823-R-08-002 

CRITICAL PATH SCIENCE PLAN 

FOR THE DEVELOPMENT OF NEW OR REVISED 

RECREATIONAL WATER QUALITY CRITERIA 

Office of Water 

Office of Research and Development 

AUGUST 31, 2007 
Critical Path Science Plan for the Development of New or Revised Recreational Water Quality Criteria

    ii August 2007

TABLE OF CONTENTS

ACRONYMS AND ABBREVIATIONS.................................................................................................. iv

CHAPTER 1 INTRODUCTION............................................................................................................. 1–1

1.0 Purpose and Scope............................................................................................................. 1–1

1.1 Statutory Background and Purpose of EPA’s Recommended Water Quality

Criteria................................................................................................................................. 1–2   

1.2 Purpose of Water Quality Criteria Components of State Water Quality  

Standards............................................................................................................................. 1–3

1.3 Goals of EPA’s Scientific Research .................................................................................. 1–4

CHAPTER 2 DEVELOPMENT OF THE CRITICAL PATH SCIENCE PLAN .............................. 2–1

2.0 Summary of EPA Research Already Completed........................................................... 2–1

2.0.1 Early Studies.......................................................................................................... 2–1

2.0.2 National Epidemiology and Environmental Assessment of Recreational

Water Study ........................................................................................................... 2–1

2.0.3 Environmental Monitoring for Public Access and Community Tracking

Study....................................................................................................................... 2–2

2.0.4 Other Completed Studies .................................................................................... 2–2

2.1 Consideration of Stakeholder Input on the 1986 Bacteria Criteria ............................. 2–3

2.2 Experts Scientific Workshop and Report........................................................................ 2–4

CHAPTER 3 KEY SCIENCE QUESTIONS EPA WILL ADDRESS UNDER THE CRITICAL

PATH SCIENCE PLAN.................................................................................................... 3–1

3.0 Peer‐Review of Draft Critical Path Science Plan ........................................................... 3–1

3.1 Assessment of Human Health Risks (Goal 1) ................................................................ 3–2

3.1.1 Description of the Key Science Question........................................................... 3–3

3.1.2 Risks from Human Sources of Fecal Contamination ....................................... 3–3

3.1.3 Risks from Non‐Human Sources of Fecal Contamination.............................. 3–5

3.2 Development of Indicators and Methods (Goals 2 and 3) ........................................... 3–7

3.2.1 Description of the Key Science Question........................................................... 3–8

3.2.2 Develop, Evaluate and Validate Indicators and Methods .............................. 3–9

3.2.3 Assess Linkages Between Indicators and Methods ......................................... 3–9

3.2.4 Characterize Temporal and Spatial Variability in Measurements................. 3–10

3.3 Extrapolation of Research Results for Developing New and Revised  

Criteria (Goal 4).................................................................................................................. 3–10

3.3.1 Description of the Key Science Question........................................................... 3–11

3.3.2 Assess Variability in Diverse Geographic and Aquatic Conditions.............. 3–11

3.3.3 Assess Methods Suitability to Different CWA Purposes ................................ 3–13

3.3.4 Develop, Evaluate and Validate Predictive Models and Tools...................... 3–13
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CHAPTER 4 FUTURE RESEARCH....................................................................................................... 4–1

4.0 Science Issues EPA Deferred for Future Research ........................................................ 4–1

CHAPTER 5 REFERENECES.................................................................................................................. 5–1

LIST OF TABLES

Table 3‒1 Science Plan Research Activities and Projects ............................................................... 3–16

Table 3‒2 Overview of Proposed Near‐term Research Activities to Support Development of

New or Revised Recreational Criteria............................................................................. 3–26
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ACRONYMS AND ABBREVIATIONS

AL    Alabama

ATP    Alternate Test Procedure

AWQC    ambient water quality criteria

BEACH Act    Beaches Environmental Assessment and Coastal Health Act

BMP    Best Management Practices

CA    California

CFR    Code of Federal Regulations

CPSP    Critical Path Science Plan

CWA    Clean Water Act

DNA    deoxyribonucleic acid

EMPACT    Environmental Monitoring for Public Access and Community Tracking

Study

EPA    U.S. Environmental Protection Agency

GI    gastrointestinal

GIS    Geographic Information System

MS    Mississippi  

NEEAR    National Epidemiological and Environmental Assessment of Recreational

    Water Study

NOAA    National Oceanic and Atmospheric Administration

NPDES    National Pollutant Discharge Elimination System

PCR    polymerase chain reaction
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POTW    publicly‐owned treatment works

QMRA    Quantitative Microbial Risk Assessment

qPCR    quantitative polymerase chain reaction

RI    Rhode Island

SCCWRP    Southern California Coastal Water Research Project

TMDL    Total Maximum Daily Load

URI    upper respiratory illness

U.S.    United States

USGS    United States Geological Survey

UV    ultraviolet

WQS    water quality standard

WWTP    Wastewater Treatment Plant
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CHAPTER 1 INTRODUCTION

On October 10, 2000, the Beaches Environmental Assessment and Coastal Health Act (BEACH

Act) was signed into law, amending the Clean Water Act (CWA). Two of the major provisions

of the BEACH Act are CWA sections 104(v) and 304(a)(9), which together require the U.S.

Environmental Protection Agency (EPA) to conduct studies associated with pathogens and

human health and to publish new or revised recreational water quality criteria for pathogens

and pathogen indicators based on those studies. These criteria will be used by States,

Territories, and Tribes to develop their water quality standards (WQS). EPA has conducted a

significant amount of research since the BEACH Act was enacted and is now in the process of

defining what additional studies EPA will conduct in order to issue new or revised CWA

criteria by 2012.  

1.0 PURPOSE AND SCOPE

Since EPA issued its current recreational water quality criteria over 20 years ago, there have

been significant scientific advances, particularly in the areas of molecular biology, virology and

analytical chemistry.  EPA believes these new scientific and technological advances need to be

considered and evaluated for feasibility and applicability in the development of new or revised

criteria for pathogens and pathogen indicators.  To this end, EPA has conducted a significant

amount of research including developing new methods for measuring microbiological

organisms in water and conducting epidemiologic studies to provide the scientific foundation

for new or revised criteria.  However, these studies are only a part of what is needed.  EPA’s

review of existing research and science has raised a series of significant questions that need to

be answered in order for EPA to move forward with criteria development.  These questions are

presented and discussed in Chapter 3.  

To address these questions, EPA has engaged a range of stakeholders representing the general

public, public interest groups, State and local government, industry, and municipal wastewater

treatment professionals.  Based on their feedback as well as detailed input and

recommendations from the scientific community, the Agency has developed a Critical Path

Science Plan for Development of New or Revised Recreational Water Quality Criteria (CPSP or Science

Plan).  The purpose of the CPSP is to articulate the essential research and science that EPA will

conduct between 2007 and the end of 2010 to establish the scientific foundation for new or

revised recreational water quality criteria to protect swimming in waters designated by a State

for that use (referred to in this document as “recreational water quality criteria” or “recreational

criteria”).  The CPSP also describes studies for which EPA is providing financial and/or

technical support. The specific near‐term critical research and science needs described in the

Science Plan were informed by the individual input of the 43 international and U.S. experts who

attended a scientific workshop held by EPA in March 2007 at the Airlie Center in Warrenton,

Virginia.  Near‐term needs were defined as specific research and science activities that could be

accomplished in 2 to 3 years to support development of new or revised criteria by 2012.  The
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Report of the Experts Scientific Workshop on Critical Research Needs for the Development of New or

Revised Recreational Water Quality Criteria is available online at www.epa.gov/waterscience.   

The CPSP represents an integrated approach to answering the key questions that EPA believes

need to be addressed to ensure that the new or revised criteria are scientifically sound.  EPA

recognizes, however, that the outcome of one study may affect the design and implementation

of those that follow.  Therefore, some contingencies have been identified in this Science Plan to

accommodate unexpected outcomes, and it is acknowledged that others may arise that have not

been foreseen.   

1.1 STATUTORY BACKGROUND AND PURPOSE OF EPA’S RECOMMENDED WATER

QUALITY CRITERIA

Section 304(a)(1) of the CWA directs EPA to publish recommended water quality criteria

reflecting the latest scientific knowledge on the effects of the presence of pollutants in water on

health and welfare.  The criteria published by EPA under section 304(a) are intended to provide

guidance to States in setting WQS to protect public health as well as to maintain and restore

water quality and ecosystem integrity.

CWA section 303 requires each State to adopt WQS for all waters of the State and to review, and

revise them as necessary, every 3 years.  A WQS is a method of expressing the desired condition

of a water body.  Such standards consist of three main elements: (1) one or more designated

“uses” of each of the State’s waters, such as recreation or propagation of fish; (2) “criteria”

expressed as pollutant concentration levels or narrative statements representing a quality of

water that supports a designated use; and (3) an anti‐degradation policy to protect existing uses

and high quality waters.  WQS serve the dual purposes of establishing the water quality goals

for a specific water body and serve as the regulatory basis for the establishment of water‐

quality‐based treatment controls and strategies beyond the technology‐based levels of treatment

required by sections 301(b) and 306 of the CWA.  In the case of WQS for pathogens or pathogen

indicators to protect the swimming use of waters, States also use WQS in their beach monitoring

and notification programs.   

The BEACH Act was enacted on October 10, 2000.  It amended the CWA in part by adding

Section 304(a)(9)(A), which provides:

“Not later than 5 years after the date of the enactment of this paragraph, after

consultation and in cooperation with appropriate Federal, State, tribal, and local officials

(including local health officials), the Administrator shall publish new or revised water

quality criteria for pathogens and pathogen indicators (including a revised list of testing

methods, as appropriate), based on the results of the studies conducted under section

104(v), for the purpose of protecting human health in coastal recreation waters.”
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Section 104(v) of the CWA was also enacted as part of the BEACH Act.  It provides that EPA

“shall initiate, and not later than 3 years after the date of enactment“ of the BEACH Act,  

“complete . . .  studies to provide additional information for use in developing —  

(1)  an assessment of potential human health risks, resulting from exposure to pathogens

in coastal recreation waters, including non‐gastrointestinal effects;

(2) appropriate and effective indicators for improving detection in a timely manner in

coastal recreation waters of the presence of pathogens harmful to human health;

(3) appropriate, accurate, expeditious, and cost‐effective  methods (including predictive

models) for detecting in a timely manner in coastal recreation waters the presence of

pathogens that are harmful to human health; and

(4) guidance for State application of the criteria for pathogens and pathogen indicators

to be published under section 304(a)(9) to account for the diversity of geographic and

aquatic conditions.”

1.2 PURPOSE OF WATER QUALITY CRITERIA COMPONENTS OF  STATE WATER QUALITY

STANDARDS

Water quality criteria when adopted into State WQSs play a critical role in implementing a

range of essential purposes and functions under the CWA.   

Water Quality Assessments. Sections 303(d) and 305(b) provide that States are required

to assess their waters on a regular basis to determine if they are meeting WQS.  The

States’ water quality criteria are an essential baseline against which States determine

whether particular waters are ʺimpaired.ʺ 

Total Maximum Daily Loads.   Total maximum daily load (TMDL) calculations are

required for all waters that have been listed as ʺimpairedʺ under section 303(d).  A

TMDL specifies the maximum amount of a pollutant that a waterbody can receive and

still meet WQS, and ʺallocatesʺ pollutant loadings among point and non‐point pollutant

sources.  TMDL calculations for impaired waters must be written to implement the

applicable State WQS.   

National Pollutant Discharge Elimination System (NPDES).     NPDES permits are

required under section 402 for point source discharges of pollutants to waters of the

United States.  NPDES permits must include effluent limitations more stringent than

required by technology regulations if necessary to meet water quality standards, which

include State water quality criteria.      

Non‐point Source Program.  Water quality standards (including criteria) play a similarly

important role under the CWA section 319 non‐point source program as part of the

listing and TMDL processes outlined above to determine whether best management
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practices (BMPs) or other risk management control strategies are needed to address non‐

point source pollution.   

Recreational Water Monitoring and Notification.  A State’s recreational water quality

criteria are used in beach monitoring and notification programs. States and beach

managers typically make decisions about whether to issue advisories or closure notices

by measuring the results of their monitoring against their WQS.  

1.3 GOALS OF  EPA’S SCIENTIFIC RESEARCH

The studies that EPA is to conduct under CWA section 104(v) are to provide additional

information for developing (1) an assessment of potential health risks resulting from exposure

to pathogens; (2) appropriate and effective indicators of the presence of pathogens; (3)

appropriate, accurate, expeditious, and cost‐effective methods for detecting the presence of

pathogens; and (4) guidance for State application of any new or revised criteria to account for

diversity of geographic and aquatic conditions. The results of these studies will support EPA’s

development of new or revised water quality criteria under CWA 304(a) to protect public health

in waters designated by States for swimming (i.e., recreational waters). Below is a general

summary of the goals of EPA’s scientific research which are consistent with the requirements of

section 104(v).  

1. Assessment of Human Health Risk.  Conduct research (e.g., epidemiologic studies and

quantitative microbial risk assessment [QMRA]) to allow for an assessment of potential

human health risks (including non‐gastrointestinal effects) in the general population,

including children, from swimming‐related exposure to different sources of fecal

contamination (human versus non‐human).  

2. Development of Indicators.1  Conduct research to identify appropriate indicators of

fecal contamination to allow for a reliable correlation between indicator concentrations

and health effects.  Develop studies to evaluate temporal and spatial variability in

indicator concentrations to appropriately characterize water quality and inform

recreational water quality management decisions.   

3. Development of Methods.2 Conduct research to develop, evaluate and validate

appropriate methods to measure indicators of fecal contamination to allow for a reliable

correlation between indicator concentrations and health effects. Assess linkages between

indicators and methods to ensure that they will be protective of the swimming use when

implemented singly or in combination.   

4. Extrapolation of Research Results for Developing New or Revised Criteria.  Conduct

appropriate studies to assess the influence of variability in geographic and aquatic

                                                     

1 Research on indicators and methods are discussed together in Chapter 3 (Section 3.2).

2 Research on methods (including models) is discussed in Chapter 3 (Sections 3.2 and 3.3).   
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conditions on indicator and method performance, and assess the suitability of indicators

and methods for various CWA purposes (e.g., beach monitoring, assessments, TMDLs,

and permitting).  Develop, evaluate and validate predictive models and tools to

understand the extent to which data from epidemiologic study sites can be extrapolated

to other geographic locations and aquatic conditions; and examine the role of models as

a tool in predicting water quality problems to assist in new or revised criteria

implementation.  

The requirements in CWA sections 104(v) and 304(a)(9)(A) are for studies and water quality

criteria related to “coastal  recreation waters” as defined in section 502(23) of the CWA (i.e.,

marine coastal waters, coastal estuaries, and Great Lakes waters).  However, some of the studies

included in this Science Plan would be used to support the development of recommended

water quality criteria that applies to both coastal recreational waters and inland waters

designated for swimming.
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CHAPTER 2 DEVELOPMENT OF THE CRITICAL PATH SCIENCE PLAN  

2.0 SUMMARY OF EPA RESEARCH ALREADY COMPLETED

2.0.1 Early Studies

Current 304(a) recreational water quality criteria are based on epidemiologic studies conducted

by EPA in the 1970s and 1980s.  The currently recommended indicators are based on methods

that involve culturing and enumerating fecal indicator bacteria (Enterococcus spp. or E. coli).  One

shortcoming of these methods is that the bacteria require at least 18 to 24 hours to grow visible

colonies for subsequent enumeration.  Recent research indicates that the quality of water that is

impacted by fecal contamination can change rapidly, and thus, criteria based on indicator

organisms and associated methods that require 18 hours or more to produce results can lead to

either unnecessary beach closings or the exposure of swimmers to water of poor quality.     

Since the enactment of the BEACH Act, EPA has undertaken several significant studies

designed to improve the scientific basis for recreational water quality criteria. Each study is

discussed below.

2.0.2 National Epidemiological and Environmental Assessment of Recreational Water

Study

EPA’s National Epidemiological and Environmental Assessment of Recreation (NEEAR) Water

Study is a collaborative research study between EPA and the Centers for Disease Control and

Prevention (CDC). EPA also coordinated this study with the U.S. Geological Survey (USGS) and

other interested agencies. A primary goal of this study is to establish a health‐based relationship

between indicators of fecal contamination and swimming‐associated illness as measured by a

variety of methods, including timely molecular methods.  To date, four Great Lakes freshwater

epidemiologic studies have been completed, one marine study3 was started but halted due to

hurricane conditions and two EPA‐conducted marine epidemiologic studies (described in

Chapter 3) are currently underway.  The Great Lakes freshwater studies were the first to

establish a relationship between the levels of fecal contamination in recreational waters

(referred to in this document as “microbial water quality”), as measured by timely methods,

and swimming‐associated health effects occurring within 10 to 12 days after a beach visit. In

these studies, molecular methods showed great promise for allowing beach managers to

potentially make more timely decisions regarding the safety of beach waters on any given day.   

                                                     

3Marine study in Biloxi, Mississippi was halted because the beach study site was destroyed by Hurricane Katrina in

2005.
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2.0.3 Environmental Monitoring for Public Access and Community Tracking Beaches

Project

The Environmental Monitoring for Public Access and Community Tracking (EMPACT) Beaches

Project (EPA, 2005) was designed to identify the characteristics of a beach environment that

have a significant impact on microbial water quality monitoring results.  Five beach

environments were examined to determine the factors that most influence the measurement of

microbial water quality at beaches.  Two ocean beaches, an estuarine beach, a Great Lakes

beach, and a riverine beach were selected to provide as broad a representation of beach

environments as possible.  The results indicated the following:  

• The greatest single determinant of fecal indicator level was found to be the depth

zone, or distance from the shoreline at which the sample was collected—fecal

indicator concentrations were substantially lower as one moved from ankle‐deep

to knee‐deep to chest‐deep water;   

• Significant declines in indicator densities from the morning to the afternoon were

observed at four of the five study beaches; and

• There was significant variability over time so that measurements of indicators on

any given day did not correlated to indicator levels on subsequent days.  

2.0.4 Other Completed Studies

The following additional studies were critical to determining which indicators and methods

were available for inclusion in the NEEAR study in the Great Lakes to provide timely

quantification of fecal contamination.    

• Method evaluation of off‐the‐shelf technologies for rapid methods for indicators of fecal

contamination;

• Method development study of quantitative polymerase chain reaction (qPCR) methods

for Enterococcus and Bacteroides; and

• Completion of a chemical indicator study evaluating other chemical substances,

including coprostanol, urobilin, caffeine, acetaminophen, cotinine and codeine as

possible indicators of human fecal contamination (from wastewater).

EPA also completed related studies to allow for the use of the epidemiologic study results to:

(1) develop a predictive modeling tool, and (2) understand whether the Great Lakes study

results could be applied beyond the study locations to other freshwaters.  These studies

included:   

• A study to develop a virtual beaches model intended to allow beach managers to collect

and analyze explanatory variables and develop a beach prediction tool; and  
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• An evaluation of the aquatic matrix effects on the performance of the qPCR method in

order to determine the methodʹs applicability in freshwaters beyond the four Great

Lakes test sites.

Additional information is needed to fulfill several important goals and objectives for new or

revised criteria.  For example, the relative health effects and associated risk levels from different

sources of fecal contamination (e.g., human versus non‐human sources of fecal contamination,

and treated versus untreated or poorly treated human sewage) are not well understood and

may vary significantly; the relationship between indicator organism concentrations and adverse

health effects in different waterbody types are not well understood; the compatibility of existing

culture methods with the newly developed rapid methods for indicator organisms is not

sufficiently understood; and the optimization of sampling, recovery, and processing of samples

using rapid methods is still under development.

2.1 CONSIDERATION OF STAKEHOLDER INPUT ON THE 1986 BACTERIA CRITERIA

Although EPA considers the science underlying the 1986 bacteria criteria to be superior to the

science underlying the previously recommended criteria for fecal coliforms, some States have

yet to adopt new or revised standards for inland waters based on the 1986 bacteria criteria.  

States and other stakeholders, including experts from the Experts Scientific Workshop have

suggested that EPA consider the following recommendations in conducting studies and

developing the new or revised criteria, based on their experience implementing the 1986

bacteria criteria.   

C Provide clear, science‐based guidance and flexibility regarding use of the single‐sample

maximum values (a feature of the 1986 criteria) and differing risk levels, or change the

approach to include specific measures to assess water quality for both the short‐term

(beach closure/advisory decisions) and the long‐term (attainment of the designated

swimming use over a length of time).  

C Consider the impact on transition from current criteria (e.g., fecal coliforms‐based

criteria or the 1986 bacteria criteria) to new criteria on impaired waters listings, existing

bacteria TMDLs, and associated discharge permits; and develop tools, strategies, and

policies to ease the transition.

C Develop EPA‐approved analytical methods for use in both ambient and wastewater for

the new indicator bacteria.

C Collect data or perform analysis to assess the applicability of the new bacteria criteria to

flowing streams.

C Conduct research to quantify the risk associated with contributions from the range of

non‐human sources of fecal contamination, and incorporate flexibility to adjust the new

criteria for water bodies that do not receive human sources of fecal contamination.

C Continue dialogue with States and other stakeholders during the development of the

new bacteria criteria to keep them informed regarding the outcomes of the research and

the effect on the criteria development approach.  
Critical Path Science Plan for the Development of New or Revised Recreational Water Quality Criteria

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2.2 EXPERTS SCIENTIFIC WORKSHOP AND REPORT

The Experts Scientific Workshop on Critical Research and Science Needs for the Development of New or

Revised Recreational Water Quality Criteria took place at the Airlie Center in Warrenton, Virginia,

from March 26 to March 30, 2007. Forty‐three U.S. and international experts from academia,

States, public interest groups, EPA, and other federal agencies, met to discuss the state‐of‐the‐

science on recreational water quality research and implementation issues.

The purpose of the workshop was for EPA to obtain input from individual members of the

broad scientific and technical community on the “critical path” research and related science

needs for developing scientifically defensible new or revised CWA Section 304(a)(9) recreational

ambient water quality criteria in the near‐term. Near‐term needs were defined as those specific

research and science activities that could be accomplished in the next 2 to 3 years so that results

would be available to EPA in time to support development of new or revised criteria by 2012.  

For additional information on the Experts Workshop Report and research identified by the

experts, go to www.epa.gov/waterscience.   
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    3–1 August 2007   

CHAPTER 3   KEY SCIENCE QUESTIONS EPA WILL RESEARCH UNDER THE  

CRITICAL PATH SCIENCE PLAN

3.0   PEER‐REVIEW OF DRAFT CRITICAL PATH SCIENCE PLAN

In developing the Science Plan, EPA considered the research needs identified by the experts

participating in the Experts Scientific Workshop. EPA then established its research priorities

based on the most significant science questions, which EPA believes it can make significant

progress toward answering in the next 2 to 3 years to support development of new or revised

recreational criteria.    

The research projects were described in a draft of the Science Plan which was peer reviewed by

three scientific experts external to EPA.4 The purpose of the peer review was to obtain expert

feedback and comments on the clarity and scientific merit of the proposed research activities,

and on the likelihood they can be completed in a 2‐ to 3‐year period and meet EPA’s goals and

objectives for the new or revised criteria.  In addition, EPA asked the peer reviewers whether or

not the proposed research activities effectively addressed the science questions and research

needs identified in the document, and to identify the noteworthy strengths and weaknesses of

the proposed research activities.  EPA requested that peer reviewers indicate any modifications

that would improve upon any particular research project or upon the science plan in its entirety.   

The reviewers provided beneficial and constructive input to EPA on the draft Science Plan.  The

reviewers confirmed that the epidemiologic studies, assay methodologies, fecal contamination

source identification studies, QMRA methods, and other studies reflected a generally

reasonable and effective approach to answering the research questions.  They supported EPA’s

focus on research related to non‐human sources of fecal contamination. They also indicated that

the plan as outlined is achievable in the 2‐ to 3‐year timeframe available.  However, they

suggested that EPA clarify the key goals and questions articulated in the  Science Plan to

increase understanding and transparency in the document (e.g., more clearly articulating the

connection between the research projects and the goals, improving individual project

descriptions and justifications, identifying how research results would be used and how the

project results may interact).  EPA concurred with many of these comments and has revised the

Science Plan accordingly.  EPA has clarified the key goals and key research questions as

presented in section 1.3 as follows:

• Assessment of Human Health Risks (Goal 1, discussed in section 3.1)

o Key Research Question: What is the risk to human health from swimming in water

contaminated with human fecal matter as compared to swimming in water

contaminated with non‐human fecal matter?   

• Development of Indicators (Goal 2) and Methods (Goal 3) (discussed in section 3.2)

                                                     

4 Peer review comments are available upon request.
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o Key Research Question: How well do culture and molecular methods for various

indicators (singly or in combination) correlate with swimming‐related illnesses?  

• Extrapolation of Research Results for Developing New or Revised Criteria (Goal 4,

discussed in section 3.3)

o Key Research Question:  Are these indicators, methods and models suitable for use

in different types of waters and for different CWA programs?

3.1 ASSESSMENT OF HUMAN HEALTH RISKS (GOAL 1)

EPA’s current CWA 304(a) recommended criteria for bacteria are based on E. coli and

enterococci as indicators of fecal contamination.  These criteria were derived largely from the

results of epidemiologic studies at beaches predominantly impacted by publicly‐owned

treatment works (POTWs) in the 1970’s and 1980’s.  At that time, human sources of fecal

contamination originating from POTWs were viewed as representing the highest relative risks

to swimmers.  While human fecal contamination may pose a higher risk, there are other sources

of fecal contamination for which the risk is not well understood. These other sources include

poorly‐ treated or untreated human fecal waste, and non‐human sources of fecal contamination

(e.g., fecal contamination from agriculturally important animals and wildlife in the watershed).  

Also, stormwater runoff in urban areas may represent a mixed source of human and animal

fecal material.  Animal sources in an urban setting may include domesticated and other animals

such as geese.   

There have been limited studies on poorly‐treated or untreated human fecal contamination, and

few studies on waters largely impacted by animal sources of fecal contamination. Many of these

studies used different indicators of fecal contamination, various (qualitative to quantitative)

approaches at differentiating sources of contamination, and different approaches or protocols to

assess health effects in the study population. The lack of studies using similar study design and

protocols focusing on various sources of fecal contamination represents a major data gap. As

such, it is difficult to determine in a quantitative manner the relative risks of swimming‐

associated illness from various sources of fecal contamination.  Specific uncertainties that EPA

intends to address include:

• Understanding what human illnesses are caused by swimming in waters contaminated

with human fecal matter from different sources, the levels of human fecal matter in these

waters that cause human illness, and the relationship between different levels of human

fecal matter in waters and human illness rates.

• Understanding what human illnesses are caused by swimming in waters contaminated

with non‐human fecal matter, the levels of non‐human fecal matter in these waters that

cause human illness, and the relationship between different levels of non‐human fecal

matter in waters and human illness rates.  

• Understanding any differences in risk to children swimming in waters contaminated

with fecal matter versus adults swimming in these waters.  
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3.1.1 Description of the Key Science Question

What is the risk to human health from swimming in water contaminated with human fecal

matter as compared to swimming in water contaminated with non‐human fecal matter?   

The research described in this section addresses Goal 1 as outlined in section 1.3 and focuses on

the following two areas:

• Risks from Human Sources of Fecal Contamination (Section 3.1.2)

• Risks from Non‐Human Sources of Fecal Contamination (Section 3.1.3)

3.1.2 Risks from Human Sources of Fecal Contamination

3.1.2.1 Treated POTW Effluent

EPA conducted prospective cohort epidemiologic studies at four Great Lakes beaches impacted

by treated wastewater discharges as part of the NEEAR studies.  EPA included several

indicators and methods of fecal contamination and assessed their relationship to the following

non‐enteric and enteric illnesses:  

(1) gastrointestinal illness (GI) , defined as any of the following:   

a) diarrhea (3 or more loose stools in a 24‐hour period), or  

b) vomiting, nausea and stomachache, or  

c) nausea or stomachache and impact on activity;  

(2) upper respiratory illness (URI), defined as any two of the following:  sore throat, cough,

runny nose, cold, fever;

(3) rash;  

(4) eye ailment, defined as either eye infection or watery eye; and  

(5) earache.   

Furthermore, EPA collected extensive demographic data which will allow for analysis of risk in

various subpopulations, including children, relative to the general population.   

Swimming‐related GI rates were found to be significantly associated with fecal contamination

(as measured by qPCR enterococci) in the Great Lakes NEEAR studies (Wade et al., 2006). EPA

intends to conduct comparable studies (using the same site selection criteria and protocols and

methods) at POTW‐impacted marine beaches to determine if a similar indicator‐illness

relationship holds.    

EPA initiated a marine epidemiologic study in Biloxi, MS in the summer of 2005 that was

curtailed due to severe weather events caused by Hurricane Katrina.  Although the study was

insufficient in terms of sample size, it represents a source of additional data that can be

analyzed along with data from ongoing and future epidemiologic studies.  At this time, the lack
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of similar epidemiologic studies in marine waters represents a data gap; EPA needs to

determine whether the relationship between fecal contamination and illness, which was

observed in the Great Lakes, is similarly applicable in marine waters. To address this gap, EPA

intends to conduct the following research activities and projects:

• Conduct an epidemiology study at a POTW‐impacted marine beach at Goddard, Rhode

Island. (P1)5

• Conduct an epidemiology study at a POTW‐impacted marine beach at Fairhope,

Alabama. (P2)  

• Conduct statistical analysis of children data (P29) to determine if there is a significant

difference in risk in all epidemiologic studies.   

• Compare 1986 to NEEAR data to better understand the relationship between fecal

contamination and illness in these data sets (P27).

If the results of these studies do not yield sufficient statistical power or if the results between

these studies (Alabama, Rhode Island, and Mississippi) are not consistent, then an additional

epidemiologic study on POTW‐ impacted marine waters (P6) would be conducted.   

When completed, these studies will fill a data gap and help EPA determine whether and how

fecal contamination is associated with illness in marine waters. Detailed descriptions of each

research activity can be found in Table 3–1, organized under a broad research category (e.g.,

epidemiology studies). Table 3–2 presents a timeline for these studies indicating when EPA

expects to initiate and complete the studies. The timeline for epidemiology studies includes

study design, study initiation and completion, data analysis, peer review, and publication.  

3.1.2.2 Poorly Treated or Untreated Wastewater

Since past research efforts have largely focused on POTW‐impacted waters, there have been few

epidemiologic studies which have addressed the relative risks of illness associated with poorly

or untreated human fecal matter.  Addressing this gap has been the focus of the Southern

California Coastal Water Research Project (SCCWRP).  A prospective cohort epidemiology

study is being conducted by SCCWRP with EPA support to assess health risks and illness‐

indicator relationships at a marine beach in California.  Avalon beach is affected by a mix of

sources of fecal contamination including bird droppings, urban runoff and leaking sanitary

sewers (including failing infrastructure and leaking collection systems). EPA is interested in this

study as an example of a beach believed to be predominantly impacted by poorly/untreated

human fecal contamination. Water samples are being tested for Enterococcus qPCR, Bacteroides

qPCR, Bacteroides thetaiotamicron qPCR, and coliphage by antibody assay in addition to

                                                     

5 Codes (P1–P32) refer to an arbitrarily assigned project number.
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traditional culture‐based assays. The study design is largely based on EPA’s current marine

study design and the data could potentially be combined with EPA conducted studies for future

analysis.  Because the focus of this SCCWRP research is expected to help fill this gap, EPA does

not intend to conduct any additional studies in this area.

SCCWRP is expected to ultimately generate data from two, other beaches: a beach that is

predominantly impacted by animal fecal contamination (Doheny, CA), and a beach that is

impacted by a mixture of animal and human fecal contamination (Malibu, CA). This data set

could potentially help EPA understand differences in illness rates under different source

conditions in the same geographic/climatic region.   These other SCCWRP studies are receiving

EPA technical input.

Summary of research activities and projects:

• Support an epidemiologic study at a beach in Avalon, CA believed to be impacted

primarily by untreated human fecal contamination. (P3)

• Conduct statistical analysis of children data (P29) to determine if there is a significant

difference in risk in the Avalon, CA epidemiologic study.  

EPA will consider the results of the SCCWRP studies to determine whether risks associated

with poorly treated or untreated human fecal matter differ greatly from risks associated with

swimming in waters in proximity to POTWs and if the risks are different, what the relative

difference is in risk of illness. A detailed description and a timeline for each study are provided

in Tables 3–1 and 3–2, respectively.  

3.1.3 Risks from Non‐Human Sources of Fecal Contamination

3.1.3.1 Animal Sources and Stormwater

Human and animal feces can both potentially contain pathogens that cause human illness.  

Some human pathogens can be shed in feces by both humans and animals, while others such as

viruses are typically host specific. As a result, the relative risks associated with animal fecal

matter are dependent somewhat on the host species. As noted in the Experts Workshop Report

(EPA, 2007), “it is widely believed that human feces pose a larger health risk than animal feces

to swimmers and other primary contact recreational waster users. This belief derives from the

basic concept that virtually all enteric pathogens of humans are infectious to other humans,

while relatively few of the enteric pathogens of animals are infectious to humans...The bottom

line is that there are few data to demonstrate whether animal feces pose a lower, greater, or

equivalent heath risk to swimmers than human feces.  If there is a difference, it would be

important to know the magnitude of the difference, in order for EPA to make appropriate

criteria recommendations.  The only way to get a better sense of the health risk to swimmers

posed by animal feces is to conduct targeted studies.”  
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EPA plans on conducting several lines of research to support such targeted studies. Initially,

EPA will conduct a state‐of‐the science review of published studies to identify major data gaps,

outline current thinking on relative risks and target animals/pathogens of concern, and identify

specific data collection needs that may influence the direction and design of field studies that

would be conducted to help answer this question. Then, EPA will:

(1) develop new and/or evaluate previously published genetic biomarker methods (or

assays) for identifying human and a particular source of animal contamination, and  

(2) collect data and conduct source and site characterization evaluations at potential study

sites.  

Based on the findings from this research, EPA will conduct at least one epidemiologic study

and/or conduct QMRA to characterize the indicator‐illness relationship at a freshwater beach

impacted by agricultural animal sources of fecal contamination for comparison to the

relationship(s) obtained at beaches impacted by human fecal contamination.

The genetic biomarker assays will be useful in characterizing the sources of fecal contamination

at recreational water sites, as an initial step prior to conducting epidemiologic or QMRA

studies.  Source and site characterization activities will be conducted concurrently with the use

of the genetic biomarker methods to identify likely agricultural sources and site characteristics

that may influence contributions of fecal contamination at the beach.  While various assays are

being researched which may in the future allow for differentiation among animal groups, only

those that differentiate human fecal material from the total fecal material, and those that

differentiate bovine fecal material from other animal fecal material, will be available given the

2‐ to 3‐year timeframe for developing the new or revised criteria.  

Source and site characterization activities will also be conducted to assess risks posed by urban

stormwater sources of contamination.  Based on these activities and an evaluation of the

preliminary results of the proposed Doheny, CA, SCCWRP study, EPA will decide whether the

potential differences in risks can be assessed through QMRA activities or whether an

epidemiologic study is needed.  If an additional epidemiologic study is warranted, EPA will use

the site/source characterization study to develop site selection criteria, and/or revise study

design if needed.  The site/source characterization study activity will also potentially support

the development of quantitative sanitary investigation tools/protocols.

Summary of research activities and projects:

• Conduct several state‐of‐the‐science reviews of published studies focusing on:  

o sources of non‐human fecal contamination (P30),  

o studies on occurrence and cross‐infectivity of specific pathogens associated with

animals (P31), and  

o components and data requirements for QMRA (P7).   
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• Develop new and/or evaluate previously published source‐identifying assays (P19) or

molecular biomarkers.  

• Evaluate human assays with water samples with different levels of fecal contamination

from wide geographic range to supplement site characterization and quantitative

sanitary investigation. (P20)

• Evaluate genetic markers for cows to supplement the site characterization and

quantitative sanitary investigation. (P21)

• Collect data and conduct source and site characterization evaluations at potential study

sites to determine the extent of specific animal sources, and factors influencing the

extent to which they would contribute to fecal contamination at the beach. (P9)

• Conduct site and source characterization studies to better understand the factors

influencing the contributions of untreated sources (e.g., urban runoff) to total fecal

contamination to ambient waters. (P11)

• Conduct at least one epidemiologic study and/or QMRA to characterize the indicator‐

illness relationship at a freshwater beach impacted by agricultural animal sources of

fecal contamination for comparison to those obtained at POTW‐impacted beaches. (P4)

• Conduct epidemiologic study in marine or fresh waters impacted by urban runoff

and/or conduct QMRA analysis. (P5)

These targeted studies will address current data gaps and uncertainties in assessing the relative

risks associated with non‐human sources of fecal contamination. A detailed description and a

timeline of each study are provided in Tables 3–1 and 3–2, respectively.

3.2 DEVELOPMENT OF INDICATORS AND METHODS (GOALS 2 AND 3)

EPA’s current CWA 304(a) recommended criteria for bacteria are based on methods that

involve culturing and enumerating E. coli and enterococci as indicators of fecal contamination.

One shortcoming of these methods is that the bacteria require at least 18 to 24 hours to grow

visible colonies for subsequent enumeration. The need for appropriate and effective indicators

and methods for timely detection of fecal pathogens is reflected in the EPA science Goals 2 and

3 described in section 1.3. As described in Chapter 2, EPA has conducted epidemiologic studies

at four Great Lakes beaches and tested a suite of indicators and methods which were available

at the time the studies were conducted and that met EPA performance criteria. The results of

those studies indicate that Enterococcus qPCR is positively correlated with GI illness. EPA has

also conducted a study evaluating the performance of this method in various settings. At

present, EPA is testing a similar suite of indicators and methods in marine waters impacted by
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human fecal contamination. The analysis of the marine studies will determine whether the same

or a different indicator and method are most appropriate for marine environments.

EPA may identify or recommend more than one indicator or method, recognizing the different

purposes served by criteria in the implementation of CWA programs (e.g., criteria are used to

determine NPDES limits, to trigger beach advisories, and to define impaired waters). If EPA

does recommend more than one indicator or method, EPA must understand the relationship

between any separately recommended indicators and methods (for the various CWA purposes)

and ensure that the recommended combination of indicators and methods will be, when

implemented, protective of the swimming use.

Recent research indicates that indicator organism concentrations can vary at a given beach on

time scales ranging from minutes to decades based on events such as changes in wastewater

treatment, meteorological events (El Niño), strength or magnitude of rainfall events, tidal

cycles, and UV‐induced mortality.  Of particular concern are the short‐term (minute to hour)

variability and heterogeneous mixing which can lead to moving hot spots of microorganisms.  

Additional research is needed to understand these processes and develop robust monitoring

protocols that will allow for adequate characterization of microbial water quality.  

EPA studies have demonstrated the utility of a new indicator and method (i.e., qPCR for

enterococci) as a predictor of swimming‐related illness in the Great Lakes. Whether this

indicator and method is applicable to other settings or appropriate for use across the range of

CWA programs is not fully understood.  Data gaps include understanding how well the various

indicators and methods perform in other settings (e.g., marine versus fresh water; human

versus non‐human sources of fecal contamination), and how they relate to one another. These

data gaps led EPA to identify the following key science question.

3.2.1 Description of the Key Science Question

How well do culture and molecular methods for various indicators (singly or in combination)

correlate with swimming‐related illnesses?  

The research activities described in section 3.2 aim to identify appropriate indicators of fecal

contamination and related methods for use in new or revised criteria.  This research addresses

Goals 2 and 3 as outlined in section 1.3. The research related to indicators is not separate from

the research related to methods. This is because in conducting epidemiologic studies to

determine the relationship between illness and indicators, methods are used to detect and

quantify the indicators. EPA will conduct health‐based studies to identify those

indicators/methods that show a positive correlation between indicator concentrations in the

water and health effects. The research in this section focuses on the following three areas:

• Develop, Evaluate and Validate Indicators and Methods (Section 3.2.2)

• Assess Linkages between Indicators and Methods (Section 3.2.3)

• Characterize Temporal and Spatial Variability in Measurements (Section 3.2.4)
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3.2.2 Develop, Evaluate and Validate Indicators and Methods

As discussed in Chapter 2, EPA conducted prospective cohort epidemiologic studies at four

Great Lakes beaches impacted by treated wastewater discharges as part of the NEEAR studies.

EPA included several validated methods available at that time and assessed their relationship to

various illness endpoints described in section 3.1.2.1. Water samples were tested for Enterococcus

using qPCR, Enterococcus using standard culture method, E. coli using a standard culture

method, and Bacteroides using qPCR.  The samples also were tested for over 30 pharmaceutical

and industrial chemicals.  Swimming‐related illness rates and qPCR measures of enterococci

were significantly associated in these studies.  EPA is conducting comparable studies in marine

waters impacted by POTWs to determine if a similar relationship holds at sites using the same

site‐selection criteria and protocols and methods used at the Great Lakes beaches. Additional

indicators and methods included in the marine study sites (section 3.1) are E. coli using qPCR,

Bacteroides using qPCR (not human‐specific), Bacteroides using qPCR (human‐specific), and

male‐specific coliphages antibody assay. EPA will evaluate each of the indicators/methods, and

should any of these prove superior to enterococci qPCR, those methods will be further studied.  

Archived samples on frozen filters from the Great Lakes epidemiologic studies will be analyzed

if appropriate for indicators and methods not originally available, but that showed promise in

marine studies, to determine whether a better correlation can be established with swimming‐

associated illness.  In addition, EPA is refining several indicators/methods (e.g., Bacteroides) and

plans to include improved techniques in any re‐analysis.  However, prior to analyzing any

archived samples, EPA plans to conduct a study to assess the effects of sample holding time,

sample storage, and preservation on sample integrity for future use (P16).   

Summary of research activities and projects:

• Study the effects of sample holding time, sample storage, and preservation on sample

integrity for future use. (P16)

• Re‐analyze archived NEEAR samples for other indicators (depending on the outcome of

M0 and the nature of the indicator/method). (P22)

• Develop, refine, validate, and publish new ambient and wastewater test methods. (P17)

3.2.3 Assess Linkages Between Indicators and Methods  

Recognizing that any single indicator or method may not be suitable for all CWA purposes,

EPA intends to conduct scientific studies to explore correlations and linkages between available

indicators and methods to ensure that they provide for equivalent or comparable public health

protection.  EPA plans to analyze each indicator and method relative to its relationship with

swimming‐associated risk of illness. Additionally, EPA plans to use this information to develop
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water quality models that can be extrapolated from one waterbody type to another. (See also

section 3.3).  

Summary of research activities and projects:

• Study various parameters that affect performance of qPCR signal for enterococci and

compare with other methods and pathogens in treated wastewater mixed with ambient

waters (enterococci, E. coli, Cryptosporidium, and enterovirus). (P8)

• Evaluate multiple indicator/method combinations to develop quantifiable relationships.

(P15)

• Pilot sanitary survey in Great Lakes. (P14)

3.2.4 Characterize Temporal and Spatial Variability in Measurements   

The NEEAR studies used a detailed sampling protocol for collecting data at various locations

and water depths at a beach several times each day.  These data were evaluated to determine

their relationship with observed rates of swimming‐associated illness.  The results of that

evaluation provide insights on the variability that one may expect spatially and temporally at a

beach.  Recent research external to EPA supports these findings (EPA, 2007).  Additional

research is needed to understand the short‐term (minute‐to‐hour) variability caused by various

processes, such as tidal cycles, as well as the effects of these processes on monitoring data.  

Accounting for this variability will lead to more robust monitoring protocols that will allow

beach managers to better characterize the water quality at their beaches.   

Summary of research activities and projects:

• Design and evaluate a monitoring approach that will characterize the quality of beach

waters that takes into account the spatial and temporal variability associated with water

sampling. (P12)

These studies will address the current data gaps and uncertainties in assessing the performance

of various indicators and methods to detect pathogens in a time manner, and how various

indicators and methods relate to one another in predicting risks. A detailed description and a

timeline of each study are provided in Tables 3–1 and 3–2, respectively.

3.3 EXTRAPOLATION OF RESEARCH RESULTS FOR DEVELOPING NEW OR REVISED

CRITERIA (GOAL 4)

As described in section 3.1, EPA is conducting or supporting epidemiological studies at select

sites.  Environmental factors, such as meteorology or the physical and chemical characteristics

of freshwater and marine environments, vary geographically and may influence the presence
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and viability of indicators and pathogens.  Consequently, they may also influence any observed

indicator‐illness relationship.  Therefore, EPA intends to conduct studies to better understand

what differences in geography and climate are significant in the context of development of new

or revised criteria.   

As described in section 3.2, EPA may identify or recommend more than one indicator or

method.  Individual CWA programs (e.g., beach monitoring, assessments, TMDLs, and

permitting) have specific purposes that may influence the selection of indicators or methods.  

For example, timeliness of obtaining test results may be critical for effective beach monitoring

and notification, but may not be essential for NPDES permitting.  Understanding the specific

attributes of various indicators and methods as they relate to different CWA programs

represents another data gap.   

The research activities described below address the major data gaps in understanding how

variations in diverse geographic and aquatic conditions can influence indicator performance,

and whether and how individual indicators and methods are suitable for various CWA

programs.  These data gaps lead EPA to identify the following key science question.  

3.3.1 Description of the Key Science Question

Are the indicators, methods and models suitable for use in different types of waters and for

different CWA programs?  

This research addresses Goal 4 as described in section 1.3 and focuses on the following three

areas:

• Assess Variability in Diverse Geographic and Aquatic Conditions (Section 3.3.2)

• Assess Methods Suitability to Different CWA Purposes  (Section 3.3.3)

• Develop, Evaluate and Validate Predictive Models and Tools (Section 3.3.4)

3.3.2 Assess Variability in Diverse Geographic and Aquatic Conditions

EPA expects that differences between freshwater and marine environments present the greatest

potential for variation in indicator performance.  Other factors that are likely to influence

variability include hydrometeorology, biogeochemistry, and temperature.   

3.3.2.1 Fresh and Marine Waters

EPA has or will be conducting or supporting several epidemiologic studies in both fresh and

marine waters.  The same protocol is being used across all epidemiologic studies to allow for an

analysis of any differences in indicator performance between waterbody types.   
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3.3.2.2 Temperature/Climatic Conditions

Temperature influences the general persistence and survival of indicators and specific

pathogens deposited or discharged into the environment.  As described in section 3.1, EPA has

or intends to conduct or support epidemiologic studies at sites representing a range of

temperature and climatic conditions. These include:  freshwater temperate (Great Lakes), a

marine subtropical beach (Fairhope, AL), a marine temperate beach on the Atlantic coast

(Goddard, RI), and a marine temperate beach on the Pacific coast (Avalon, CA).  The same

protocol is being used across all epidemiologic studies to allow for analysis of any differences

between temperature and climatic conditions and indicator performance as predictors of illness.    

In the near term, EPA is not intending to conduct an epidemiology study in tropical waters.  

This is because available data indicate that the characterization of indicators and pathogens in

tropical climates and the factors influencing their existence, persistence, and behavior (e.g., re‐

growth, naturally occurring sources) are not sufficiently characterized to pursue targeted

research in the near‐term.  There has been extensive research in recent years in an attempt to

understand the behavior of pathogens and pathogen indicators in tropical waters, but this

research has yielded ambiguous results as to what may actually be influencing the presence and

growth of indicators and pathogens.  If EPA were to conduct an epidemiologic study in tropical

waters within 2‐3 years, and differences between tropical and temperate waters were observed,

EPA would not be able to use its results in developing new or revised criteria without a better

understanding of the factors influencing the presence and growth of indicators and pathogens.  

Additional research is needed to characterize organism ecology and fate before an appropriate

study design can be developed for an epidemiologic study. (Refer to Chapter 4 for further

discussion on deferred research at tropical beaches.)  

Instead, EPA will conduct a comprehensive literature review to determine the extent to which

indicators may perform differently in a tropical environment compared to temperate or

subtropical environments, and to better understand the underlying causes for any differences.

EPA is also open to evaluating epidemiologic and other data generated at tropical locations by

other entities to determine if an alternative indicator is appropriate.

Summary of research activities and projects (for tropical waters):

• Conduct literature review, and evaluate and interpret available data on indicator

behavior in tropical climates: (e.g., water, sand, and sediments). (P32)

3.3.2.3 Extrapolation to Other Fresh Waters

EPA is interested in evaluating whether it is scientifically valid to extrapolate results from

studies conducted in Great Lakes freshwater environments to other freshwater environments

that may differ from the Great Lakes.   
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Sites can vary in the type and magnitude of contamination sources and their relative

contribution to the mix of individual pathogens, and they may differ with respect to site‐specific

environmental factors (e.g., hydrology, meteorology).  Given the numerous factors to be

considered, it is not feasible to conduct field studies that can adequately control for all

parameters.  Collecting weather information along with physical and chemical water

characteristics data during epidemiology studies provides the opportunity to utilize water

quality models to examine any correlation of these data with health effects.  Utilizing existing or

developing new predictive water quality models, one can evaluate whether and how the

epidemiologic data can be extrapolated to estimate potential health effects across different

geographic areas.  (Refer to section 3.3.4 for research activities related to development,

evaluation and validation of predictive models and tools.)  

Summary of research activities and projects:

• Evaluate applicability of NEEAR Great Lakes data to inland waters. (P28)

• Expand spatial scale of collection of site‐specific data at epidemiologic study locations to

characterize watershed and support research into development of predictive models and

QMRA. (P10)

3.3.3 Assess Methods Suitability to Different CWA Purposes

Individual CWA programs (e.g., beach monitoring, assessments, TMDLs, and permitting) have

specific purposes that may influence selection of indicators or methods.  For example, timeliness

of obtaining test results may be critical for effective beach monitoring and notification, but may

not be essential for NPDES permitting.  Understanding the specific attributes of various

indicators and methods as they relate to different CWA programs represents a data gap.

Summary of research activities and projects:

• Evaluate the suitability of individual combinations of indicators and methods for

different CWA programs. (P18)   

3.3.4      Develop, Evaluate and Validate Predictive Models and Tools

Statistical models that relate water quality to environmental factors like wind speed, prior

rainfall, and tide level are valuable tools for making beach closure or advisory decisions.  Site‐

validated models predict water quality problems reliably and in a more timely fashion than

traditional bacterial indicator monitoring alone.  Once a model is site‐validated, traditional

water monitoring could be reduced and targeted.  

As described in Sections 3.2 and 3.3.2, EPA is conducting research to understand those factors

that contribute to variability of indicator and pathogen behavior across diverse aquatic
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conditions including those that influence sources of indicators and pathogens, their persistence,

and their concentrations at beaches. As a result of these studies, EPA intends to refine an

existing predictive model (virtual beach) based largely on the Great Lakes studies for use in

beach monitoring at specific sites.  EPA intends to test and validate this model and other

existing models in various freshwater and marine environments in different geographic

conditions, and in waters impacted by a wide range of fecal sources of contamination for site

specific application. A technical protocol for site‐specific application of the model(s) would then

be developed to assist States and tribes with implementation of new or revised criteria.  In

addition to predictive models, EPA intends to develop tools such as sanitary surveys to

facilitate the collection and evaluation of data for site‐specific applications.  

The research activities described below provide useful tools for extrapolating data from

epidemiologic study sites to other geographic locations and aquatic conditions, and predicting

water quality problems to assist in beach monitoring and notifications programs.  Potentially,

these tools may also prove useful in predicting water quality problems in other CWA programs

for which criteria are intended.   

Summary of research activities and projects:

• Pilot test Virtual Beach model for beach notification and advisories/closures. (P23)

• Refine and validate other existing water quality models for freshwater and marine beach

notification and advisories/closures. (P24, P25)

• Develop technical protocol for site‐specific application of predictive models to be used in

making beach advisory decisions. (P26)

• Develop, refine and evaluate quantitative sanitary investigation method – sanitary

survey protocol for recreational waters. (P13)
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3–15 

Table 3‒1. Science Plan Research Activities and Projects 

GOALS ADDRESSED BY RESEARCH 

PROJECT TITLE RESEARCH DESCRIPTION 

Epidemiology Studies/QMRA 

1 ─ 4 Conduct epidemiologic studies at POTW-impacted 

marine beaches in Fairhope, Alabama and Goddard, Rhode Island (P1, P2) 

Prospective cohort epidemiology studies designed to evaluate the ability of raindicators of recreational water quality to predict swimming-associated illness sites impacted by treated wastewater effluent discharge. The study design is 

to the recently completed Great Lakes studies (Wade et al., 2006), and very 

recently completed and ongoing in California (Colford, 2007). Water samples Enterococcus using qPCR, Enterococcus using standard culture method, E. Bacteroides using qPCR (not human specific), Bacteroides using qPCR (hummale-specific coliphages by antibody assay. Additional tests include over 30 and industrial chemicals. Water quality measures will be compared to illness exposure-response relationships between indicator measures and illness rep

beachgoers. Study will have a multi-station sampling grid with multiple sampday to capture local temporal and spatial variability. 

1 ─ 4 Support epidemiologic study at a beach in Avalon, CA 

considered to be impacted primarily by untreated human fecal contamination (P3) 

Prospective cohort epidemiology study being conducted by SCCWRP with Eassess health risks and illness/indicator relationship in marine beach primariluntreated human wastewater (as compared to treated human sources from ostudies). Avalon beach is affected by a mix of sources of fecal contamination droppings, urban runoff and leaking sanitary sewers (including failing infrastr

leaking collection systems). Water samples are tested for Enterococcus qPC

qPCR, Bacteroides thetaiotamicron qPCR, and coliphage by antibody assay. is based on EPA’s current marine study design. The intent is for data to be cfuture analysis. This study is part of a three beach “suite” in California. SCCultimately have data from a beach that is predominantly impacted by animal fcontamination (Doheny) and a beach predominantly impacted by a mixture ohuman fecal contamination (Malibu). This data set could help EPA understanillness rates under different source conditions in the same geographic/climati

SCCWRP studies are receiving EPA technical input to ensure the usability of developed. Study will have a multi-station sampling grid similar in design to tstudies with multiple samples taken each day to capture local temporal and s

1 ─ 4 Conduct epidemiologic study (ies) and/or QMRA to 

characterize the indicator-illness relationship at a freshwater beach impacted by agricultural animal sources of fecal contamination for comparison to those obtained at POTW-impacted beaches (location to be determined) (P4) 

Evaluate the ability of indicators to predict swimming-associated illness and cresults with those at POTW-impacted beaches. Use a prospective cohort apfeasible. Collect information to support predictive modeling. Study will have a sampling grid with multiple samples taken daily to capture local temporal and variability. 
Critical Path Science Plan for the Development of New or Revised R

3–16 

GOALS ADDRESSED BY RESEARCH 

PROJECT TITLE RESEARCH DESCRIPTION 

1 ─ 4 Conduct epidemiologic study in fresh or marine waters 

impacted by urban runoff and/or conduct QMRA analysis (P5) 

Evaluate the ability of indicators to predict swimming-associated illness and cresults with those at POTW-impacted beaches. Use a prospective cohort apfeasible. Collect information to support predictive modeling. Study will have a sampling grid with multiple samples taken daily to capture local temporal and variability. 

1 ─ 4 Conduct epidemiology study on POTW-impacted marine 

waters (location to be determined) (P6) 

Conduct epidemiologic study at a POTW-impacted beach to increase statisticat a location similar to one of the previous marine studies or at a location in -account for geographic differences to assess indicator illness. Utilize the samcohort approach and same study design. Study will have a multi-station sammultiple samples taken daily to capture local temporal and spatial variability. 

1, 4 Determine data/components needed (e.g., monitoring 

and exposure) for QMRA applications (P7) 

The overall objective of this project is to identify the data and information thause QMRA techniques to interpret and interpolate the epidemiologic data thahave available by 2011, and if necessary extrapolate to conditions for which 

epidemiologic data have not been collected or are not planned. A research twith QMRA and recreational water will collaborate with EPA scientists and epidentify critical data and information to support QMRA, evaluating how data f

studies can be utilized, and identify additional data could be collected in concplanned epidemiologic studies to leverage the interpretation of those studies interpolation and/or extrapolations. For example, epidemiologic studies of retypically relate water quality characteristics (density of indicator organisms) to illness among recreators, and to interpret these studies via QMRA, additionathe volume of water ingested during recreational activities and the critical etiomay need to be collected as part of and/or in parallel with the planned epidemStudy will consider site-specific spatial and temporal sampling conditions tha

in QMRA to assess swimmer exposure to indicators/pathogens. 

Site Characterization Studies

2 ─ 4 Study various parameters that affect performance of 

qPCR signal for enterococci and compare with other methods and pathogens in treated wastewater mixed with ambient waters (enterococci, E. coli, Cryptosporidium, and enterovirus) (P8) 

The objective of this project is to understand what happens to the Enterococc

during wastewater treatment, after release into the environment and relationsEnterococcus qPCR signal to other indicators and pathogens. This project is because it will establish whether and under what conditions EPA could recomuse Enterococcus qPCR as an indicator/method in new or revised criteria thadefensible for the broad CWA uses of criteria, including NPDES permitting of treatment plans. Understanding if and how the qPCR signal changes as a rekinds of wastewater treatment, and the relationship between treatment and wthe water at end-of-pipe, will allow EPA to understand the controls that would place during treatment to meet the criteria at the beach. This study will evalu
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GOALS ADDRESSED BY RESEARCH 

PROJECT TITLE RESEARCH DESCRIPTION 

enterococci, E. coli, and F-specific (F+) coliphage as well as specific pathoge

and Cryptosporidium) through wastewater treatment. In addition, the decay will after treatment be examined after mixing with surface water under labora

1 ─ 3 Collect data and conduct source and site 

characterization evaluations at potential study sites to determine the extent of specific animal sources, and factors influencing the extent to which they would contribute to fecal contamination at the beach (P9) 

This project will generally address the need to characterize non-human sourcand conditions in watersheds that can result in pathogen contamination of reThis activity would contribute to the hazard identification and exposure assesQMRA. Simple models that correlate watershed activities (presence of treatmeffluents, types of agricultural activities, and domesticated animals) and attribtype, vegetation cover climate, soil moisture) will be used to determine the suwatershed to pathogen impairment. Geographic Information System (GIS)-basuch as Digital Watershed and available beach survey data will be used to expatterns in a watershed and help evaluate, for example, whether animal sourFactors that modulate contributions of animal wastes to pathogen loads in waadjacent recreational waters coupled with meteorological factors (e.g., rainfaspeed/direction, etc.) will also be investigated. Source differentiation assays bovine fecal matter being developed and evaluated as a part of this Science other assays (e.g., avium) available in the published literature or being indep

developed externally, could be used along with traditional fecal indicator meacharacterize the potential fecal input from animal feeding operations and pas

spatial and temporal variability will be captured by multi-sample station grids samples taken during the day that would impact on assessing exposure risks

2 ─ 4 Expand spatial scale of collection of site-specific data at 

epidemiology study locations to characterize watershed and support research into development of predictive models and QMRA (P10) 

This project will build on the base studies to provide more extensive fecal indhydrometeorological and biogeochemical data to develop predictive models t

to predict fecal indicator levels based on weather and physical/chemical wate

and provide the opportunity to assess any potential direct correlation betweeweather/physical water characteristics data and health effects being documeepidemiologic studies. This project will also allow for development of models extrapolate potential for health effects in geographic areas which possess socharacteristics of the settings of epidemiologic study locations, based on corr

weather and other data with health effects at epidemiology study sites. GIS-such as Digital Watershed and available beach survey data will be used to idthe expanded studies. Where possible, measurement of the hydrometeoroloautomated with equipment that is compatible with data loggers to increase frereduce man-hours required for data collection Parameters such as current vdirection, water temperature, wave height, tides, irradiance, turbidity, salinity, dissolved organic matter, and chlorophyll all can be logged automatically. Th

use data from nearby National Oceanic and Atmospheric Administration (NO
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GOALS ADDRESSED BY RESEARCH 

PROJECT TITLE RESEARCH DESCRIPTION 

Data Buoy Center observation stations and the Weather Service to help devenowcast and forecast fecal indicator levels at the epidemiologic sites. Data wspatial and temporal variables impact beaches. These variables will be used sampling locations and sampling times/frequencies for QMRA and new or rev

1 ─ 3 Conduct site and source characterization studies to 

better understand the factors influencing the contribution of untreated sources (e.g., urban runoff) to total fecal contamination to ambient waters (P11) 

If an additional epidemiologic study is necessary EPA will use the site/source study to select the study location based upon the site selection criteria, and/odesign. Data will inform sampling requirements to capture spatial and temporbased on upstream fecal contamination. 

3, 4 Design and evaluate a monitoring approach that will 

characterize the quality of beach waters that takes into account the spatial and temporal variability associated with water sampling (P12) 

Utilize data from the literature, e.g., the EMPACT study, or develop new datamolecular methods, to provide sufficient information for use by a limited numdesign a sampling plan or plans at a focused workshop. Future EPA epidemiother related studies will incorporate mutli-site grids with multiple samples takepidemiology studies. These will be used to determine how temporal and spabe used for future ambient recreational water quality criteria. 

3, 4 Develop, refine and evaluate quantitative sanitary 

investigation method - sanitary survey protocol for recreational waters (P13) 

The sanitary survey protocol should provide users with a set of tools to help t

sources of bacterial contamination. This information can be used to make bedecisions on remediation. The protocol and set of tools should be broad enomodular form so that it can be applied to all geographies and beach environmenough to provide a variety of tools to be used if resources are limited. Sanwill consider sampling of upstream waters to quantify the contribution of feca

that will impact beaches and the spatial and temporal factors that will need to criteria informed by the sanitary inspections. The approach to develop these tools is: 1) Analyze results of Great Lakes Beach Sanitary Survey Pilot Project with sofollowing questions in mind: -identification of specific avenues of investigation that produce results in the there are any, -identification of structure of survey forms and database that is easiest to use 2) Assess on-going beach sanitary survey activities non Great Lakes waters. water beach sanitary surveys, three west coast marine, three east coast matropical marine). -identify approaches in a variety of geographies and climates, -identify approaches with a spectrum of resource availability (national data comay not be available, local information on septic tanks or storm water infrastrmay not be available, manpower for field investigations may or may not be avwords, does the simple stuff work as well as the high tech stuff?) 
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GOALS ADDRESSED BY RESEARCH 

PROJECT TITLE RESEARCH DESCRIPTION 

3) Combine results of above assessments into a nationwide protocol and set 

2 ─ 4 Pilot sanitary survey in Great Lakes (P14) This project is a 3-year effort to design and implement beach sanitary survey

recreational waters. Major milestones include: (1) developing a draft sanitary survey form and receiving comments from GreManagers and public health officials; (2) developing grant criteria and award to pilot and implementing sanitary surveys; (3) pilot testing Beach Sanitary S

piloting the use of a data entry template to ensure consistent data entry for eanalysis; and (5) evaluating pilot studies and publishing a final beach sanitary 

use by beach managers. Studies will consider spatial and temporal factors frcontamination events that will contribute to similar spatial and temporal variabeaches as reflected in criteria. 

Indicators/Methods Development and Validation Studies

2 ─ 3 Evaluate multiple indicator/method combinations to 

develop quantifiable relationships (P15) 

Multiple indicator/method combinations are being or will be tested in the marstudies. The illness response to exposure relationship for each method will bdevelop a quantifiable relationship among the results derived using the varioindicator/method combinations. The relationships derived will serve as a bas

that results using the differing approaches can be compared to determine thalevels are being attained. 

2, 3 Study the effects of sample holding time, sample 

storage, and preservation on sample integrity for future use (P16) 

The objective of the study is to determine feasibility of using freezer-archived determining quantitative relationships between levels of target deoxyribonuclsequences from new and/or improved water quality indicators and health datNEEAR epidemiologic studies. The effect of holding time of fresh samples oefficiency by qPCR will also be investigated. Analyses will be performed on fwater sample filter retentates and DNA extracts of water sample filter retentaepidemiologic studies using previously employed assays for target DNA sequAdditional analyses will be performed on replicate freezer-archived sample fifrom common water samples after storage for incremental time periods. The used to assess comparability of performance levels of the initial and subsequTime point analysis (up to overnight) to investigate the effect of holding fresh qPCR signal will also studied. 

2 ─ 4 Develop, refine, validate, and publish new ambient and 

wastewater test methods (P17) 

Once the epidemiologic studies identify those indicator/methods that are bettswimming-related illness, those methods will be further developed and validasingle- and/or multi-lab validation studies for monitoring in ambient water and This activity involves considering those methods for promulgation in 40 Code Regulations (CFR) Part 136. Additionally, this activity involves developing an Procedure (ATP) protocol to facilitate addition of new molecular methods to P
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GOALS ADDRESSED BY RESEARCH 

PROJECT TITLE RESEARCH DESCRIPTION 

methods mature. Included in this approach will be elements of training of the to ensure proper levels of understanding of the validation plan and protocols. 

2 ─ 4 Evaluate the suitability of individual combinations of 

indicators and methods for different CWA programs (P18) 

The overall objective of this project is to identify and evaluate indicator/methofor their strengths and limitations with respect to fecal source identification (hperformance in different waterbody types. The important features of each indwill be described and the strengths and weaknesses of those features will be evaluated. The ideal set of features will be proposed so that the indicator/mecompared to a hypothetical ideal indicator/method. The indicators/methods uconsideration will be ranked for each feature with respect to ability to differen

sources, performance in different waterbody types, and appropriateness for d

purposes. EPA plans to use the results of this evaluation to inform the deciswhich indicator/methods will be included in the new or revised criteria and unconditions those indicators/methods will be recommended. 

1 ─ 3 Develop new and/or evaluate previously published 

source-identifying assays (P19) 

This project will develop human-specific qPCR assays and evaluate the perfoassays and other currently available qualitative and quantitative PCR-based designed to discriminate between human and non-human sources of fecal poPerformance measures will include specificity, sensitivity, precision and rangquantification, as well as genetic marker geographic continuity and abundancbetween human populations. Top performing qualitative PCR assays, providhuman fecal pollution, will be recommended for use in epidemiology study sicharacterizations. If possible, qPCR assays will be recommended that prove calculating a meaningful ratio of human to non-human fecal load in environm

1 ─ 4 Evaluate human assays with water samples with 

different levels of fecal contamination from wide geographic range to supplement site characterization and quantitative sanitary investigation (P20) 

This project will assemble a collection of human fecal impacted water samplewide geographic range and compare detection levels between select humanassays and currently recommended water quality fecal indicators. Water samcollected from both fresh and marine sites where applicable with the goal of asamples from each EPA region. Parallel tests will also be completed to mea

enterococci cell densities. Results from PCR studies will be compared to ba

to characterize any relationships between human-specific genetic methods afecal indicator approaches. 

1 ─ 3 Evaluate genetic markers for cows to supplement the 

site characterization and quantitative sanitary investigation (P21) 

This project will evaluate the performance of currently available ruminant- anqualitative and quantitative PCR assays. Top performing qualitative PCR aspossible qPCR assays will be recommended for use in epidemiology study scharacterizations. Select host-specific qualitative and quantitative PCR assamethods) will be evaluated in regards to specificity, sensitivity, precision and quantification, as well as genetic marker geographic continuity and abundanc
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GOALS ADDRESSED BY RESEARCH 

PROJECT TITLE RESEARCH DESCRIPTION 

between host populations. 

1 ─ 4 Re-analyze archived NEEAR samples for other 

indicators (depending upon the outcome of P16 and the nature of the indicator/method) (P22) 

Determine quantitative relationships between absolute and/or relative levels sequences from new water quality indicators and health data from previous estudies based on analyses of freezer-archived samples. As many as eight neincluding presumptive human-specific indicators, several new Bacteroides sp

perfringens and E. coli may be analyzed for in frozen archived samples from 

and 2007 NEEAR epidemiologic studies. 

Modeling

2 ─ 4 Pilot test Virtual Beach model for beach notification and 

advisories/closures (P23) 

This project is pilot testing models in current use in the Great Lakes, includinBeach model, to provide early warnings about fecal indicator levels that pose beach communities. The synthesized system will forecast fecal indicator levetime and location. The project is limited to two beaches in Lake Erie and Lakthe models will be validated for predicting culturable E. coli or fecal enterococmodels for static and dynamic nowcasting of indicator bacteria at beaches wobservations of variables by buoy/sonde, current instrumentation and optical meteorological data. These observations include water quality and dynamic v(temperature, turbidity, currents, density stratification), optical (UV and visible scattering) and meteorological (wave height, wind speed, rainfall) parameterswill be pursued in conjunction with NOAA forecasts of the environmental and variables that are used as model inputs, to forecast exceedance of recreationstandards a day in advance. 

2 ─ 4 Refine and validate existing water quality models for 

freshwater beach notification and advisories/closures (P24) 

This project will validate the ability of Virtual Beach and other selected statist

predictive models in current use from our base studies to provide early warniindicator levels that pose health risks to a wider range of beach communities by POTWs around the Great Lakes. Five beaches in the Great Lakes will be modeling in collaboration with Region 5 and local State and municipal beach based software such as Digital Watershed and available beach survey data widentify the POTW-impacted beaches. In all beaches, models will be develop

either culturable E. coli, or fecal enterococci. One beach will be used for pre

E. coli, fecal enterococci and Enterococcus qPCR detection methods. Model

Virtual Beach model for static and dynamic nowcasting and forecasting of indbeaches, along with other modeling configurations being successfully used in will be integrated to include observations of variables by buoy/sonde, current optical systems and meteorological data that will be automated where possibmodels will be developed to evaluate concentrations of fecal indicator bacterculturable and qPCR methods at several points in a POTW-contaminated str
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GOALS ADDRESSED BY RESEARCH 

PROJECT TITLE RESEARCH DESCRIPTION 

in a small catchment that runs into beach areas along southern Lake Michiga

2 ─ 4 Refine and validate other existing water quality models 

for marine beach notification and advisories/closures (P25) 

This project will evaluate the ability of Virtual Beach and other selected prediour base studies to provide warnings with an acceptable level of statistical re

fecal indicator levels that pose health risks to coastal marine beach communaffected by POTWs and other sources. The project will be applied to at least beaches to be selected in collaboration with Region 4, Region 9, and Region and local State and municipal beach managers. GIS-based software such as Watershed and available beach survey data will be used to identify the POTWbeaches. Models will be developed at all study beaches for predicting (nowcaforecasting) culturable E. coli, fecal enterococci and one beach for predicting or fecal enterococci and Enterococcus qPCR detection methods. The predict

static and dynamic nowcasting and forecasting of indicator bacteria at beachtheir statistic bases observations of variables by buoy/sonde, current instrumsystems and meteorological data that will be automated where possible. Obsmade in the project include water quality and oceanographic variables (tides, temperature, turbidity, currents, density stratification, wave height), optical (Uirradiance, light scattering) and meteorological (humidity, clouds, temperatureparameters. EPA will pursue other studies regarding the ability of NOAA foreenvironmental and meteorological variables that are used as model inputs to exceedance of recreational water standards a day in advance. These studieevaluation of the accuracy of the forecasts as a function of distance of the wefrom the beach of interest relative to the parameters measured in situ during 

4 Develop technical protocol for site-specific application of 

predictive models to be used in making beach advisory decisions (P26) 

Develop a guide to assist States and localities in using Virtual Beach and othmodels in their beach advisory programs to support criteria implementation. 

Appropriate Level of Public Health Protection

1 ─ 4 Compare 1986 to NEEAR to better understand the 

relationship between fecal contamination and illness in these data sets (P27) 

Obtain raw data from the 1986 studies (if available). Conduct statistical analyknown differences in the two studies such as recall period, age distribution brates, and illness definition to attempt to create comparable definitions. Once illness definitions are created, it may be possible to use this information to de"new" acceptable risk levels that do not exceed those from 1986, accounting 

the studies. 

3, 4 Evaluate applicability of NEEAR Great Lakes data to 

inland waters (P28) 

Assess the similarities and differences between coastal freshwaters and inlaestablish whether there are or not significant differences to justify additional s

applicability of criteria to inland waters. Additional studies could include an e
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GOALS ADDRESSED BY RESEARCH 

PROJECT TITLE RESEARCH DESCRIPTION 

study or QMRA application in flowing inland water. 

1 Conduct statistical analysis of children data from 

epidemiologic studies (P29) 

Conduct statistical analyses of data collected for children during epidemiologdetermine if there is a significant difference in risk to children. 

Literature Reviews

1 Conduct state-of-the-science reviews of published 

studies to characterize relative risks from different sources (P30) 

Search the epidemiologic literature (international and domestic journals and reports) for references to illness resulting from exposure to fecal materials fro

sources. Particular emphasis will be placed on animal-derived waste. The li

information will be evaluated to determine the extent to which it supports chadifferences in illness resulting from exposure to waters contaminated with fec

different sources. While recreational exposures are the primary focus, attentbe paid to contaminated drinking water and reported illness. Report detailinidentified and an evaluation of what they indicate relative to illness resulting f

different sources of fecal contamination. 

1 Conduct state-of-the-science review on occurrence and 

cross-infectivity of specific pathogens associated with animals (P31) 

Search available literature (international and domestic journals, waterborne dsurveillance reports, and other government reports) on organisms that occur that are pathogenic to humans, which of these organisms are also present in populations, and the extent to which strains found in animals can be transmitThe product will be a report discussing the issues above with an evaluation owhich the information identified can be used to support the differentiation of rand human sources of fecal contamination. 

4 Conduct literature review, and evaluate and interpret 

available data on indicator behavior in tropical climates (e.g., water, sand and sediments) (P32) 

Determine the extent to which indicators perform differently in a tropical envircompared to a temperate environment, investigate the underlying cause if a didentified, and consider possible alternative indicators for future developmenappropriate. The domestic and international literature will be searched to idenarticles and reports that discuss and evaluate the extent to which indicator orother accompanying organisms derived from fecal sources are impacted by t

regime (e.g., temperate vs. tropical). In addition, the literature will also be qu

information on what other parameters, such as resuspension or regrowth, maamount of indicators measured in compliance monitoring. Finally, the review 

potential alternative indicators that may provide more meaningful results in trenvironments if the current indicators are determined to be limited in applicatenvironment. 

Note: Codes (P1–P32) refer to an arbitrarily assigned project number.
Critical Path Science Plan for the Development of New or Revised R

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Table 3‒2. Overview of Proposed Near-term Research Activities to Support Development of New or Revised Recreational Crite

Broad Research 

Category 

Completed 2007 2008 2009 

P1: Conduct epidemiologic study on POTW–impacted marine beach in Goddard, Rhode Island.P2: Conduct epidemiologic study on POTW–impacted marine beach in Fairhope, Alabama.P3: Support epidemiologic study at a beach in Avalon, CA considered to beprimarily impacted by untreated human fecal contamination. 

P4: Conduct epidemiologic study(ies) indicator-illness relationship at a freshagricultural animal sources of fecal cthose obtained at POTW-impacted beP5: Conduct epidemiologic study in frurban runoff and/or conduct QMRA a

P6: Conduct epidemiology study on POTW-impacted marine waters. 

Epidemiology Studies/QMRA 

Great Lakes NEEAR freshwater studies Incomplete marine study in Biloxi, MS

P7: Determine data/components needed (e.g., monitoring and exposure) for QMRA applications.

P8: Study various parameters that affect performance of qPCR signal for enterococci and compare with other methods and pathogens in treated wastewater mixed with ambient waters (enterococci, E. coli, 

Cryptosporidium, and enterovirus).

P9: Collect data and conduct source and site characterization evaluations at potential study sites to determine the extent of specific animal sources, and factors influencing the extent to which they would contribute to fecal contamination at the beach.

P10: Expand spatial scale of collection of site-specific data at epidemiologic study locations to characterize watershed and support research into development of predictive models and QMRA.

Site Characterization P14: Pilot Great Lakes 

sanitary survey

P11: Conduct site and source characterization studies to better understand the factors influencing the contribution of untreated sources (e.g., urban runoff) to total fecal contamination to ambient waters.

6 Note: The timeline for epidemiologic studies includes study design, study initiation and completion, data analysis, peer review, and pu
Critical Path Science Plan for the Development of New or Revised R

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Broad Research 

Category 

Completed 2007 2008 2009 

P12: Design and evaluate design a monitoring approach that will characterize the quality of beach waters that takes into account temporal and spatial variability associated with water sampling.

 P13: Develop, refine and 

evaluate quantitative sanitary investigation tools/protocols.

P14: Pilot sanitary survey in Great Lakes. 

P15: Study equivalency between enterococci qPCR and various indicators and methods. 

P16: Study the effects of sample holding time, sample storage, and preservation on sample integrity for future use. P17: Develop, refine, validate, and publish new ambient and wastewater test P18: Evaluate the suitability of individual combinations of indicators and methods for different CWA programs.P19: Develop new and/or evaluate of previously published sourceidentifying assays.

P20: Evaluate human assays with water samples with different levels of fecal contamination from wide geographic range to supplement site characterization and quantitative sanitary investigation.P21: Evaluate genetic markers for cows to supplement site characterization and quantitative sanitary investigation.

Indicators/Methods Development and Validation 

Test methods through epidemiology studies Conduct lab validation of enterococci qPCR in freshwater Publish wastewater culture method for enterococci and E. coli in 40 Code of Federal Regulations (CFR) Part 136 

P22: Re-analyze archived NEEAR samples for other indicators 

(depending on the outcome of P16 and the nature of the indicator/method)

Modeling Virtual Beach model and 

other existing models P23: Pilot test Virtual Beach model for beach notification and advisories/closures 
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Broad Research 

Category 

Completed 2007 2008 2009 

P24: Refine and validate other existing water quality models for freshwater beach notification and advisories/closures. 

P25: Refine and validate other existing water quality models for marine beach notification and advisories/closures. 

P26: Develop technical protocol for site-specific application of predictive models to be used in making beach advisory decisions. P27: Compare 1986 to NEEAR data between fecal contamination and illne

P28: Evaluate applicability of NEEAR Great Lakes data to inland waters. 

Appropriate Level of 

Public Health Protection 

Analysis of Great Lakes NEEAR freshwater epidemiology data for general population and subgroups (e.g., children and elderly) 

P29: Conduct statistical analysis of children data from epidemiologic studies.

P30: Conduct state-of-thescience review of published studies to characterize relative risks from different. P31: Conduct state-of-the -science review on occurrence and crossinfectivity of specific pathogens associated with animals.

Literature Reviews 

P32: Conduct literature review and evaluate and interpret available data on indicator behavior in tropical climates (e.g., water, sand and sediments). 

Note: Codes (P1–P32) refer to an arbitrarily assigned project number.
Critical Path Science Plan for the Development of New or Revised Recreational Water Quality Criteria

    4–1 August 2007

CHAPTER 4 FUTURE RESEARCH

4.0    SCIENCE ISSUES EPA DEFERRED FOR FUTURE RESEARCH

EPA limited the scope of the Science Plan to science and research activities that could be

completed within 2 to 3 years.  The completion of research by the end of 2010, which would

include data collection, analysis and reporting, is critical to EPA’s goal of publishing new or

revised criteria by the end of 2012.  EPA recognizes that a number of science issues will be

deferred for future criteria efforts because the current state‐of‐the‐science does not support their

inclusion in the shorter term effort, or because preliminary research must be completed before

remaining science issues can be addressed.  For example, the Science Plan partially addresses

the differentiation of non‐human sources, and places emphasis on addressing what is expected

to be the greatest sources of risk first.  Additional research to potentially differentiate between

non‐human sources of fecal contamination (e.g., wildlife versus agricultural animals such as

cows) cannot be completed in the proposed timeframe.   Such longer‐term research ─ for

example, developing source identification tools that reflect avian and wildlife sources of fecal

contamination ─ will continue on a separate track.  These tools may be useful in revising the

criteria in the future.

Understanding the etiology of illness arising from recreational water exposures was identified

by EPA as a desired outcome of future research.  This information would allow EPA to better

evaluate the effectiveness of its current regulatory policies regarding waste treatment, and the

relationship between discharges and beach closures.  It would also improve the ability to

extrapolate data from epidemiology studies to locations with different site characteristics.  The

tools to permit easier collection of etiology data in conjunction with illness data are not yet

sufficiently developed to permit their inclusion in near term studies.  They will not be available

within the 2 to 3 year timeframe for the current criteria development effort.   

The concern that different fecal indicators may be more appropriate for use in tropical or

subtropical versus temperate environments was raised during the Experts Scientific Workshop.   

EPA is addressing the need for studies to develop guidance to account for the diversity of

geographic conditions of marine waters by conducting epidemiology studies along diverse

locations on the east, west and gulf coasts of the United States.  An epidemiologic study at a

tropical site is not specifically included in the Science Plan because (1) indicators of fecal

contamination for temperate and subtropical waters may not be suitable for tropical waters; and

(2) additional preparatory research would need to be completed prior to conducting a tropical

study. The additional research activities EPA would need to complete before conducting a

tropical epidemiology study include: (1) evaluating the results of marine epidemiology studies

to determine if the indicators used would be suitable for tropical sites; (2) identifying and

developing new potential indicators for tropical waters; (3) identifying an appropriate study

site to conduct tropical epidemiology study; and (4) establishing a partnership with the

municipality where the study would be conducted. These research activities are sequential and
Critical Path Science Plan for the Development of New or Revised Recreational Water Quality Criteria

    4–2 August 2007

will require more than 3 years to complete. Therefore, they are being deferred for future

research.

EPA will conduct a comprehensive literature review to determine the extent to which indicators

perform differently in a tropical environment compared to the temperature environment and

the underlying cause if there is a difference. EPA is also open to evaluating epidemiologic and

other data generated at tropical locations by other entities to determine if an alternative

indicator is appropriate.

Scientific uncertainty regarding the re‐growth of fecal indicators and the impact of this

phenomenon on water quality as well as beach sand was also identified as having a potential

impact on the utility of indicators as a measure of fecal contamination in recreational water,

especially in tropical climates.  EPA has not included any specific research activity in this topic

in the current Science Plan but will conduct a literature review to determine: how significant is

this issue, if regrowth of indicators is just an issue in tropical environments, if regrowth of

indictors is due to nutrient contamination, and the impact of indicator regrowth on human

health risk. EPA will evaluate the results of the literature search to identify any subsequent

steps that may be helpful to address this issue. This research will not be conducted to support

the current criteria development because of the short timeframe available.
Critical Path Science Plan for the Development of New or Revised Recreational Water Quality Criteria

    5–1 August 2007

CHAPTER 5 REFERENCES

Colford, J.M., Jr., T.J. Wade, K.C. Schiff, C.C. Wright, J.F. Griffith, S.K Sandhu, S. Burns, M.

Sobsey, G. Lovelace, and S.B. Weisberg. 2007. Water quality indicators and the risk of illness at

beaches with nonpoint sources of fecal contamination. Epidemiology 18(1):27‐35.   

Dick, L.K., and K.G. Field. 2004. Rapid estimation of numbers of fecal Bacteroides by use of a

quantitative PCR assay for 16S rRNA genes. Applied and Environmental Microbiology 70:5695‐

5697.  

Kim, J.H. and S.B. Grant.  2004.  Public mis‐notification of coastal water quality: A probabilistic

evaluation of posting errors at Huntington Beach, California. Environmental Science and Technology

38(9):2497‐2504.

Layton, A., L. McKay, D. Williams, V. Garrett, R. Gentry, and G. Sayler. 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 72:4214‐4224.   

U.S. Environmental Protection Agency. 1999. Review of Potential Modeling Tools and Approaches to

Support the BEACH Program. 823‐R‐99‐002, March 1999.

U.S. Environmental Protection Agency. 2005. The EMPACT Beaches Project Results from a Study on

Microbiological Monitoring in Recreational Waters. EPA 600/R‐04/023, August 2005.  

U.S. Environmental Protection Agency. 2007 Report of the Experts Scientific Workshop on Critical

Research Needs for the Development of New or Revised Recreational Water Quality Criteria. EPA 823‐

R‐07‐006, June 2007.

Wade, T.J., R.L. Calderon, E. Sams, M. Beach, K.P. Brenner, A.H. Williams, and A.P. Dufour,

2006.  Rapidly Measured Indicators of Recreational Water Quality are Predictive of Swimming‐

Associated Gastrointestinal Illness. Environmental Health Perspectives, 114(1): 24‐28.