracted by using the Qiagen QIAamp® DNA 

Mini Kit (Qiagen, USA), following the manufacturers protocol. DNA concentrations and purity were determined with a 

NanoDrop spectrophotometer (Thermo Scientific, USA). DNA 

was then stored at −20 °C until needed for Polymerase Chain 

Reaction (PCR) analysis for the selected gene targets (table 3). 

Polymerase Chain Reaction Assays for Pathogen 

Detection

Samples were analyzed by using PCR to determine the 

occurrence of pathogen gene markers for Shigella sonnei, 

Campylobacter jejuni and coli, Salmonella, and STEC. The 

primer sequences, positive controls, reaction details, and quality-control procedures used for the detection of the pathogens 

by PCR listed in table 3 were based on previously published 

studies (Haack and others, 2013).

All PCR assays were performed by using 1 microliter 

of DNA solution, representing 0.1–85 nanograms of template 

DNA, which was isolated from the appropriate growth enrichment. Results from these analyses indicated whether the target 

genes were present or absent in the sample above the method 

detection limit; however, PCR does not quantify the genes 

present. In order for the gene to be detected, the organism had 

to grow on the appropriate medium, and therefore must have 

been viable in the sample. 

Laboratory filtration blanks were processed daily with 

every set of samples on all growth media and enrichments 

to ensure that the laboratory equipment was sterile and that 

aseptic laboratory techniques were being followed. One set 

of laboratory replicates was processed weekly on all growth 

media and enrichments to quantify method variability. If contamination was found in the laboratory blanks, either sample 

results were discarded or samples were rerun. 

Standard quality-assurance and quality-control procedures were followed for all PCR reactions (EPA, 2004). 

Detection limits for all PCR reactions were determined by 

using serial dilution of DNA from control organisms. For 

approximately every 20 samples of any given PCR assay, PCR 

positive controls (DNA extracted from bacteria known to contain the target gene) and PCR negative controls (no template 

reactions) were included. 

Results of Microbiological Analyses

Of the 177 water samples collected, 12 samples were 

omitted from the data analysis because of holding-time violations and 64 of the samples were collected for the analysis of 

quality control. The 165 samples included in the analyses were 

assessed for occurrence and distribution of FIB during normal 

and high flows and for whether the samples exceeded the 

water quality criteria. These samples were also analyzed for 

specific pathogen genes by using PCR. Fecal indicator bacteria 

results are included in the USGS National Water Information 

System (NWIS) database. 

Occurrence and Distribution of Fecal Indicator 

Bacteria

Fecal coliform concentrations ranged from < 2 to 950 

colony-forming units per 100 mL (CFU/100 mL), E. coli

concentrations ranged from < 2 to 26,000 CFU/100 mL, 

and enterococci concentrations ranged from < 2 to 31,000 

CFU/100 mL. Fecal indicator bacteria concentrations for all 

samples are presented in appendix 1.

The lowest E. coli concentrations were recorded at the Au 

Sable River near Au Sable, MI (AU) (during high and normal 

flows), and the St. Joseph River at Niles, MI (during normal 

flow) (SJ). The highest E. coli concentrations were recorded at 
Results of Microbiological Analyses 7

the River Rouge at Detroit, MI (during high flow) (RR). The 

lowest enterococci concentrations were recorded at the Au 

Sable River near Au Sable, MI (AU) (during high and normal 

flows), and the Oswego River at Lock 7 at Oswego, NY (OS) 

(during high flow). The highest enterococci concentrations 

were recorded at the River Rouge at Detroit, MI (RR) (during 

high flow). The lowest E. coli and enterococci concentrations 

were found at sites dominated by forest and agricultural land 

cover, whereas the highest E. coli and enterococci concentrations were recorded at sites dominated by urban development.

Enterococci and E. coli concentrations were evaluated 

on the basis of whether the data met or exceeded the 1986 

EPA criterion for moderate full body contact recreation for 

freshwater for a single sample (Dufour and Ballantine, 1986). 

The moderate full body contact recreation criterion was 

considered most applicable for this study given the type of 

recreation typically found on rivers; for example, kayaking, 

canoeing, and fishing. The moderate full body contact criterion 

for enterococci for a single sample is greater than or equal to 

78 CFU/100 mL; and for E. coli, the recreation criterion is 

greater than or equal to 298 CFU/100 mL for a single sample. 

Of 112 samples analyzed for FIB concentrations, 21 percent of 

samples exceeded the EPA recreation criterion for E. coli, and 

40 percent of samples exceeded the criterion for enterococci. 

During high-flow events, 43 percent of all samples 

exceeded the EPA recreation criterion for E. coli, and 61 percent of samples exceeded the criterion for enterococci. During 

normal-flow conditions, about 2 percent of samples exceeded 

the criterion for E. coli, and about 21 percent of samples 

exceeded the criterion for enterococci. 

Table 2. Growth media, target organisms, and incubation temperature requirements for the Great Lakes 

Restoration Initiative (GLRI) pathogens study.

[mL, milliliters; °C, degrees Celsius; E. coli, Escherichia coli]

Growth media Organism or method Volume 

filtered (mL)

Incubation temperature and time 

requirement

mFC Fecal coliform bacteria 

(E. coli, Shigella)

50 44.5 °C ± 0.5 °C for 22–24 hours

Modified mTEC E. coli 50, 10, 1 35–37 °C for 2 hours, then 44.5 °C 

± 0.5 °C for 20–22 hours

mEI Enterococci 50, 10, 1 41 °C ± 0.5 °C for 22–24 hours

Bolton Broth (BB) with Preston1

supplement

Campylobacter 50 37 °C for 4 hours, then 42 °C 

for 40–44 hours

Gram Negative Broth (GN) Salmonella 50 37°C ± 1.0 °C for 22–24 hours

1

Oxoid, Cambridge, United Kingdom.

Pathogen Gene target Virulence trait

E. coli eaeA Attachment

E. coli stx2 Severe toxin

E. coli stx1 Moderate toxin

E. coli rfbO157 Common outbreak strain

Shigella ipaH Invasion

Salmonella invA Invasion

Salmonella spvC Multiple virulence traits

Campylobacter jejuni and coli 16s rDNA (Campy) Pathogenic species marker

Table 3. Selected pathogen gene targets and virulence traits of the organism.

[E. coli, Escherichia coli]
8 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries

Occurrence and Distribution of Bacterial 

Pathogen Gene Markers

Data from the E. coli pathogen analysis showed that 68 

percent of samples contained the eaeA gene, 20 percent of 

samples contained the stx2 gene, 12 percent of samples contained the stx1 gene, and 11 percent of samples contained the 

rfbO157 gene (fig. 3). Data from the Shigella analysis showed 

that 6 percent of samples contained the ipaH gene. Data from 

the Salmonella analysis showed that 7 percent of samples contained the invA gene and 14 percent of samples contained the 

spvC gene. Data from the Campylobacter analysis showed that 

9 percent of samples contained the 16s rDNA gene (fig. 3). 

Detections of bacterial pathogen gene markers by site and by 

sample are listed in appendix 3.

The frequency of pathogen gene markers detected in 

each sample is summarized in table 4. The greatest number of 

pathogen gene markers detected in any one sample was seven 

(River Rouge at Detroit, MI, during a May 26, 2011, high-flow 

event). This same May 26, 2011 sample from the River Rouge 

also contained the highest E. coli and enterococci concentrations of samples collected during this project (E. coli value 

of 26,000 CFU/100 mL; enterococci value, 31,000 CFU/100 

mL). 

0

10

20

30

40

50

60

70

80

eaeA stx2 stx1 rfb0157 ipaH invA spvC C. coli/C. jejuni

Positive samples, in percent

Gene marker

Figure 3. Frequency of samples testing positive for pathogen gene markers (C. coli, Campylobacter coli; 

C. jejuni, Campylobacter jejuni).

Figure 3. Frequency of samples testing positive for pathogen gene markers (C. coli, Campylobacter coli; C. 

jejuni, Campylobacter jejuni).

Table 4. Summary of the frequency of pathogen gene detections in a single sample.

[<, less than]

Flow conditions

Number of bacterial pathogen genes present

0 1 2 3 4 5 6 7 8

Percentage of samples in which the indicated number of genes were detected

High flow 10 12 13 2 3.5 6 0 1 0

Normal flow 16 25 10 1 <1 0 0 0 0

Total percent detection 26 37 23 3 4 6 0 1 0
Results of Microbiological Analyses 9

For those samples in which 3 or more genes were present, 14 of the 16 samples were collected during high-flow 

conditions. 

Pathogen frequency was analyzed in relation to hydrologic condition among all sites, as illustrated in figure 4. 

Overall, a higher percentage of samples tested positive for 

pathogens under high-flow conditions than during normal-flow 

conditions. For Campylobacter, the differences in the percentage of samples that were positive for pathogens between highand normal-flow conditions were less obvious. The invA gene 

for Salmonella was found only during high flows.

 The frequencies of pathogen gene occurrence in samples 

that met and exceeded the EPA criteria for moderate full body 

contact recreation for E. coli and enterococci were compared 

for the 22 sites (table 5). Fisher’s Exact Test was run to determine if there was a significant difference (p-value less than 

0.05) between gene detection in samples that met or exceeded 

the water quality criteria. Overall, there was a greater occurrence of pathogen gene markers in samples that exceeded the 

moderate full body contact recreation criteria for both E. coli 

and enterococci, the exception being a greater occurrence of 

the ipaH gene marker for Shigella in samples that met the 

criterion for E. coli. 

0

10

20

30

40

50

60

70

80

eaeA stx2 stx1 rfb0157 ipaH invA spvC C. coli/C. jejuni

Percent age of samples

Gene Marker

Percentage of normal-flow samples

Percentage of high-flow samples

Figure 4. Percentage of pathogen gene markers in relation to water quality criteria (C. coli, Campylobacter coli; 

C. jejuni, Campylobacter jejuni).

Table 5. Percentage of samples that tested positive for pathogenic gene markers during high-flow and normal-flow conditions.

[C. coli, Campylobacter coli; C. jejuni, Campylobacter jejuni, E. coli, Escherichia coli; n, number of samples; <, less than; nsd, no significant difference; 

p-value, p-value less than 0.05 = significant difference between groups, Fisher’s Exact Test]

Water quality criteria1

status n eaeA stx2 stx1 rfb0157 ipaH invA spvC C. coli/C. jejuni

Meet E. coli criterion 88 60 11 3 5 7 0 9 6

Exceed E. coli criterion 24 96 50 42 33 4 33 33 21

p-value — <0.05 <0.05 <0.05 <0.05 nsd <0.05 <0.05 <0.05

Meet enterococci 

criterion

67 54 10 5 3 6 0 3 2

Exceed enterococci 

criterion

45 91 33 22 22 7 18 31 20

p-value — <0.05 <0.05 <0.05 <0.05 nsd <0.05 <0.05 <0.05

1

Water quality criteria = EPA Water Quality Criteria for Moderate Full Body Contact (Dufour and Ballantine, 1986).
10 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries

Quality-Control Results

To assess for bias and precision, 21 field blanks, 21 

source solution blanks, and 22 field replicates were collected 

and processed in the same manner as the regular field samples. 

All field blanks and source solution water blanks were negative (no growth) for all FIB except for a sample collected at 

the River Raisin on August 30, 2011, which had an enterococci count of 2E (appendix 2). For PCR analysis, all no-template controls (negative controls) were found to be negative, 

and all positive assay controls yielded appropriate responses. 

However, the eaeA, rfb0157, and ipaH genes were infrequently detected in the field blanks and source solution blanks, 

most likely as a result of contamination in the source solution 

blank water (appendix 4). There were two dates—September 7, 2011, and August 24, 2011—for which environmental 

samples were collected in association with the source solution 

blank and field blank samples where there may have been 

possible contamination. The environmental sample, source 

solution blank, and field blank samples from these dates have 

been qualified with a “V” (analyte was detected in both the 

environmental sample and the associated blanks) as a result of 

possible contamination and data were not included in analyses 

(appendixes 3 and 4). 

For all FIB field replicates, a relative standard deviation 

(RSD) was calculated and a mean RSD was computed (table 

6) by using the formula below: 

In all cases, the average RSD fell below the recommended 36 percent according to the initial and ongoing 

precision and recovery acceptance criteria that were used as 

a benchmark for replicate environmental samples (table 6) 

(EPA, 2009a).

For pathogen analysis, which yields only a presence or 

absence result, the frequencies of agreement between replicates were determined by dividing the number of paired replicates in agreement by the total number of replicates (table 7). 

The field blank and source solution blank data results 

are presented in appendixes 2 and 4. All replicate data are 

presented in appendixes 1 and 3, along with the associated 

environmental sample.

Summary

A total of 177 environmental samples were collected at 

USGS streamgaging stations during both normal-flow and 

high-flow conditions in 22 tributaries to the Great Lakes and 

were analyzed for the presence of FIB concentrations and 

to determine the occurrence of pathogen gene markers for 

Shigella species, Campylobacter jejuni and coli, Salmonella 

species, and pathogenic E. coli, including STEC. Results from 

a total of 165 samples were evaluated because 12 samples did 

not meet quality-control measures.

E. coli concentrations ranged from less than 2 to 26,000 

CFU/100 mL. Enterococci concentrations ranged from less 

than 2 to 31,000 CFU/100 mL. Fecal coliform bacteria 

concentrations ranged from less than 2 to 950 CFU/100 ml. 

Data from E. coli pathogen analyses showed that 68 percent 

of samples contained the eaeA gene, 20 percent of samples 

contained the stx2 gene, 12 percent of samples contained the 

stx1 gene, and 11 percent of samples contained the rfbO157

gene. Data from the Shigella analysis showed that 6 percent of 

samples contained the ipaH gene. Data from the Salmonella

analysis showed that 7 percent of samples contained the invA

gene and 14 percent of samples contained the spvC gene. Data 

from the Campylobacter analysis showed that 9 percent of 

samples contained the 16S rDNA gene of Campylobacter coli

and Campylobacter jejuni.

Table 6. Relative standard deviation of field replicates for 

quantitative microbial methods in the Great Lakes Restoration 

Initiative (GLRI) pathogens study.

[E. coli, Escherichia coli; RSD, relative standard deviation]

Statistic E. coli Enterococci Fecal 

coliforms

Average RSD, in percent 25.3 28.4 31.1

Number of field replicates 22 22 22

Table 7. Frequency of agreement between field replicates for qualitative microbial methods in the Great Lakes Restoration 

Initiative (GLRI) pathogens study.

[C. coli, Campylobacter coli; C. jejuni, Campylobacter jejuni]

Statistic Pathogen gene markers

eaeA stx2 stx1 rfb0157 ipaH invA spvC C. coli/C. jejuni

Percent agreement 82 95 95 82 100 95 91 95

Number of field replicates 22 22 22 22 22 22 22 22

S

X X X X X X

n

= −+ −+ − +

−

( ) 1 2 ( ) ( ) 3 ...

1

2 2 2
References Cited 11

There were no samples in which all eight pathogen gene 

markers were detected; however, 88 percent of the samples 

that had three or more pathogen gene markers present were 

collected during high-flow conditions. Overall, there were a 

higher percentage of samples that tested positive for pathogens 

during high-flow conditions than normal-flow conditions, and 

there was a greater occurrence of pathogen gene markers in 

samples that exceeded the EPA moderate full body contact 

recreation criteria for E. coli and enterococci (Dufour, 1986) 

than in samples that met the EPA criteria; the exception was 

a greater occurrence of the ipaH gene marker for Shigella in 

samples that met the EPA criterion for E. coli than in samples 

that exceeded the EPA criterion for E. coli.

Acknowledgements

This study was funded by the Great Lakes Restoration 

Initiative. We wish to acknowledge the many USGS personnel 

from Indiana, Michigan, Minnesota, Ohio, New York and Wisconsin who collected the water samples for this project and 

communicated with the Michigan Bacteriological Research 

Laboratory.

References Cited

American Public Health Association, American Water Works 

Association, and Water Environment Federation, 1998, 

Standard methods for the examination of water and wastewater (20th ed.): Washington, D.C., American Public Health 

Association, p. 9–1 to 9–76.

Centers for Disease Control and Prevention (CDC), 2012a, 

Campylobacter: CDC Web page, accessed April 17, 2012, at 

http://www.cdc.gov/nczved/dfbmd/diseases/campylobacter/.

Centers for Disease Control and Prevention (CDC), 2012b, 

Recreational Water Illnesses (RWIs): CDC Web page, 

accessed April 17, 2012, at http://www.cdc.gov/healthywater/swimming/rwi/.

Centers for Disease Control and Prevention (CDC), 2012c, 

Salmonella: CDC Web page, accessed April 17, 2012, at 

http://www.cdc.gov/salmonella.

Centers for Disease Control and Prevention (CDC), 2012d, 

STEC: CDC Web page, accessed April 17, 2012, at http://

www.cdc.gov/ecoli/index.html.

Dufour, A.P., and Ballantine, R.K., 1986, Ambient water 

quality criteria for bacteria, 1986—Bacteriological ambient 

water quality criteria for marine and freshwater recreational 

waters: Washington, D.C., EPA 440/5–84–002.

Great Lakes Information Network (GLIN), 2013, Great Lakes 

facts and figures: GLIN Web page, accessed May 6, 2013, at 

http://www.glin.net/lakes/ref/lakefact.html.

Haack, S.K., Fogarty, L.R., Stelzer, E.A., Fuller, L.M, Brennan, A.K, Isaacs, N.M., and Johnson, H.E. 2013, Geographic setting influences great lakes beach microbiological 

water quality: Environmental Science & Technology, v. 47, 

no. 21, p. 12054–12063.

Myers, D.N., Stoeckel, D.M., Bushon, R.N., Francy, D.S., and 

Brady, A.M.G., 2014, Fecal indicator bacteria (ver. 2.1): 

U.S. Geological Survey Techniques of Water-Resources 

Investigations, book 9, chap. A7, section 7.1, May 2014, 

accessed June 2014 at http://pubs.water.usgs.gov/twri9A/.

U.S. Environmental Protection Agency (EPA), 2004, Quality 

assurance/quality control guidance for laboratories performing PCR analysis on environmental samples: Office of 

Water, EPA 815-B-04-001, 56 p.

U.S. Environmental Protection Agency (EPA), 2009a, Method 

1603 “Escherichia coli in water by membrane filtration 

using modified membrane-thermotolerant Escherichia coli

agar”: Washington, D.C., EPA–821–R–09–007 

[variously paged].

U.S. Environmental Protection Agency (EPA), 2009b, Method 

1600 “Enterococci in water by membrane filtrations using 

membrane-Enterococcus indoxyl-β-D-glucoside agar”: 

Washington, D.C., EPA–821–R–09–016 [variously paged].

U.S. Environmental Protection Agency (EPA), 2012, Recreational water quality criteria: Office of Water, 

EPA 815–F–12–058, 63 p.

U.S. Environmental Protection Agency (EPA) and U.S. 

Geological Survey (USGS), 2012, National Hydrography 

Dataset Plus - NHDPlus version 2.1, accessed May 2012 at 

http://www.horizon-systems.com/NHDPlus/NHDPlusV2_

home.php.

U.S. Geological Survey (USGS), 2006, Collection of water 

samples (ver. 2.0): U.S. Geological Survey Techniques of 

Water-Resources Investigations, book 9, chap. A4, September 2006, accessed June 1, 2014, at http://pubs.water.usgs.

gov/twri9A4/. 

U.S. Geological Survey (USGS), 2011, National Land Cover 

Database (NLCD) 2006 Land Cover, accessed April 3, 

2012, at http://www.mrlc.gov/nlcd06_data.php.

U.S. Geological Survey (USGS), Great Lakes Restoration Initiative (GLRI), 2014, Forecast/nowcast Great Lakes nutrient 

and sediment loadings: USGS/GLRI Web page, accessed 

March 6, 2014, at http://cida.usgs.gov/glri/projects/nearshore_health/forecast_loadings.html.

Appendix 13

Appendixes

1. Fecal indicator bacteria concentrations in Great Lakes tributaries, 2011........................14

2. Quality-control data—Fecal indicator bacteria concentrations in Great Lakes 

tributaries, 2011...........................................................................................................................20

3. Pathogen gene detection in Great Lakes tributaries, 2011..................................................22

4. Quality-control data—Pathogen gene detection in Great Lakes tributaries, 2011 .........28
14 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries Appendix 1. Fecal indicator bacteria concentrations in Great Lakes tributaries, 2011.—Continued [Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmen- tal sample; E. coli, Escherichia coli; CFU/100 mL, colony-forming units per 100 milliliters; ns, no sample; unc, uncountable; E, estimated value; <, less than; >, greater than] USGS station ID Field ID Sample collection date Flow conditions Sample type Assoc. environ. sample Fecal coliforms (CFU/100mL) Remark code E. coli (CFU/ 100 mL) Remark code Enterococci (CFU/100 mL) Remark code 04137500 AU-01 3/15/2011 Normal Regular 2 < 2 < 2 < 04137500 AU-04 6/15/2011 Normal Regular 2 E 2 E 2 < 04137500 AU-05 7/13/2011 Normal Regular 74 2 < 2 < 04137500 AU-06 7/13/2011 Normal Replicate AU-05 34

E 2 E 2 E

04137500 AU-07 8/23/2011 Normal Regular 2 E 2 < 4 E

04137500 AU-10 9/13/2011 Normal Regular 4 E 2 E 2 <04027000 BD-04 7/12/2011 Normal Regular 84 44 23

E

04027000 BD-05 7/12/2011 Normal Replicate BD-04 58 52 18

E

04027000 BD-08 8/16/2011 Normal Regular 160

E 220 25

E

04027000 BD-09 9/20/2011 Normal Regular unc 66 28

E

04095090 BN-01 3/30/2011 Normal Regular 22

E 8 E 8 E

04095090 BN-05 7/12/2011 Normal Regular 120

> 140 140

E

04095090 BN-08 8/11/2011 Normal Regular 430

E 140 120

04095090 BN-09 8/11/2011 Normal Replicate BN-08 340

E 150 140

E

04208000 CY-06 8/31/2011 Normal Regular unc 220 150

E

040851385 FX-02 8/16/2011 Normal Regular 130

E 23

E 8 E

040851385 FX-03 8/16/2011 Normal Replicate FX-02 110 30

E 13

E

04231600 GS-01 4/5/2011 Normal Regular 120

> 520 230

E

04231600 GS-09 7/18/2011 Normal Regular 180

E 6 E 2 E

04231600 GS-10 7/18/2011 Normal Replicate GS-09 190

E 2 E 2 E

04231600 GS-13 8/8/2011 Normal Regular 84 32

E 13

E

04193500 MA-02 4/19/2011 Normal Regular 42 88 76

04193500 MA-03 7/27/2011 Normal Regular 120

> 18

E 20

E

04193500 MA-04 7/27/2011 Normal Replicate MA-03 120

> 26

E 390

04067500 MM-02 7/7/2011 Normal Regular 100 10

E 690

E

04067500 MM-03 9/7/2011 Normal Regular 6 E 8 E 7 E
Appendix 15

Appendix 1. Fecal indicator bacteria concentrations in Great Lakes tributaries, 2011. —Continued[Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, Escherichia coli; CFU/100 mL, colony-forming units per 100 milliliters; ns, no sample; unc, uncountable; E, estimated value; <, less than; >, greater than]

Sample Assoc. Fecal E. coli USGS Field Flow Sample Remark Remark Enterococci Remark collection environ. coliforms (CFU/ station ID ID conditions type code code (CFU/100 mL) code date sample (CFU/100mL) 100 mL)

04067500 MM-04 9/7/2011 Normal Replicate MM-03 20 E 2 E 6 E

04085427 MN-03 9/8/2011 Normal Regular 72 68 140 E04085427 MN-04 9/8/2011 Normal Replicate MN-03 94 120 140 E04087170 MW-02 9/20/2011 Normal Regular 48 30 E 8 E04087170 MW-03 9/20/2011 Normal Replicate MW-02 50 39 E 5 E04040000 ON-01 3/23/2011 Normal Regular 40 50 72

04040000 ON-02 4/5/2011 Normal Regular 28 E 35 E 94

04040000 ON-03 4/26/2011 Normal Regular 6 E 6 E 7 E04040000 ON-04 5/25/2011 Normal Regular 52 74 4404040000 ON-05 6/6/2011 Normal Regular 10 E 5 E 4 E04040000 ON-07 7/14/2011 Normal Regular 340 E 30 E 5804040000 ON-08 8/17/2011 Normal Regular 16 E 10 E 38 E04040000 ON-09 9/13/2011 Normal Regular 38 E 35 E 27 E

04040000 ON-10 9/13/2011 Normal Replicate ON-09 32 E 15 E 20 E04249000 OS-02 4/7/2011 Normal Regular 30 E 22 E 4 E

04249000 OS-05 6/8/2011 Normal Regular 86 68 43 E04249000 OS-10 7/18/2011 Normal Regular 150 E 33 E 7604249000 OS-11 7/18/2011 Normal Replicate OS-10 120 > 140 22004249000 OS-14 8/8/2011 Normal Regular 12 E 20 E 7 E04102500 PP-01 4/11/2011 Normal Regular 42 82 38 E04102500 PP-06 9/8/2011 Normal Regular 170 E 72 12004166500 RR-03 8/17/2011 Normal Regular 120 > 140 32004166500 RR-04 8/17/2011 Normal Replicate RR-03 420 E 430 44004176500 RS-01 6/16/2011 Normal Regular 100 110 6604176500 RS-02 8/23/2011 Normal Regular 52 20 E 46004176500 RS-03 8/23/2011 Normal Replicate RS-02 44 44 370
16 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries Appendix 1. Fecal indicator bacteria concentrations in Great Lakes tributaries, 2011. —Continued [Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmen- tal sample; E. coli, Escherichia coli; CFU/100 mL, colony-forming units per 100 milliliters; ns, no sample; unc, uncountable; E, estimated value; <, less than; >, greater than] Sample Assoc. Fecal E. coli USGS Field Flow Sample Remark Remark Enterococci Remark collection environ. coliforms (CFU/ station ID ID conditions type code code (CFU/100 mL) code date sample (CFU/100mL) 100 mL) 04157000 SG-01 3/15/2011 Normal Regular 210

E 66 160

E

04157000 SG-05 6/16/2011 Normal Regular 150

E 36

E 42

04157000 SG-06 7/14/2011 Normal Regular 950

E 25

E 12

E

04157000 SG-07 7/14/2011 Normal Replicate SG-06 850 E 20

E 13

E

04157000 SG-08 8/23/2011 Normal Regular 52 30

E 12

E

04157000 SG-11 9/14/2011 Normal Regular 110 60 4004101500 SJ-02 4/7/2011 Normal Regular 26

E 2 < 7 E

04101500 SJ-07 7/27/2011 Normal Regular 110 74 5204101500 SJ-08 8/24/2011 Normal Regular 370

E 130 52

04269000 SR-01 3/24/2011 Normal Regular 16

E 6 E 2 E

04269000 SR-04 4/26/2011 Normal Regular 14

E 8 E 2 E

04269000 SR-07 6/21/2011 Normal Regular ns ns ns04269000 SR-08 7/26/2011 Normal Regular 170

E 130 46

04269000 SR-09 7/26/2011 Normal Replicate SR-08 210 E 140 5204269000 SR-13 9/20/2011 Normal Regular 150

E 180

E 110

04024000 ST-01 3/15/2011 Normal Regular 8 E 2 E 2 E04024000 ST-02 4/20/2011 Normal Regular 2 E 4 E 5 E04024000 ST-04 6/14/2011 Normal Regular 12

E 3 E 2 E

04024000 ST-05 6/23/2011 Normal Regular 26

E 18

E 44

E

04024000 ST-06 7/21/2011 Normal Regular 120 26

E 28

E

04024000 ST-07 7/21/2011 Normal Replicate ST-06 110 42 42

04024000 ST-11 8/31/2011 Normal Regular 74 40 20

E

04024000 ST-12 9/13/2011 Normal Regular 42 25

E 10

E

04137500 AU-02 4/12/2011 High Regular 2 < 2 < 2 <04027000 BD-01 4/11/2011 High Regular 110 82

E 280

04027000 BD-02 4/11/2011 High Replicate BD-01 140 E 56 270
Appendix 17

Appendix 1. Fecal indicator bacteria concentrations in Great Lakes tributaries, 2011. —Continued[Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, Escherichia coli; CFU/100 mL, colony-forming units per 100 milliliters; ns, no sample; unc, uncountable; E, estimated value; <, less than; >, greater than]

Sample Assoc. Fecal E. coli USGS Field Flow Sample Remark Remark Enterococci Remark collection environ. coliforms (CFU/ station ID ID conditions type code code (CFU/100 mL) code date sample (CFU/100mL) 100 mL)

04027000 BD-03 5/24/2011 High Regular 340 E 510 150 E04095090 BN-02 4/28/2011 High Regular 120 > 1400 E 1100 E04095090 BN-03 5/25/2011 High Regular 610 E 710 E 35004095090 BN-04 6/8/2011 High Regular 46 17 E 7 E04095090 BN-10 9/7/2011 High Regular 94 48 5604165500 CL-01 5/16/2011 High Regular 120 > 2500 380004165500 CL-02 8/17/2011 High Regular 230 E 200 10004165500 CL-03 8/17/2011 High Replicate CL-02 160 E 140 8404208000 CY-01 4/27/2011 High Regular 490 E 590 25004208000 CY-02 7/26/2011 High Regular 120 > 180 10004208000 CY-03 7/26/2011 High Replicate CY-02 120 > 250 7804208000 CY-07 9/20/2011 High Regular 120 > 6100 8000 E04208000 CY-08 10/26/2011 High Regular 430 E 430 420040851385 FX-01 5/4/2011 High Regular 14 E 64 4 E04119400 GR-01 4/29/2011 High Regular 310 E 290 28004119400 GR-02 5/18/2011 High Regular 140 E 230 34 E04119400 GR-03 6/2/2011 High Regular 70 48 17 E04119400 GR-04 6/29/2011 High Regular 240 E 82 12 E04119400 GR-05 6/29/2011 High Replicate GR-04 270 E 80 8 E04119400 GR-06 8/2/2011 High Regular 130 E 90 17 E04231600 GS-02 4/26/2011 High Regular 400 E 320 27004231600 GS-03 5/17/2011 High Regular 120 > 1200 E 1400 E04231600 GS-04 6/2/2011 High Regular unc 390 12004193500 MA-01 3/8/2011 High Regular 570 E 650 980 E04085427 MN-02 7/6/2011 High Regular 410 E 70 5004087170 MW-01 5/3/2011 High Regular 28 E 58 27 E
18 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries Appendix 1. Fecal indicator bacteria concentrations in Great Lakes tributaries, 2011. —Continued [Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmen- tal sample; E. coli, Escherichia coli; CFU/100 mL, colony-forming units per 100 milliliters; ns, no sample; unc, uncountable; E, estimated value; <, less than; >, greater than] Sample Assoc. Fecal E. coli USGS Field Flow Sample Remark Remark Enterococci Remark collection environ. coliforms (CFU/ station ID ID conditions type code code (CFU/100 mL) code date sample (CFU/100mL) 100 mL) 04040000 ON-06 6/23/2011 High Regular 120

> 920

E 570

04249000 OS-01 3/9/2011 High Regular 150

E 100 64

04249000 OS-03 4/27/2011 High Regular 70 88 6604249000 OS-04 5/9/2011 High Regular 4 E 18

E 2 <

04249000 OS-15 9/7/2011 High Regular 70 15

E 11

E

04195500 PO-01 3/8/2011 High Regular 580

E 650 570

04195500 PO-02 4/20/2011 High Regular 120

> 1400

E 3600

04195500 PO-03 7/27/2011 High Regular 120

> 240 310

04195500 PO-04 7/27/2011 High Replicate PO-03 120 > 220 28004102500 PP-02 4/21/2011 High Regular 120

> 790 1200

E

04102500 PP-03 6/1/2011 High Regular 96 100 7204102500 PP-04 7/19/2011 High Regular 120

> 4800 6700

E

04102500 PP-05 8/3/2011 High Regular 410

E 630 420

E

04102500 PP-08 10/4/2011 High Regular 120 70 8204166500 RR-01 5/16/2011 High Regular 120

> 2600 5700

04166500 RR-02 5/26/2011 High Regular 120

> 26000

E 31000

E

04157000 SG-02 4/6/2011 High Regular 240

E 220 440

04157000 SG-03 5/2/2011 High Regular 100 190

E 98

04157000 SG-04 5/16/2011 High Regular 120

> 1200

E 960

E

04101500 SJ-01 3/9/2011 High Regular unc 96 44004101500 SJ-03 4/21/2011 High Regular 120

> 860

E 1300

E

04101500 SJ-04 4/28/2011 High Regular 120

> 1400

E 870

E

04101500 SJ-05 6/28/2011 High Replicate SJ-06 260 E 100 2304101500 SJ-06 6/28/2011 High Regular 380

E 58 40

04269000 SR-02 4/6/2011 High Regular 16

E 5 E 14

E

04269000 SR-03 4/12/2011 High Regular 50 40

E 33

E
Appendix 19

Appendix 1. Fecal indicator bacteria concentrations in Great Lakes tributaries, 2011. —Continued[Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, Escherichia coli; CFU/100 mL, colony-forming units per 100 milliliters; ns, no sample; unc, uncountable; E, estimated value; <, less than; >, greater than]

Sample Assoc. Fecal E. coli USGS Field Flow Sample Remark Remark Enterococci Remark collection environ. coliforms (CFU/ station ID ID conditions type code code (CFU/100 mL) code date sample (CFU/100mL) 100 mL)

04269000 SR-05 5/5/2011 High Regular 24 E 46 17 E04269000 SR-06 5/24/2011 High Regular 30 E 60 30 E04269000 SR-12 8/23/2011 High Regular 220 E 220 21004024000 ST-03 5/1/2011 High Regular 16 E 17 E 6 E04024000 ST-10 8/3/2011 High Regular 580 E 790 360
20 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries Appendix 2. Quality-control data—Fecal indicator bacteria concentrations in Great Lakes tributaries, 2011.—Continued [Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, Escherichia coli; CFU/100 mL, colony-forming units per 100 milliliters; E, estimated value; <, less than; >, greater than; N/A; not applicable; ns, no sample] USGS station ID Field ID Sample collection date Sample type Assoc. environ. sample Fecal coliforms (CFU/100 mL) Remark code E. coli (CFU/100 mL) Remark code Entero-cocci (CFU/100 mL) Remark code 04137500 AU-08 8/23/2011 Field blank AU-07 2 < 2 < 2 < 04027000 BD-06 7/12/2011 Field blank BD-04 2 < 2 < 2 < 04095090 BN-06 7/12/2011 Field blank BN-05 2 < 2 < 2 < 04165500 CL-04 11/1/2011 Field blank ns 2 < 2 < 2 < 04208000 CY-04 7/26/2011 Field blank CY-02 2 < 2 < 2 < 040851385 FX-04 9/19/2011 Field blank ns 2 < 2 < 2 < 04119400 GR-07 10/31/2011 Field blank ns 2 < 2 < 2 < 04231600 GS-11 7/18/2011 Field blank GS-09 2 < 2 < 2 < 04193500 MA-05 7/27/2011 Field blank MA-03 2 < 2 < 2 < 04067500 MM-05 9/7/2011 Field blank MM-03 2 < 2 < 2 < 04085427 MN-05 9/8/2011 Field blank MN-03 2 < 2 < 2 < 04087170 MW-04 9/20/2011 Field blank MW-02 2 < 2 < 2 < 04040000 ON-12 9/20/2011 Field blank ns 2 < 2 < 2 < 04249000 OS-12 7/18/2011 Field blank OS-10 2 < 2 < 2 < 04195500 PO-05 7/27/2011 Field blank PO-03 2 < 2 < 2 < 04166500 RR-05 10/31/2011 Field blank ns 2 < 2 < 2 < 04176500 RS-04 8/30/2011 Field blank ns 2 < 2 < 2 E 04157000 SG-09 8/23/2011 Field blank SG-08 2 < 2 < 2 < 04101500 SJ-09 8/24/2011 Field blank SJ-08 2 < 2 < 2 <

04269000 SR-10 7/26/2011 Field blank SR-08 2 < 2 < 2 <04024000 ST-08 7/21/2011 Field blank ST-06 2 < 2 < 2 <

04137500 AU-09 8/22/2011 Source solution blank ns 2 < 2 < 2 <

04027000 BD-07 7/12/2011 Source solution blank BD-04 2 < 2 < 2 <

04095090 BN-07 7/12/2011 Source solution blank BN-05 2 < 2 < 2 <

04165500 CL-05 11/1/2011 Source solution blank ns 2 < 2 < 2 <04208000 CY-05 7/26/2011 Source solution blank CY-02 2 < 2 < 2 <
Appendix 21

Appendix 2. Quality-control data—Fecal indicator bacteria concentrations in Great Lakes tributaries, 2011.—Continued[Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, 

Escherichia coli; CFU/100 mL, colony-forming units per 100 milliliters; E, estimated value; <, less than; >, greater than; N/A; not applicable; ns, no sample]

Sample Assoc. Fecal USGS Field Remark E. coli Remark Entero-cocci Remark collection Sample type environ. coliforms station ID ID code (CFU/100 mL) code (CFU/100 mL) code date sample (CFU/100 mL)

040851385 FX-05 9/19/2011 Source solution blank ns 2 < 2 < 2 <

04119400 GR-08 10/31/2011 Source solution blank ns 2 < 2 < 2 <

04231600 GS-12 7/18/2011 Source solution blank GS-09 2 < 2 < 2 <04193500 MA-06 7/27/2011 Source solution blank MA-03 2 < 2 < 2 <04067500 MM-06 9/19/2011 Source solution blank ns 2 < 2 < 2 <04085427 MN-06 9/19/2011 Source solution blank ns 2 < 2 < 2 <04087170 MW-05 9/20/2011 Source solution blank MW-02 2 < 2 < 2 <04040000 ON-11 9/20/2011 Source solution blank ns 2 < 2 < 2 <04249000 OS-13 7/18/2011 Source solution blank OS-10 2 < 2 < 2 <04195500 PO-06 7/27/2011 Source solution blank PO-03 2 < 2 < 2 <04166500 RR-06 10/31/2011 Source solution blank ns 2 < 2 < 2 <04176500 RS-05 8/30/2011 Source solution blank ns 2 < 2 < 2 <04157000 SG-10 8/23/2011 Source solution blank SG-08 2 < 2 < 2 <04101500 SJ-10 8/24/2011 Source solution blank SJ-08 2 < 2 < 2 <04269000 SR-11 7/26/2011 Source solution blank SR-08 2 < 2 < 2 <04024000 ST-09 7/21/2011 Source solution blank ST-06 2 < 2 < 2 <
22 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries Appendix 3. Pathogen gene detection in Great Lakes tributaries, 2011.—Continued [Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, Escherichia coli; +, gene present in sample; —, gene absent in sample; ns, no sample; V– remark code indicating possible contamination (analyte was detected in both the environmental sample and the associated blanks)] USGS station ID Field ID Sample collection date Flow conditions Sample type Assoc. environ. sample E. coli gene data Shigella gene data Salmonella gene data Campylobacter gene data eaeA stx2 stx1 rfb O157 ipaH invA spvC C. coli/ C. jejuni 04137500 AU-01 3/15/2011 Normal Regular

—

—

—

—

—

—

—

—

04137500 AU-04 6/15/2011 Normal Regular

—

—

—

—

—

—

—

—

04137500 AU-05 7/13/2011 Normal Regular

+

—

—

—

—

—

—

—

04137500 AU-06 7/13/2011 Normal Replicate AU-05

+

—

—

—

—

—

—

—

04137500 AU-07 8/23/2011 Normal Regular

—

—

—

—

+

—

—

—

04137500 AU-10 9/13/2011 Normal Regular

—

—

—

—

—

—

—

—

04027000 BD-04 7/12/2011 Normal Regular

+

—

—

—

—

—

—

—

04027000 BD-05 7/12/2011 Normal Replicate B-04

+

—

—

—

—

—

—

—

04027000 BD-08 8/16/2011 Normal Regular

+

—

—

—

—

—

—

—

04027000 BD-09 9/20/2011 Normal Regular

+

—

—

—

—

—

+

—

04095090 BN-01 3/30/2011 Normal Regular

+

—

—

—

—

—

—

—

04095090 BN-05 7/12/2011 Normal Regular

+

—

—

—

—

—

+

—

04095090 BN-08 8/11/2011 Normal Regular

+

—

—

—

—

—

—

—

04095090 BN-09 8/11/2011 Normal Replicate BN-08

+

—

—

—

—

—

—

—

04208000 CY-06 8/31/2011 Normal Regular

+

—

—

—

—

—

—

+

040851385 FX-02 8/16/2011 Normal Regular

—

—

—

—

—

—

—

—

040851385 FX-03 8/16/2011 Normal Replicate FX-02

—

—

—

—

—

—

—

—

04231600 GS-01 4/5/2011 Normal Regular

+

—

—

—

—

—

—

+

04231600 GS-09 7/18/2011 Normal Regular

—

—

—

—

—

—

—

—

04231600 GS-10 7/18/2011 Normal Replicate GS-09

—

—

—

—

—

+

—

—

04231600 GS-13 8/8/2011 Normal Regular

—

—

—

—

—

—

—

—

04193500 MA-02 4/19/2011 Normal Regular

+

—

—

—

—

—

—

—

04193500 MA-03 7/27/2011 Normal Regular

+

—

—

+

—

—

—

—

04193500 MA-04 7/27/2011 Normal Replicate MA-03

+

—

—

+

—

—

—

—

04067500 MM-02 7/7/2011 Normal Regular

—

—

—

—

—

—

—

—
Appendix 23

Appendix 3. Pathogen gene detection in Great Lakes tributaries, 2011.—Continued[Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, 

Escherichia coli; +, gene present in sample; —, gene absent in sample; ns, no sample; V– remark code indicating possible contamination (analyte was detected in both the environmental sample and the associated blanks)]

Shigella Salmonella Campylobacter E. coli gene data Sample Assoc. gene data gene data gene data USGS Field Flow collection Sample type environ. station ID ID conditions date sample rfb C. coli/ eaeA stx2 stx1 ipaH invA spvC O157 C. jejuni

04067500 MM-03 9/7/2011 Normal Regular +V — — — — — — —

04067500 MM-04 9/7/2011 Normal Replicate MM-03 + — — + — — — —04085427 MN-03 9/8/2011 Normal Regular — — — — — — — +

04085427 MN-04 9/8/2011 Normal Replicate MN-03 + — — — — — — +04087170 MW-02 9/20/2011 Normal Regular + — — + — — — —

04087170 MW-03 9/20/2011 Normal Replicate MW-02 + — — — — + — —04040000 ON-01 3/23/2011 Normal Regular — — + — — — — —

04040000 ON-02 4/5/2011 Normal Regular + — — — — — — —

04040000 ON-03 4/26/2011 Normal Regular — — — — — — — —

04040000 ON-04 5/25/2011 Normal Regular + — — — — — — —

04040000 ON-05 6/6/2011 Normal Regular + — — — — — — —

04040000 ON-07 7/14/2011 Normal Regular — — — — — — — —

04040000 ON-08 8/17/2011 Normal Regular — — — — + — — —

04040000 ON-09 9/13/2011 Normal Regular + — — — — — — —

04040000 ON-10 9/13/2011 Normal Replicate ON-09 + — — — — — — —04249000 OS-02 4/7/2011 Normal Regular — — — — — — — —

04249000 OS-05 6/8/2011 Normal Regular + — — — — — — —

04249000 OS-10 7/18/2011 Normal Regular — — — — — — — —

04249000 OS-11 7/18/2011 Normal Replicate OS-10 + — — — — — — —04249000 OS-14 8/8/2011 Normal Regular + — — — — — — —

04102500 PP-01 4/11/2011 Normal Regular + + — — — — — —

04102500 PP-06 9/8/2011 Normal Regular + + — — — — + +

04166500 RR-03 8/17/2011 Normal Regular + — — + — — + —

04166500 RR-04 8/17/2011 Normal Replicate RR-03 + — — — — — + +04176500 RS-01 6/16/2011 Normal Regular + + — — — — — —
24 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries Appendix 3. Pathogen gene detection in Great Lakes tributaries, 2011.—Continued [Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, Escherichia coli; +, gene present in sample; —, gene absent in sample; ns, no sample; V– remark code indicating possible contamination (analyte was detected in both the environmental sample and the associated blanks)] Shigella Salmonella Campylobacter E. coli gene data Sample Assoc. gene data gene data gene data USGS Field Flow collection Sample type environ. station ID ID conditions date sample rfb C. coli/ eaeA stx2 stx1 ipaH invA spvC O157 C. jejuni 04176500 RS-02 8/23/2011 Normal Regular + — — — + — — — 04176500 RS-03 8/23/2011 Normal Replicate RS-02 + — — — + — — — 04157000 SG-01 3/15/2011 Normal Regular + — — — — — — — 04157000 SG-05 6/16/2011 Normal Regular — — — — — — — — 04157000 SG-06 7/14/2011 Normal Regular — — — — — — — — 04157000 SG-07 7/14/2011 Normal Replicate SG-06 + — — — — — — — 04157000 SG-08 8/23/2011 Normal Regular + — — — — — — — 04157000 SG-11 9/14/2011 Normal Regular + — — — — — — — 04101500 SJ-02 4/7/2011 Normal Regular — — — — — — — — 04101500 SJ-07 7/27/2011 Normal Regular + — — — — — — — 04101500 SJ-08 8/24/2011 Normal Regular

+V — — — — — — —

04269000 SR-01 3/24/2011 Normal Regular — — + — — — — —

04269000 SR-04 4/26/2011 Normal Regular — — — — — — — —

04269000 SR-07 6/21/2011 Normal Regular + — — — — — — —

04269000 SR-08 7/26/2011 Normal Regular + — — — — — — —

04269000 SR-09 7/26/2011 Normal Replicate SR-08 + — — — — — — —04269000 SR-13 9/20/2011 Normal Regular + — — — — — + —

04024000 ST-01 3/15/2011 Normal Regular — — — — — — — —

04024000 ST-02 4/20/2011 Normal Regular — — — — — — — —

04024000 ST-04 6/14/2011 Normal Regular + + — — — — — —

04024000 ST-05 6/23/2011 Normal Regular + — — — — — — —

04024000 ST-06 7/21/2011 Normal Regular — — — — — — — —

04024000 ST-07 7/21/2011 Normal Replicate ST-06 + — — — — — — —04024000 ST-11 8/31/2011 Normal Regular — — — — — — — +

04024000 ST-12 9/13/2011 Normal Regular + — — — — — — —
Appendix 25

Appendix 3. Pathogen gene detection in Great Lakes tributaries, 2011.—Continued[Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, 

Escherichia coli; +, gene present in sample; —, gene absent in sample; ns, no sample; V– remark code indicating possible contamination (analyte was detected in both the environmental sample and the associated blanks)]

Shigella Salmonella Campylobacter E. coli gene data Sample Assoc. gene data gene data gene data USGS Field Flow collection Sample type environ. station ID ID conditions date sample rfb C. coli/ eaeA stx2 stx1 ipaH invA spvC O157 C. jejuni

04137500 AU-02 4/12/2011 High Regular — — — — — — — —

04027000 BD-01 4/11/2011 High Regular — — — — — — — —

04027000 BD-02 4/11/2011 High Replicate BD-01 — — — — — — — —04027000 BD-03 5/24/2011 High Regular + — — — — — — —

04095090 BN-02 4/28/2011 High Regular + — + + — + — +

04095090 BN-03 5/25/2011 High Regular + — — — — + — —

04095090 BN-04 6/8/2011 High Regular — — — — — — — —

04095090 BN-10 9/7/2011 High Regular + — — — — — — —

04165500 CL-01 5/16/2011 High Regular + + + + — — + —

04165500 CL-02 8/17/2011 High Regular + — — — — — + —

04165500 CL-03 8/17/2011 High Replicate CL-02 + — — + — — + —04208000 CY-01 4/27/2011 High Regular — — — — — — — —

04208000 CY-02 7/26/2011 High Regular + — — — — — — —

04208000 CY-03 7/26/2011 High Replicate CY-02 + + — — — — — —04208000 CY-07 9/20/2011 High Regular + + + + — — + —

04208000 CY-08 10/26/2011 High Regular + — — — — — — —

040851385 FX-01 5/4/2011 High Regular + — — — — — — —

04119400 GR-01 4/29/2011 High Regular + + — — — — — —04119400 GR-02 5/18/2011 High Regular + — — — — — — —04119400 GR-03 6/2/2011 High Regular + — — — + — — —04119400 GR-04 6/29/2011 High Regular + — — — — — + —04119400 GR-05 6/29/2011 High Replicate GR-04 + — + — — — — —04119400 GR-06 8/2/2011 High Regular + + + — + — — —

04231600 GS-02 4/26/2011 High Regular + — + — — — — —

04231600 GS-03 5/17/2011 High Regular + — + + — — — —
26 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries Appendix 3. Pathogen gene detection in Great Lakes tributaries, 2011.—Continued [Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, Escherichia coli; +, gene present in sample; —, gene absent in sample; ns, no sample; V– remark code indicating possible contamination (analyte was detected in both the environmental sample and the associated blanks)] Shigella Salmonella Campylobacter E. coli gene data Sample Assoc. gene data gene data gene data USGS Field Flow collection Sample type environ. station ID ID conditions date sample rfb C. coli/ eaeA stx2 stx1 ipaH invA spvC O157 C. jejuni 04231600 GS-04 6/2/2011 High Regular + + — — — — — — 04193500 MA-01 3/8/2011 High Regular + + — — — + + + 04085427 MN-02 7/6/2011 High Regular + — — — — — — — 04087170 MW-01 5/3/2011 High Regular — — — — — — — — 04040000 ON-06 6/23/2011 High Regular + — — + — — — — 04249000 OS-01 3/9/2011 High Regular — — — — — — — — 04249000 OS-03 4/27/2011 High Regular — + — — — — — — 04249000 OS-04 5/9/2011 High Regular — — — — — — — — 04249000 OS-15 9/7/2011 High Regular + — — — — — — — 04195500 PO-01 3/8/2011 High Regular + — — — — — — + 04195500 PO-02 4/20/2011 High Regular + + — + — + — — 04195500 PO-03 7/27/2011 High Regular + — — — — — — — 04195500 PO-04 7/27/2011 High Replicate PO-03 + — — — — — — — 04102500 PP-02 4/21/2011 High Regular + + — — — + + + 04102500 PP-03 6/1/2011 High Regular + + — — — ns ns — 04102500 PP-04 7/19/2011 High Regular + + + — — + + — 04102500 PP-05 8/3/2011 High Regular + + — — — — — — 04102500 PP-08 10/4/2011 High Regular + — — — — — — —

04166500 RR-01 5/16/2011 High Regular + + + — — — + —

04166500 RR-02 5/26/2011 High Regular + + + + + + + —

04157000 SG-02 4/6/2011 High Regular + — — + — — — —

04157000 SG-03 5/2/2011 High Regular + — — — — — — —

04157000 SG-04 5/16/2011 High Regular + + — — — — + —

04101500 SJ-01 3/9/2011 High Regular + — — — — — — +

04101500 SJ-03 4/21/2011 High Regular + + + + — + — —
Appendix 27

Appendix 3. Pathogen gene detection in Great Lakes tributaries, 2011.—Continued[Streamgaging stations corresponding to station IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, 

Escherichia coli; +, gene present in sample; —, gene absent in sample; ns, no sample; V– remark code indicating possible contamination (analyte was detected in both the environmental sample and the associated blanks)]

Shigella Salmonella Campylobacter E. coli gene data Sample Assoc. gene data gene data gene data USGS Field Flow collection Sample type environ. station ID ID conditions date sample rfb C. coli/ eaeA stx2 stx1 ipaH invA spvC O157 C. jejuni

04101500 SJ-04 4/28/2011 High Regular + — + — — — — —

04101500 SJ-05 6/28/2011 High Replicate SJ—06 + + — — — — — —04101500 SJ-06 6/28/2011 High Regular + + — — — — — —

04269000 SR-02 4/6/2011 High Regular + — — — — — — —

04269000 SR-03 4/12/2011 High Regular — — — — — — — —

04269000 SR-05 5/5/2011 High Regular — — — — — — — —

04269000 SR-06 5/24/2011 High Regular — — — — — — — —

04269000 SR-12 8/23/2011 High Regular + + — — + — + —

04024000 ST-03 5/1/2011 High Regular — — — — — — — —

04024000 ST-10 8/3/2011 High Regular + — — — — — — —
28 Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries Appendix 4. Quality-control data—Pathogen gene detection in Great Lakes tributaries, 2011.—Continued [Streamgaging stations corresponding tostation IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, Escherichia coli; +, gene present in sample; -, gene absent in sample; ns, no sample; v – value qualifier code (analyte detected in laboratory blank); V – value qualifier code (contamination, analyte was detected in both the environmental sample and the associated blanks)] USGS station ID Field ID Sample collection Date Sample type Assoc. environ. sample E. coli gene data Shigella gene data Salmonella gene data Campylobacter gene data eaeA stx2 stx1 rfb O157 ipaH invA spvC C. coli/ C. jejuni 04137500 AU-08 8/23/2011 Field blank AU-07

—

—

—

—

—

—

—

—

04027000 BD-06 7/12/2011 Field blank BD-04

—

—

—

—

—

—

—

—

04095090 BN-06 7/12/2011 Field blank BN-05

—

—

—

—

—

—

—

—

04165500 CL-04 11/1/2011 Field blank ns

—

—

—

—

—

—

—

—

04208000 CY-04 7/26/2011 Field blank CY-02

—

—

—

—

—

—

—

—

040851385 FX-04 9/19/2011 Field blank ns

+v —

—

—

—

—

—

—

04119400 GR-07 10/31/2011 Field blank ns

—

—

—

—

+v —

—

—

04231600 GS-11 7/18/2011 Field blank GS-09

—

—

—

—

—

—

—

—

04193500 MA-05 7/27/2011 Field blank MA-03

—

—

—

—

—

—

—

—

04067500 MM-05 9/7/2011 Field blank MM-03

+V —

—

+V —

—

—

—

04085427 MN-05 9/8/2011 Field blank MN-03

—

—

—

—

—

—

—

—

04087170 MW-04 9/20/2011 Field blank MW-02

—

—

—

—

—

—

—

—

04040000 ON-12 9/20/2011 Field blank ns

—

—

—

—

—

—

—

—

04249000 OS-12 7/18/2011 Field blank OS-10

—

—

—

—

—

—

—

—

04195500 PO-05 7/27/2011 Field blank PO-03

—

—

—

—

—

—

—

—

04166500 RR-05 10/31/2011 Field blank ns

+v —

—

—

—

—

—

—

04176500 RS-04 8/30/2011 Field blank ns

—

—

—

—

+v —

—

—

04157000 SG-09 8/23/2011 Field blank SG-08

—

—

—

—

—

—

—

—

04101500 SJ-09 8/24/2011 Field blank SJ-08

—

—

—

—

—

—

—

—

04269000 SR-10 7/26/2011 Field blank SR-08

—

—

—

—

—

—

—

—

04024000 ST-08 7/21/2011 Field blank ST-06

—

—

—

—

—

—

—

—

04137500 AU-09 8/22/2011 Source solution blank ns

—

—

—

—

+v —

—

—

04027000 BD-07 7/12/2011 Source solution blank BD-04

—

—

—

—

—

—

—

—

04095090 BN-07 7/12/2011 Source solution blank BN-05

—

—

—

—

—

—

—

—

04165500 CL-05 11/1/2011 Source solution blank ns

—

—

—

—

—

—

—

—

04208000 CY-05 7/26/2011 Source solution blank CY-02

—

—

—

—

—

—

—

—
Appendix 29

Appendix 4. Quality-control data—Pathogen gene detection in Great Lakes tributaries, 2011.—Continued[Streamgaging stations corresponding tostation IDs and field IDs are listed in table 1 in the main report. USGS, U.S. Geological Survey; Assoc. environ. sample, associated environmental sample; E. coli, Escherichia coli; +, gene present in sample; -, gene absent in sample; ns, no sample; v – value qualifier code (analyte detected in laboratory blank); V – value qualifier code (contamination, analyte was detected in both the environmental sample and the associated blanks)]

Shigella Salmonella Campylobacter

E. coli gene data gene gene gene Sample Assoc. USGS station data data data Field ID collection Sample type environ. ID Date sample rfb C. coli/ eaeA stx2 stx1 ipaH invA spvC O157 C. jejuni

040851385 FX-05 9/19/2011 Source solution blank ns — — — — — — — —

04119400 GR-08 10/31/2011 Source solution blank ns +v — — — — — — —

04231600 GS-12 7/18/2011 Source solution blank GS-09 — — — — — — — —

04193500 MA-06 7/27/2011 Source solution blank MA-03 — — — — — — — —04067500 MM-06 9/19/2011 Source solution blank ns — — — — — — — —04085427 MN-06 9/19/2011 Source solution blank ns — — — — — — — —04087170 MW-05 9/20/2011 Source solution blank MW-02 — — — — — — — —04040000 ON-11 9/20/2011 Source solution blank ns +v — — — — — — —

04249000 OS-13 7/18/2011 Source solution blank OS-10 — — — — — — — —

04195500 PO-06 7/27/2011 Source solution blank PO-03 — — — — — — — —04166500 RR-06 10/31/2011 Source solution blank ns — — — — — — — —04176500 RS-05 8/30/2011 Source solution blank ns — — — — — — — —04157000 SG-10 8/23/2011 Source solution blank SG-08 — — — — — — — —04101500 SJ-10 8/24/2011 Source solution blank SJ-08 +V — — — — — — —

04269000 SR-11 7/26/2011 Source solution blank SR-08 — — — — — — — —

04024000 ST-09 7/21/2011 Source solution blank ST-06 — — — — — — — —

Brennan and others—Fecal Indicator Bacteria and Gene Markers of Pathogenic Bacteria in Great Lakes Tributaries, March–October 2011—Open File Report 2015–1013

ISSN 2331-1258 (online)

http://dx.doi.org/10.3133/ofr20151013