U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2013–3071

October 2013

Research on Pathogens at Great Lakes Beaches—Sampling, 

Influential Factors, and Potential Sources

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The overall mission of this work is to provide science-based information and methods that will allow beach managers to more 

accurately make beach closure and advisory decisions, understand the sources and physical processes affecting beach contaminants, 

and understand how science-based information can be used to mitigate and restore beaches and protect the public. 

The U.S. Geological Survey (USGS), in collaboration with many Federal, State, and local agencies and universities, has conducted research on beach health issues in the Great Lakes Region for more than a decade. The work consists of four science elements 

that align with the USGS Beach Health Initiative Mission: real-time assessments of water quality; coastal processes; pathogens and 

source tracking; and data analysis, interpretation, and communication. The ongoing or completed research for the pathogens and 

source tracking topic is described in this fact sheet.

Pathogens at Great Lakes Beaches

Beach advisories and closings, based 

on the fecal indicator bacteria (FIB) 

Escherichia coli (E. coli) and enterococci, are intended to protect the public 

from coming into contact with pathogenic 

(disease-causing) organisms. FIB are 

not necessarily pathogenic themselves, 

but they may indicate the presence of 

pathogenic organisms. The United States 

(U.S.) Centers for Disease Control and 

Prevention (CDC) report that between 

1999 and 2008, four major pathogens 

were associated with outbreaks of illness 

acquired from ambient (as opposed to 

swimming pools) recreational water: 

the bacteria E. coli and Shigella, Cryptosporidium (protozoa), and norovirus 

(virus). In up to 21.9 percent of reported 

cases, the pathogen that caused the illness 

was not determined (Centers for Disease Control and Prevention, 2011). The 

bacteria Salmonella and Campylobacter, 

together with a few rarely occurring 

pathogens, accounted for fewer than 

8 percent of cases. Methicillin-resistant 

Staphylococcus aureus (MRSA) have 

been detected at marine beaches. With 

the exception of MRSA, these pathogens 

typically cause gastrointestinal illness of 

varying severity, and enter recreational 

water through dissemination of human 

and animal wastes. MRSA are typically 

skin-associated, are reported to arise from 

swimmers themselves, and are of considerable concern because their resistance to 

antibiotic treatment leads to life-threatening infections. The USGS has conducted 

studies of pathogens at 12 representative 

Great Lakes beaches, in storm drains 

that deliver runoff to beaches, and in a 

focused study at Lake Michigan beaches.

Developing New Methods to Test 

for Pathogens

The FIB are used to indicate the 

possible presence of pathogens, but may 

not have the same survival properties as 

all pathogens. For example, FIB in the 

environment may not survive as long as 

pathogens, falsely indicating safety, or 

FIB may survive or grow longer than 

pathogens, falsely indicating risk. There 

have been only a few studies of pathogens at Great Lakes beaches, because 

each pathogen requires a separate test, 

and traditional methods require the 

organism in question to be cultured in the 

laboratory and confirmed with several 

tests. It would be costly and time consuming to routinely analyze for a large 

suite of pathogens, and even if none are 

detected for this analysis, there could 

be other pathogens present that were 

not part of the suite that were analyzed. 

However, new methods that rely on 

the detection of genes associated with 

specific pathogens are widely applied to 

food, and to clinical samples in hospitals, 

to determine the cause of illness. These 

methods include polymerase chain reaction (PCR) and quantitative PCR (qPCR), 

by which many thousands of copies of a 

signature gene for the pathogen can be 

created. The qPCR can be conducted in a 

few hours, and offers potential for more 

rapid determination of recreational water 

quality than growth-based methods, such 

as for the FIB, which typically take 18 

to 24 hours to process. The USGS has 

developed and used both PCR and qPCR 

to detect or enumerate bacterial pathogens and viruses at Great Lakes beaches. 

Study of Twelve Representative 

Great Lakes Beaches

The USGS conducted studies in 

2010 to identify factors that influence 

bacterial pathogen and microbial source 

tracking (MST) genes at beaches, and 

relate pathogen and source-tracking gene 

occurrence to concentrations of E. coli

and enterococci. In cooperation with 

multiple local partners, approximately 

30 samples were collected over a range 

of environmental conditions from each 

of 12 beaches in Wisconsin, Michigan, 

Ohio, and New York, on Lakes Michigan, 

Huron, and Erie, and daily environmental 

data were recorded (fig. 1). 

Figure 1. Over 300 samples from 12 

representative Great Lakes beaches were 

tested for the presence of selected bacterial 

pathogens, by culture, combined with genetic 

methods.
Land cover was determined for 

beach catchments and adjacent river 

watersheds using geographic information 

systems. The PCR was used to detect 

genes indicating the following bacteria: 

Shigella spp., pathogenic Salmonella 

spp., Shiga toxin-producing E. coli, 

Campylobacter jejuni and Campylobacter

coli, and MRSA. Variables influencing 

frequency of occurrence of gene markers 

were determined using multiple statistical 

approaches. Although FIB concentrations 

and total pathogen count were significantly highest at beaches that exceeded 

any of several recreational water-quality 

criteria, pathogen genes still were 

detected in waters that met all criteria. 

Wave height and water velocity along the 

beach were important factors influencing 

FIB concentrations, as were various indicators of urban development, and runoff 

from rainfall events. Additionally, the 

qPCR was used to detect source-tracking 

markers in a subset of samples. No beach 

had only a single source identified, and 

the sources indicated changed by date, 

further emphasizing the complexity of 

beach indicator bacteria and pathogen 

dynamics. This study was the first to 

examine Staphylococcus aureus and the 

occurrence of MRSA at Great Lakes 

beaches. Likewise, this study was the first 

to evaluate the occurrence of pathogen 

genes in storm drain waters that flow 

into Great Lakes beaches. Study results 

should be available in several publications in 2013. 

Focused Study at Three Lake 

Michigan Beaches

A subset of three Lake Michigan 

beaches was sampled using large-volume 

glass-wool filtration for the qPCR analysis of 22 waterborne pathogens including 8 human viruses, 8 bovine viruses, 

4 bacteria, and Cryptosporidium parvum 

(fig. 2). 

Bacterial pathogens analyzed 

were Campylobacter jejuni, Salmonella 

enterica, enterohemorrhagic E. coli and

Mycobacterium avium subsp. paratuberculosis. These three beaches were chosen 

to represent a range of land uses in the 

surrounding watershed (rural, agricultural, and urban). A total of 71 samples 

were collected during summer 2010 at 

these three beaches. There was very highdetection frequency of human viruses 

and pathogenic bacteria, no detection 

of protozoa, and lower detection and 

concentration of bovine viruses than that 

of human viruses. All three beaches had 

detections of human and bovine viruses 

and pathogenic bacteria indicating the 

influence of multiple sources at these 

beaches. Human viruses and bacterial 

pathogens were present in a sufficient 

number of samples to explore results with 

statistical analysis using various measures 

of water quality, hydrology, and weather 

conditions to explain variability in pathogen concentrations. This included data 

from water samples collected concurrently with the pathogen samples as well 

as data retrieved from the USGS, NOAA, 

and the National Weather Service through 

the Environmental Data Discovery 

and Transformation (EnDDaT) system 

(http://cida.usgs.gov/enddat/). Data used 

in statistical analysis included E. coli,

turbidity (measure of water clarity), 

specific conductance, rainfall, water and 

air temperature, water and wind velocity and direction, lake level, wave height 

and direction, and cloud cover. Variables 

found to have the greatest influence on 

human virus occurrence and concentrations were water temperature, wave direction, and air temperature. Variables found 

to have the greatest influence on bacterial 

pathogen concentrations included cloud 

cover, rainfall, wave direction, and wave 

height. 

HCl

pH conditioning 

pump

pump

water

intake

flow control 

valve

P G

filter set

pH 

sensor

graduated 

cylinder and

stopwatch

Figure 2. Large-volume glass-wool filtration 

system. Sample water is mixed with dilute 

hydrochloric acid to achieve an optimal and 

uniform pH, then pumped to the filter set, 

which consists of a pre-filter (P) and a glasswool filter (G). The rate of flow is measured 

in the graduated cylinder, and pH is recorded 

throughout the sample duration.

Application of qPCR to Bacterial 

Pathogens in Water, Sediment, and 

Algae at Great Lakes Beaches

Previous research has shown that 

beach sediment, and the nuisance alga 

Cladophora, may harbor bacterial pathogens. A focused study was designed to 

evaluate the quantities of genes indicating typical bacterial pathogens in these 

matrixes, and in water from the same 

beach. The qPCR assays for quantification of Shigella, Campylobacter, and 

Shiga-toxin producing E. coli were 

performed on 5–15 samples of water, 

sediment, and algae from each of 7 Great 

Lakes beaches. This study will provide 

important information about potential 

numbers of bacterial pathogens at different beaches; the relation between 

numbers of bacterial-pathogen genes and 

FIB concentrations; and the relative role 

of water, sediment, and algae as reservoirs of bacterial pathogens at beaches. 

Results of this study should be available 

in a publication in 2013.

Evaluating Sampling Methods for 

Pathogens

Sampling methods for pathogens 

are not yet well established. Because 

pathogens are typically found in low 

numbers in environmental waters, methods are needed to concentrate pathogens 

from large volumes of water. It would be 

advantageous and cost effective to use 

a method that can simultaneously target 

all types of pathogens (viruses, bacteria, 

and protozoa), provided the method can 

reliably measure each pathogen. The 

USGS conducted studies that compare 

the reliability of different approaches to 

pathogen sampling. 

Five filtration methods (see box) 

were tested for recovery of viruses and 

protozoa artificially added to samples, 

and for naturally occurring bacterial indicators in seven experiments (fig. 3). 

Figure 3. Filtering 10 liters of lake water in 

the laboratory using NanoCeram© filtration.
In each experiment, 10 liter lakewater samples were collected from 

beaches around the Great Lakes and 

brought back to the laboratory for 

artificial additions of viruses and further 

processing. The numbers of each type of 

microorganism were determined before 

and after filtration; the difference between 

these two numbers was calculated as 

the recovery. The variability in recovery 

was determined by running some of the 

experiments in triplicate (three runs of 

each filtration method instead of one). 

In addition to recovery experiments, 

eight samples were collected during field 

deployment experiments at seven beaches 

in Ohio and Wisconsin. These experiments were done to evaluate the practicality and efficiency in using filtration 

for large-volume sampling at recreational 

beaches. 

Median percent recoveries of microorganisms in lake-water samples for the 

five filtration methods are presented in 

table 1. In evaluating filter performance 

in terms of both recovery and variability, 

the automatic ultrafiltration (UF) method 

generally resulted in the highest recoveries while maintaining low variability 

for all nine microorganisms (Francy and 

others, 2013). 

Glass-wool filtration and automatic 

UF were used to demonstrate that filtration can be scaled up to the collection of 

200 liter lake-water samples from multiple public beaches in two States. The 

issue of filter clogging from high turbidity or algae was identified and reduced 

Filtration Methods for Pathogens 

at Beaches 

• Glass-wool fiber filter (special order 

from the USGS, Marshfield, Wisconsin) 

• NanoCeram® filter (Argonide, Inc., 

Sanford, Florida) 

• Continuous flow centrifugation 

(CFC) with ViroCap® capsule filter 

(CFC+ViroCap) (Scientific Methods, 

Granger, Indiana) 

• An automatic ultrafiltration sampler 

provided by the EPA, National Homeland Security Research Center (Teledyne Isco, Lincoln, Nebraska) 

• Dead-end ultrafiltration 

Table 1. Median percent recoveries of microorganisms in seeded lake-water samples. 

[CFU, colony forming units; gc, genomic copies; results from the filtration method yielding the highest 

recovery for each organism are shaded]

Median recoveries (percent)

Glass 

wool

NanoCeram©

Continuous 

flow 

centrifugation + 

ViroCap

Automatic 

ultrafiltration

Dead-end 

ultrafiltration

Escherichia coli (CFU) 2.1 0.8 68.3 64.6 62.1

Enterocooci (CFU) .9 .4 27 45.8 80.5

MS2 coliphage (plaque 

forming units)

4.6 84 20.5 67.7 58.7

Adenovirus (gc) 4.7 .02 .04 1.4 .6

Norovirus GII (gc) 2.0 0 .06 2.4 2.1

Enterovirus (gc) 10.5 14.5 11.3 3.5 .9

Avian influenza virus (gc) 0 .007 .002 .01 .02

Cryptosporidium (oocysts) 10.7 0 54.0 35.3 41.0

Giardia (cysts) 12.1 0 32.4 22.7 57.0

by using an end connector, such as the 

one pictured in figure 4. The use of one 

or two filters to effectively concentrate all 

types of microorganisms makes filtration 

efficient for regional studies of publichealth risk at beaches. 

Figure 4. Field equipment used to reduce clogging of filtration systems by algae and other 

particles in lake-water samples. The 40-centimeter long polyvinyl chloride end connector with 

0.254 millimeter slotted openings prevents particles from entering the filtration system.
Microbial Source Tracking

Physical and biological processes at 

beaches can influence the occurrence and 

abundance of FIB and pathogens. Great 

Lakes beaches may vary widely in the 

nature of materials that form the beach, 

their proximity to sources of fecal pollution such as rivers, the numbers of birds 

or people that visit the beach, and the 

influence of offshore waters on the beach. 

However, the relations between these 

environmental factors and FIB concentrations or pathogen occurrence are not well 

understood. In recent years, DNA-based 

laboratory methods have been developed to distinguish between human and 

animal fecal contamination. These MST 

methods rely on the qPCR to generate 

copies of genes found in bacteria that 

tend to inhabit one host organism, such 

as humans or gulls. The USGS has used 

the qPCR/MST methods to evaluate the 

influence of humans, gulls, and ruminants 

(typically cattle or deer) on microbial 

contamination at Great Lakes beaches. 

Sinigalliano, C.D.; Fleisher, J.M.; Gidley, 

M.L.; Solo-Gabriele, H.M.; Shibata, 

Tomoyuki; Plano, L.R.W.; Elmir, S.M.; 

Wanless, David; Bartkowiak, Jakub; 

Boiteau, Rene; Withum, Kelly; Abdelzaher, A.M., He, Guoqing; Ortega, 

Cristina; Zhu, Xiaofang; Wright, 

M.E.; Kish, Jonathan; Hollenbeck, 

Julie; Scott, Troy; Backer, L.C.; and 

Fleming, L.E., 2010, Traditional and 

molecular analyses for fecal indicator 

bacteria in non-point source subtropical recreational marine waters: Water 

Research, v. 44, no. 13, p. 3763–3772.

Program Information 

Funding for USGS beach projects 

and research in the Great Lakes comes 

from a variety of sources including the 

Ocean Research Priority Plan, the USGS, 

the Great Lakes Restoration Initiative, the 

EPA), the NOAA Center for Great Lakes 

and Human Health, and many State and 

local partner agencies and organizations 

throughout the region. 

Contact

James R. Morris, Director 

USGS Michigan and Ohio 

 Water Science Centers

614-430-7700

http://greatlakesbeaches.usgs.gov/

Microbial Source Tracking 

Markers

Microbial source tracking (MST) 

is a term used for identifying sources of 

fecal contamination in the environment. 

MST techniques are based on the concept 

that intestinal systems of different warmblooded animals are associated with specific microbial populations in response 

to differences in diet and physiology. A 

widely used MST method is the use of 

host-associated MST markers. Quantitative polymerase chain reaction (qPCR) is 

a laboratory method that targets, amplifies, and quantifies genetic sequences of 

DNA for these markers. The following 

qPCR MST marker assays were used by 

USGS researchers at beaches on inland 

lakes (Francy and Stelzer, 2012) and at 

12 Great Lakes beaches:

• General Bacteroides marker present in 

most warm-blooded animals—AllBac 

(Layton and others, 2006) 

• Human-associated Bacteroides

marker—HF183 (Seurinck and others, 

2005) 

• Ruminant-associated Bacteroides

marker—BoBac (Layton and others, 

2006) 

• Gull-associated marker from the species Catellicoccus marimammalium—

Gull2 (Sinigalliano and others, 2010)

These assays are applied as experimental methods in the emerging field of 

MST. Most experts agree that MST markers are one tool that should be used along 

with other methods to characterize fecal 

contamination at a site. 

References

Centers for Disease Control and Prevention, 2011, Surveillance for waterborne 

disease outbreaks and other health 

events associated with recreational 

water—United States, 2007–2008 and

surveillance for waterborne disease 

outbreaks associated with drinking 

water—United States, 2007–2008: 

Morbidity and Mortality Weekly 

Report, Surveillance Summaries, v. 60, 

no. 12, 78 p.

Francy, D.S., and Stelzer, E.A., 2012, 

Microbial source tracking markers at 

three inland recreational lakes in Ohio, 

2011: U.S. Geological Survey OpenFile Report 2012–1222, 8 p.

Francy, D.S., Stelzer, E.A., Brady, 

A.M.G., Huitger, Carrie, Bushon, R.N., 

Ip, H.S., Ware, M.W., Villegas, E.N., 

Gallardo, Vincente, and Lindquist, 

H.D.A., 2013, Comparison of filters 

for concentrating microbial indicators 

and pathogens in lake-water samples: 

Applied and Environmental Microbiology, v. 79, no. 4, p. 1342–1352.

Layton, Alice; McKay, Larry; Williams, 

Dan; Garrett, Victoria; Gentry, Randall; and Sayler, Gary, 2006, Development of Bacteroides 16S rRNA 

gene TaqMan-based real-time PCR 

assays for estimation of total, human, 

and bovine fecal pollution in water: 

Applied and Environmental Microbiology, v. 72, no. 6, p. 4214–4224.

Seurinck, Sylvie; Defoirdt, Tom; Verstraete, Willy; and Siciliano, S.D., 2005, 

Detection and quantification of the 

human-specific HF183 Bacteroides

16S rRNA genetic marker with realtime PCR for assessment of human 

faecal pollution in freshwater: Environmental Microbiology, v. 7, no. 2, 

p. 249–259.