1

1

2

3

4

5

6

7

8

9

10

11

12

13

14

A B C

# Comment Text Comment Response

Charge Question 1. Does the document adequately present the logic and 

scientific support behind its conclusions? Please comment on the 

document’s transparency, the completeness of the presentations, and 

any shortfalls in the material presented. Are uncertainties for technical 

conclusions transparent? Do you have any suggestions on how we could 

improve this document? Please explain your responses. 

General

1.1

Add an executive summary to the criteria document that contains a road 

map. Emphasize what is staying the same from the 1986 criteria and what 

is changing. 

Section 1.0 has been expanded to cover the function of an executive summary.

1.2

It would be useful to the reader for EPA to explain the components of a 

criterion. Provide basic definitions/explanations. Avoid using “criteria” as 

the microbe being measured and the density of the microbe not to be 

exceeded. Have a glossary to define terms and define the term when first 

used in the document.

All usages of the word "criteria" were reviewed and edited for clarity where necessary.

EPA has determined that a glossary is not necessary

1.3

Stress that feacal indicator bacteria (FIB) are health risk indicators, not 

necessarily pathogen indicators. The later portions of the criteria 

document wholly focused on the link between FIB and health, so there is 

little need for emphasis in the earlier portion of the document on an FIB 

pathogen relationship. Statements regarding FIB pathogen relationship in 

the water body type section might be better placed in the QMRA section.

Although termed pathogen indicator in the BEACH Act, we have defined pathogen 

indicators as indicators of fecal pollution. Section 3.1 states that FIB are not necessarily 

indicators of pathogens.

1.4

Release the topic specific guidance documents at the same time as the 

RWQC. If these won’t be available, there should be some indication of the 

basic contents of the topic specific guidance (TSG) documents. 

EPA is developing a number of technical tools and documents to aid states and other 

stakeholders implement the 2012 RWQC. Many of the documents will be updates of 

existing guidance which we intend to issue in 2012, concurrent with publication of the 

RWQC. Others require additional studies or analyses that will not be complete in 2012 

and will be issued later. 

1.5

Write the document from the perspective of the end user, who is more 

interested in implementation than in the process/history by which the 

criteria were developed. Rather than writing in a retrospective framework, 

be prospective about the findings and science.

The historical perspective is important for a document of this type. Implementation is 

the focus of other documents.

1.6

Add text to the Introduction indicating that water quality monitoring and 

notification programs are critical but are not the only elements to 

protecting public health. Water quality monitoring is one component in a 

beach management strategy.

We agree there are other components to beach management strategies. For example, 

sanitary surveys are important in identifying the sources of contamination. Controlling 

these sources protects public health. EPA will consider addressing this in our update to 

the beach guidance.

Application of Criteria to Inland Waters

1.7

Reorganize the structure of the Water body Type section to emphasize 

public health protection first. De-emphasize the suggested similarity of 

coastal and inland waters. As written, the RWQC suggests that the 

variability in FIB (or FIB-pathogen associations) in inland vs. coastal water 

distinctions is smaller than the variability across coastal sites. This 

discussion is most appropriate in Section 5.2.2 under QMRA. 

The text has been edited to acknowledge that there is limited data on inland waters at 

this time. EPA expects that criteria inclusive of inland waters would be protective of 

human health. Supplemental information is provided for sites where States can 

demonstrate that the national RWQC would be overprotective. Although EPA believes 

that the RWQC are protective of human health, States have the ability to adopt stricter 

standards.

1.8

The reviewers endorsed extending coastal water criteria to inland waters, 

based upon protection of public health. However, they recommend that 

EPA acknowledge the paucity of health data upon which to base the 

extension of coastal derived indicator criteria to inland waters. The 

information presented on this topic in the RWQC should consider the 

findings presented in the Inland Waters Workshop, including the 

conclusion of workshop experts that coastal-derived criteria should be 

protective of public health in inland waters impacted by POTWs. Proceed 

with using coastal water criteria in the interest of protecting public health 

based on the best available information available at this time. 

Text has been edited to include information from the Inland Waters Workshop. 

Tropical and Subtropical Waters

1.9

Be transparent about the lack of usable data from the NEEAR studies in 

tropical waters.

EPA has discussed NEEAR study findings from Boquerón, Puerto Rico in the RWQC 

document. The health effects study conducted at the beach in Boquerón, Puerto Rico 

suggest consistency with previous EPA studies that were conducted using culture-based 

methods to measure water quality. These results show that low fecal indicator levels 

measured by Enterococcus CFU ( only one day exceeded a geometric mean of 35 CFU 

per 100 ml) and the frequency of observing evidence of gastrointestinal illness in 

swimmers was also low to non-detectable. Therefore, there was not a lack of usable 

data, but rather a lack of qPCR measured water quality data (an issue which has since 

been resolved).
2

15

16

17

18

19

20

A B C

1.10

Cite findings from the Tropical Indicator Workshop. Mention different 

season lengths that could impact sampling requirements. 

EPA cannot require sampling. The tropical indicators workshop (Fujioka, R. and 

Byappanahalli, M., Draft Final Report, U.S EPA, Office of Water, Washington D.C., 2003) 

that was convened in 2003 had as its objective to determine whether the EPA 

recommended bacterial indicators of fecal contamination are appropriate for 

monitoring bathing beach waters in tropical climates. The conclusions of the workshop, 

based on the consensus of 18 experts, after they had listened to several presentations, 

including two papers on epidemiological studies that were conducted in tropical 

climates (Trinidad-Tobago and Hawaii ), were, among other conclusions, that “the 

inherent environmental characteristics of the tropics affect the relationship between 

indicators of fecal contamination and health effects observed in bathers, which may 

compromise the efficacy of EPA guidelines.” (88.8% consensus). This conclusion was 

voted on in spite of the two reports of successful epidemiological studies conducted in 

tropical environments. Other consensus conclusions related mainly to bacterial 

indicators and the environment.

1.11

Have a separate section addressing specific issues facing tropical (and 

subtropical) waters. It would be appropriate to include studies from Hawaii 

on this issue.

Two epidemiology studies have been conducted in Hawaii, one a retrospective study to 

determine if Staphylococcus infections were related to swimming exposures (Charoenca, 

N and Fujioka, RS, Association of Staphylococcal Skin Infections and Swimming, Water, 

Science and Technology, 31(5-6):11-17, 1995 ) and the second was a prospective pilot 

study, to determine if illness was related to swimming activity (Morens, DM, Roll, KK and 

Fujioka, RS, A Pilot Epidemiology Study of Health, Risks Associated with Swimming at 

Kuhio Beach, Water Resources Research Center, University of Hawaii at Manoa, 

Honolulu, Hawaii, 1994). This latter study was conducted at a beach affected by a 

storm drain and no excess health effects were observed. These studies did not provide 

information to show that environmental characteristics of tropical climates 

compromised the use of EPA guidelines. Furthermore, the issues with the current fecal 

indicator system in Hawaii were mainly experienced because Hawaii had promulgated a 

water quality standard of 7 enterococci per 100 ml, a standard that was difficult to 

attain. Two years ago the State of Hawaii relaxed the standard to 35 enterococci per 

hundred ml, the water quality value recommended by the USEPA.

1.12

States that currently implement more stringent criteria should be 

encouraged to continue doing so. Given the lack of useable data from 

NEEAR tropical sites, EPA should partner with tropical and subtropical 

states to develop new indicators, particularly rapid ones, as potential 

criteria. This is important given the high level of beach usage in these 

states.

Thank you for your comment. 

Quiescent and High Energy Beaches

1.13

Acknowledge that all NEEAR studies, as well as the Mission Bay study, have 

been done in enclosed beach or embayments, except for Surfside Beach, 

SC. The proposed criteria should be applicable at high energy beaches but 

the differences should be noted. 

See comments 1.14 and 1.16.

1.14

Acknowledge the possibility that had NEEAR studies been conducted at 

high energy beaches, respiratory illness may have been more frequent.

It is possible that if the NEEAR studies had been conducted at high energy beaches 

(Ocean Beaches with a strong surf) more respiratory symptoms may have been 

observed. It is too speculative to imply that the respiratory illness may have been in 

excess of that observed in non-swimmers or that the illness may have been related to 

measures of water quality. A cursory examination of the epidemiological literature on 

hand revealed 15 ocean, high-energy beaches. Six of the studies indicated that the 

swimmer populations suffered respiratory illness that was in excess of that observed in 

non-swimmers. Only three of the six beaches where excess respiratory illness was 

observed showed that the illness was related to the level of fecal indicator bacteria in 

the water.

 One can conclude from this very cursory look at the literature that significant 

respiratory illness in swimmers exposed at high energy beaches does not occur 

frequently (40% of the high-energy beaches reviewed in the epidemiological literature). 

The frequency of respiratory illness at 50% of these high-energy beaches did not relate 

to the level of fecal indicator bacteria in the water.

 The conclusion that can be drawn is that excess respiratory illness does occur at highenergy beaches, but not at a high frequency and that it is likely that the criteria and 

monitoring tools developed for gastrointestinal illness will also protect swimmers from 

respiratory illness.
3

21

22

23

24

25

26

27

28

29

30

31

32

33

34

35

A B C

1.15

Work to ensure that Southern California Water Research Project (SCCWRP) 

studies are included in the RWQC because they include good information 

about high energy beaches. 

SCCWRP data can not be included at this time because it is unpublished.

1.16

EPA may wish to explain its rationale for selecting beaches for NEEAR 

studies. Such an explanation - the requirement of a range of FIB levels and 

POTW proximity - may explain blunt criticism regarding the absence of highenergy marine sites.

EPA has added the beach selection criteria to the RWQC document. Whether beaches 

were low or high energy was not part of the selection criteria. Additionally, the Great 

Lake sites that had higher wave action did not demonstrate increased respiratory health 

effects.

Singla Sample Maximum (SSM) vs. Statistical Threshold Value (STV)

1.17 Needs to be more clearly presented. Highlight what has changed and what 

is staying the same.

This section has been edited for clarity.

1.18 Justify the assumption of log normal distribution of FIB data (for both 

culture-based and qPCR data) as related to calculation of STV. 

Text has been edited to explain why EPA chose to use the geometric mean.

1.19

The discussion needs to be more clearly laid out for the loss of tiers. 

Address the impact resulting from the loss of tiers. 

Almost all of the states, territories, and tribes with coastal recreation waters currently 

use an equivalent, or similar, SSM value to issue their beach advisories or closings. EPA’s 

review shows that approximately 31 of the 37 BEACH rule states, territories, and tribes 

use the same value as the proposed STV. (These states either have a SSM of 104 cfu/100 

ml for enterococcus in marine waters, or of 235 cfu/100 ml for E. coli in fresh waters; 

this is the 75th percentile SSM value). 

1.20 The uses of GM vs STV for beach notification vs other CWA purposes need 

to be clarified.

The GM/STV construct has been clarified fro beach notification, permitting, and 

assessment purposes.

1.21

The change in sampling frequency for the GM from at least 5 per 30 days 

should translate to at least 15 per 90 days, rather than 12 per 90 days.

EPA is not recommending specific sampling frequency guidance. Instead EPA is 

presenting an analysis of how sample size affects whether the calculated geometric 

mean represents the actual geometric mean.

1.22

Specify acceptance of other water quality assessment approaches, such as 

the frequency of beach closure approach used by the State of California 

dependent upon increased stringency.

Text has been revised to clarify supplemental information that is being provided to 

states. 

1.23

Provide guidance on sampling frameworks that promote accurate 

representation of beaches over wide ranging conditions (e.g., wet weather 

vs dry weather). 

Epidemiology results accounting for wet weather events. EPA added a sentence on wet 

weather in Section 3.6 and indicated that for Attainment purposes, sampling of 

waterbodies should be representative of meteorological conditions (e.g., wet and dry 

weather) for the recreational season.

1.24

There was general agreement that the concept of STV – that a substantial 

percent of single samples would be expected to exceed the GM – is more 

appropriate than the term “single sample maximum”, which may be 

misconstrued to mean FIB densities that should never be violated.

Thank you for the comment.

Minimum Sampling Requirements (Wet Weather)

1.25

A poorly designed sampling framework can result in under protection of 

public health and inaccurate 303(d) listing. Strive for a common set of 

minimum sampling requirements across states for all CWA purposes. In 

other words, sampling requirements informed by site-specific variability in 

FIB values would be useful, though more challenging from an 

implementation standpoint. 

EPA reviewed the literature on temporal and spatial variability of fecal indicator 

organisms for implications for designing sampling plans in its report, Sampling and 

Consideration of Variability (Temporal and Spatial) for Monitoring Recreational Waters, 

December 2010. EPA will use this report as the basis for technical support materials 

(TSM) with information and recommendations regarding sampling frequency, location, 

and other parameters. However, the RWQC document is a guidance document, not a 

rule. As such, it will not include binding requirements.

1.26

States should be directed to sample at locations and during periods of high 

use, such as weekends, regardless of antecedent weather conditions. 

Minimum spatial and temporal sampling frequencies, should be specific 

enough so that it would not be possible for water samples to be collected 

(for GM calculation) selectively on days expected to have low FIB values 

(i.e., we do not want beach managers to avoid sampling the day or two 

following rainfall). 

EPA reviewed the literature on temporal and spatial variability of fecal indicator 

organisms for implications for designing sampling plans in its report, frequency, location, 

and other parameters. However, the RWQC document is a guidance document, not a 

rule. As such, it will not include binding requirements. Sampling and Consideration of 

Variability (Temporal and Spatial) for Monitoring Recreational Waters, December 2010. 

EPA will use this report as the basis for topic specific guidance with information and 

recommendations regarding sampling. 

E. coli
4

36

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

53

54

55

56

A B C

1.27

Be transparent about the lack of NEEAR E. coli qPCR study data. EPA believes this is already stated clearly (Culturable E. coli was not included in the 

NEEAR epidemiological studies, because EPA was evaluating a single indicator to be 

applied broadly. )

1.28

Acknowledge the strength of health risk as related to E. coli by culture 

concentrations in fresh water epidemiology studies.

The document has been edited to include citations for epidemiological studies that 

demonstrate the strength of E. coli as an indicator in freshwater.

1.29 More fully address the options for rapid method implementation for E. coli. Section 5.2.3 now includes E. coli qPCR as an example alternative method.

1.30 Increase consistency of messages about the use of E. coli as an effective 

indicator in fresh waters.

EPA's messaging of E. coli as an indicator is positive in the criteria document. We did not 

find anything to contradict our position in the Appendices.

qPCR

1.31

Increase the amount of information regarding strength of relationship 

between qPCR for Enterococcus and health outcomes at NEEAR fresh 

water beaches. Include visual representation. 

EPA believes the qPCR data from the NEEAR studies is adequately addressed in the 

document, including visual representation. 

1.32

Failure to propose mandatory qPCR criteria at Great Lakes beaches is 

surprising given the results of the NEEAR studies. Because prior day culture 

measures are poor predictors of illness, explain why culture based 

methods are being put forward as the first choice and qPCR are an option. 

Clarifying edit made in Section 3.1 and Section 4, indicating minimal to no inhibition 

seen in the Great Lakes. However, it is EPA’s mandate to develop RWQC that can be 

applied nationally. Overall, there is a lack of experience with qPCR and a lack of 

understanding with how it performs in various waterbody types. EPA has clarified 

throughout the document that qPCR may be used to develop site-specific criteria, 

including in the Great Lakes. While culture methods give next day results, the criteria 

provide protection of the swimming use over the course of a season. EPA is also 

indicating predictive modeling can be used for same day notification.

1.33

If the proposed RWQC are not revised to mandate qPCR monitoring at 

Great Lakes beaches, justification for failing to promote the better and 

faster method is necessary.

Clarifying edit made in Section 3.1 and Section 4, indicating minimal to no inhibition 

seen in the Great Lakes. However we also noted that it is EPA's mandate to develop 

RWQC that can be applied nationally. Thus qPCR may be used to develop site-specific 

criteria, including in the Great Lakes.

1.34

Reviewers like the inclusion of the indicator bacteria and methods section 

(Section 3.1), but the written material needs to be more detailed and in 

relation to culture-based methods vs rapid methods needs to be more 

balanced. Inhibition information is too detailed and presented too early in 

the document. Reverse the order of Sections 3.1 and 3.2. 

Section 3.1 has been divided into two sections, one for fecal indicators and one for 

enumeration methods. The text was edited to balance the discussion between culture 

and qPCR. 

QMRA

1.35 Explain “scientifically defensible” as related to QMRA in developing site 

specific criteria.

EPA will provide more information on QMRA in technical support materials.

1.36 Acknowledge that EPA did not deliver a side-by-side QMRA with the NEEAR 

Boquerón study.

EPA is planning to publish a Boquerón QMRA case study. The risk analysis is currently 

ongoing and will be included in technical support materials.

1.37

Without QMRA/epidemiology validation study, the accuracy of QMRA 

estimates remains to be determined.

EPA's QMRA efforts have used the available epidemiology data as a benchmark for 

estimating human health effects from exposure to fecal contamination. QMRA is not 

envisioned as a standalone tool, but rather a tool to expand the applicability of existing 

data, and to develop bounding estimates. The use of QMRA has been vetted with the 

EPA and other federal agencies, and has been used successfully by the international 

1.38

Need to justify QMRA as an alternative to epidemiology studies in 

developing site specific criteria rather than a water body management 

tool. QMRA is a good management tool, encourage states to use it as way 

to evaluate options for water management, but the option to use QMRA to 

develop criteria should be backed up by validation studies.

QMRA supplements the currently available epidemiology data and allows for prediction 

of risks in locations where there are no epidemiology studies. EPA is currently 

developing 1) case-studies to show how QMRAs relate to available epidemiology data 

and 2) technical support materials for States wanting to implement QMRA on a sitespecific basis. QMRA will be especially useful for less frequently visited beaches.

1.39

EPA has an opportunity to take the lead in QMRA science, particularly in 

the development of accurate quantification approaches for pathogens.

We agree.

1.40

Need to provide a conceptual framework figure and examples/case 

studies. 

EPA will provide more information on QMRA in technical support materials. EPA's 

"Microbiological Risk Assessment (MRA) Tools, Methods, and Approaches for Water 

Media" is now cited in the document. 

1.41 Increase breadth of potential “tools” to include resuspension and regrowth 

studies, as presented in Section 5.2. 

This is beyond the scope of the criteria.

1.42

Technical support documents will be critical for appropriate use of specific 

QMRA. modeling approaches and inputs.

EPA agrees that the technical support materials will be critical. The document refers to 

planned technical support materials in lieu of one overarching document.

1.43 Text about sources of fecal contamination as related to QMRA is missing. EPA believes that the 4 paragraphs in section 5.2.2 (QMRA section) that discuss fecal 

sources is adequate for this document.

Charge Question 2. Are you aware of any important peer review literature 

or applicable data that not have been incorporated in this document and 

should be included?

Reviewers recommended adding the following references to the RWQC:
5

57

58

59

60

61

62

63

64

65

66

67

68

69

A B C

2.1

WHO/EPA Annapolis protocol (WHO 1999, WHO 2003)

Explain why not being used, but note that extension to 90 days for GM 

calculation takes these criteria close toward that protocol's beach grading 

component. Also discuss consideration of a "traffic light" notification 

approach. 

During development of the RWQC EPA discussed the Annapolis Protocol at length and 

determined that the approach is not compatible with the requirements of the Clean 

Water Act.

2.2

Kay et al. (2004)—including discussion (Wymer et al. 2005) and Reply (Kay 

et al. 2006)

Explain reasons for not adopting the "UK ecologic exposure model" for 

"guideline" development.

EPA uses a different approach for criteria development. Thus these cites do not need to 

be discussed in the RWQC document.

2.3

Dufour et al. (2006)

Children more at risk than adults 

- this could be - Dufour, A. P., O. Evans, T. D. Behymer, and R. Cantu. 2006. 

Water ingestion during swimming activities in a pool: a pilot study. Journal 

of Water and Health. Dec. 4(4): 425-430.

This reference has been added to the document.

2.4

Heaney (2009), Heaney (2011)

NEEAR study swimmers illness may be influenced by sand exposure. 

Heaney (2011). Details to come (Rachel)

EPA has clarified that 304(a) CWA, AWQC do not address exposures to sand. 

Additionally language has been added to the RWQC document indicating that NEEAR 

epidemiology studies controlled for sand exposure.

2.5

Pratap et al. (2011)

Need for effective communication also needed for disease prevention 

Thank you for the comment. This topic is appropriate for implementation guidance.

2.6

Bambic et al. (2011)

Bacteroidales measured by qPCR as alternate indicator and fecal source 

identifier were highly correlated with Enteroccoccus and E. coli when 

either traditional (cultivation dependent) or qPCR methods were used.

Norovirus GI and GII were reasonable predictors of other pathogens like 

Adenovirus 40/41, Adenovirus C, Giardia and Cryptosporidium measured 

by qPCR. 

This reference has been added to the document.

2.7

Fewtrell et al. (1992), Harrington et al. (1993)

Health effects (respiratory) of white-water canoeing and surfing 

EPA did not believe it was necessary to add this reference to the RWQC document.

2.8

Sinton et al. (2002), Noble et al. (2004)

Differing interpretations on relative microbial inactivation rates in 

freshwater cf. coastal waters. 

EPA did not believe it was necessary to add these references to the RWQC document.

2.9

French et al. (2011)

Wild bird feces (via Campylobacter) demonstrated to be less virulent to 

humans, cf feces from farmed animals.

EPA did not believe it was necessary to add this reference to the RWQC document.

2.10 SCCWRP epidemiology studies/Colford et al. submitted

SCCWRP results to be used as soon as available. 

SCCWRP data can not be included at this time because it is unpublished.

2.11

Lavender & Kinzelman (2010)

Implementation of already available rapid methods, especially equivalence 

between culture based and rapid methods for E. coli. 

Lavender & Kinzelman (2010) Details to come (Rachel)

This reference has been added to the document.

2.12

Viau et al. (2011)

Example of application of QMRA in tropical waters.

This reference has been added to the document.

2.13 Doervitch et al., (2011) Epidemiologic study of limited contact water 

recreation at inland waters
6

70

71

72

73

74

75

76

77

78

79

80

81

82

83

84

85

A B C

References 

Bambic, D.; McBride, G.; Miller, W.; Stott, R.; Wuertz, S. (2011). Final 

Report: Quantification of Pathogens and Sources of Microbial Indicators for 

QMRA in Recreational waters. Report by University of California (Davis), 

AMEC Earth and Environmental and NIWA to WERF (USA Water 

Environment Research Foundation) for the project PATH2R08. 375 p.

This reference has been added to the document.

Dorevitch S, Pratap P, Wroblewski M, Hrohorczuk DO, Li H, Liu LC, Scheff 

PA: Health risks of limited contact water recreation. Environmental Health 

Perspectives, 2011, in press.

Fewtrell, L.; Godfree, A.F.; Jones, F.; Kay, D.; Salmon, R.L.; Wyer, M.D. 

(1992). Health effects of white-water canoeing. The Lancet 339: 

1587–1589. Their results for Site B refer.

French, N.P.; Marshall, J.; Mohan, V. (2011). Campylobacter in food and the 

environment: new and emerging data on typing of Campylobacter strains 

in animals, environmental matrices and humans. Final report 07 10436, 

Molecular Epidemiology and Public Health Laboratory, Massey University, 

Palmerston North, New Zealand. Prepared for the New Zealand Food 

Safety Authority and Ministry for the Environment. 

http://www.foodsafety.govt.nz/elibrary/industry/examining-link-withpublic-health/new-and-emerging-data-on-typing-of-campylobacter.pdf. 

Harrington, J.F.; Wilcox, D.N.; Giles, P.S.; Ashbolt, N.J.; Evans, J.C.; Kirton, 

H.C. (1993). The health of Sydney surfers: an epidemiological study. Water 

Science and Technology 27(3–4): 175–181.

Heaney, C.D.; Sams, E.; Wing, S.; Marshall, S.; Brenner, K.; Dufour, A.P.; and 

Wade, T.J. (2009). Contact With Beach Sand Among Beachgoers and Risk of 

Illness. American Journal of Epidemiology 70(2): 164–172.

Kay, D.; Bartram, J.; Prüss, A.; Ashbolt, N.; Wyer, M.D.; Fleisher, J.M.; 

Fewtrell, L.; Rogers, A.; Rees, G. (2004). Derivation of numerical values for 

the World Health Organization guidelines for recreational waters. Water 

Research 38: 1296–1304.

Kay, D.; Ashbolt, N.; Wyer, M.D.; Fleisher, J.M.; Fewtrell, L.; Rogers, A.; 

Rees, G. (2006). Reply to comments on "Derivation of numerical values for 

the World Health Organization guidelines for recreational waters". Water 

Research 40: 1921–1925. 

Lavender, J.S.; Kinzelman, J.L. (2009). A cross comparison of QPCR to agarbased or defined substrate methods for determination of Escherichia coli 

and enterococci in municipal water quality monitoring programs. Water 

Research 43(19):4967–4979.

Noble, R.T.; Lee, I.M.; Schiff, K.C. (2004). Inactivation of indicator microorganisms from various sources of faecal contamination in seawater and 

freshwater. Journal of Applied Microbiology 96: 464–472

Pratap, P.L.; Desai, P.; and Dorevitch S. (2011). Beach communications: a 

need for evaluation of current approaches. Journal of Water and Health 

9(3): 556-568.

Sinton, L.W.; Hall, C.H.; Lynch, P.A.; Davies-Colley, R.J. (2002). Sunlight 

inactivation of fecal indicator bacteria and bacteriophages from waste 

stabilization pond effluent in fresh and saline water. Applied and 

Environmental Microbiology 68(3): 1122–1131

Viau, E.J.; Lee, D.; Boehm, A.B. (2011). Swimmer Risk of Gastrointestinal 

Illness from Exposure to Tropical Coastal Waters Impacted by Terrestrial 

Dry-Weather Runoff. Environmental Science & Technology. 

dx.doi.org/10.1021/es200984b 

WHO (1999). Health-based monitoring of recreational waters: the 

feasibility of a new approach (the “Annapolis Protocol”). World Health 

Organization, Geneva (http://www.who.int/water_sanitation_ 

health/bathing/Annapolis.pdf)

WHO (2003). Guidelines for safe recreational waters volume 1 - Coastal 

and fresh waters. World Health Organization, Geneva 

(http://www.who.int/water_sanitation_health/bathing/srwe1/en/).

Wymer, L.J.; Dufour, A.P.; Calderon, R.L.; Wade, T.J.; Beach, M. (2005). 

Comment on "Derivation of numerical values for the World Health 

Organization guidelines for recreational waters". Water Research 39: 

2774–2777.
7

86

87

88

89

90

91

92

93

94

95

A B C

Charge Question 3. Do the analyses comparing the NEEAR freshwater and 

marine culture-based indicator data aggregated by days of similar water 

quality corroborate that the NEEAR culture data are generally consistent 

with the 1986 regression models?

3.1

Much needed clarity was provided during the peer review for comparing 

freshwater and marine culture data to 1986 data. Since the purpose is to 

establish the targeted level of risk used in developing the 1986 criteria to 

qPCR methods, the RWQC should be clarified/reorganized. Change the title 

of Section 3.2.4 to “Establishing a comparable target level of risk for 

defining culture and qPCR criteria values”.

The section has been re-titled "Establishing a comparable illness rate for defining culture 

and qPCR thresholds"

3.2

Peer reviewers found that some aspects of the section, especially Figures 

1a and 1b, undermine EPA’s effort to arrive at a targeted level of risk that 

applies to both PCR and culture measures of water quality. Specifically, the 

information currently in document suggests an inverse/negative 

relationship between culture measures of indicator bacteria and health risk 

when analyzed using the seasonal aggregation approach.

Figures 1a and 1b have been removed from the document.

3.3

EPA could acknowledge that the raw data used to establish the 1986 

criteria are no longer available for analysis. For that reason the two data 

sets (1986 and NEEAR) cannot both be analyzed using NEEAR methods. 

This limits EPA’s ability to identify qPCR values associated with the same 

targeted level of risk defined by specific CFU values.

EPA has address this transparently in earlier documents. This information is not 

necessary for the RWQC document.

3.4

Given the unavailability of data used to develop the 1986 criteria EPA faced 

two options: 1) to analyze the NEEAR culture data using the 1986 approach 

and compare it to the 1986 data analysis or 2) analyze culture data only 

from the NEEAR study using the same methods published by Wade et al. 

for the qPCR data. 

Results of Option 1 are presented in the RWQC. The limitations of that 

analytic method were not clearly acknowledged. Specifically, these 

analyses do not include individual level covariates. Given that a variety of 

exposures, such as digging in sand, are associated with GI illness, and that 

these are not accounted for in the analysis, confounding is a significant 

possibility. 

ORD staff clarified that EPA has conducted the option 2 analyses, but has 

not reported them. Those analyses reportedly show weak relationships 

between culture measures of indicators and GI illness. Those results 

should be presented in the RWQC.

All associations between illness and culture indicators have been previously published 

(Wade 2008, Wade 2010). For the NEEAR analyses, Enterococcus CFU (culture) 

associations to illness were analyzed in the same, rigorous manner as the qPCR 

measured indicators. The approach was as follows. 1) Determine whether there was a 

statistically significant association between swimming associated illness and the 

indicator density. 2) For those indicators which showed a significant association, 

exposure response relationships were derived as shown in publications by Wade et al. 

and in the RWQC. Since Enterococcus CFU associations with GI illness were not 

statistically significant, no regression lines were developed.

3.5

Since the ORD analysis (Option 2) shows a weak association between 

culture measures of FIB and health outcome, EPA must acknowledge that 

any targeted level of risk selected is inherently imprecise (i.e., it’s difficult 

to establish with confidence the FIB CFU or qPCR CCE values associated 

with a narrowly-defined targeted risk level). Figures presenting results of 

those analyses (analogous to Figure 1 of Wade 2008 and Figure 2 of Wade 

2010) should be included in the document.

EPA has added a figure (and accompanying text) comparing the illness rates of NGI/HCGI 

on days above and below 33 CFU/100ml and 35 CFU/100ml for fresh and marine sites, 

respectively. EPA believes this provides the most appropriate representation of the 

data.

3.6

Since a clear threshold between safe and unsafe levels of FIB is not 

apparent in the data, EPA may want to consider other graded approaches 

(e.g., red, yellow, green) for beach notification purposes.

EPA has determined that a graded approach is not possible for 304(a) CWA AWQC.

3.7

Since the criteria values of 33 and 35 CFU/100 ml are not changing, 

justification of these numbers is less important than if EPA had proposed 

alternate values. In Wade 2008 (Table 6) and Wade 2010 (Table 6) data are 

presented that support these culture-based criteria values, including tables 

in the RWQC would bolster EPA’s decision to retain those thresholds. 

The suggested tables have been adapted and added to the RWQC document. Section 

3.2.3 has been edited for clarity.

3.8

In order to establish threshold values of qPCR Enterococcus FIB, EPA could 

define expected case of illness per 1,000 swimmers at 33 and 35 CFU using 

NEEAR culture data analyzed the same way as NEEAR qPCR data. Then 

apply those targets to establish qPCR thresholds.

See comment 3.5.

3.9

Figures 2 and 3 should present confidence intervals instead of prediction 

intervals. Figure 2 of Wade 2010 and Figure 1 of Wade 2008 present graphs 

of Enterococcus data in marine and freshwater, respectively. It would be 

useful to include them in the RWQC document.

Figure 3 was changed to confidence intervals. Figure 2 retains prediction intervals and 

an explanation of why has been added. See response to comment 4.4 for explanation of 

why marine and freshwater data are not presented separately.
8

96

97

98

99

100

101

102

103

104

105

106

107

108

109

A B C

Charge Question 4. Do the characterization and explanation of the qPCR 

method reflect that of the scientific literature? If not, what additional 

information should be included? Is the derivation of the qPCR value using 

the EPA data scientifically supported and adequately explained? Please 

discuss why or why not?

4.1

Be more transparent about the strength of the relationship between NGI 

risk and qPCR and health risk measures in NEEAR freshwater studies as 

compared to culture methods.

EPA believes this information is already adequately covered in the document.

4.2 Investigate possible incorporation of SCCWRP study results for marine 

waters. 

SCCWRP data can not be included at this time because analyses available at this time are 

preliminary in nature and subject to change.

4.3

Even though qPCR in the RWQC is not specified as a “criteria”, EPA could 

specifically note that associations between qPCR and illness are stronger 

than those between culture methods and illness in freshwater.

EPA believes this information is already adequately covered in the document.

4.4

Present graphical representation of qPCR data in relation to illness for 

freshwater and marine beaches.

 EPA used the combined freshwater and marine data to arrive at one epidemiological 

curve for deriving the qPCR value. The evaluation of separate maine and freshwater 

epidemiological curves found there was no statistically significant difference between 

the fresh and marine relationship between indicators and GI illness (See Appendix B.3). 

Additionally, the combined curve is graphically presented in the RWQC document. For 

these reasons, EPA is not including graphical representation of the separate fresh and 

marine curves in the criteria document. These relationships are however published in 

Wade et al 2008 and Wade et al 2010. 

4.5 Acknowledge the similarity between CE and CCE quantification approaches 

in predicting health outcomes. 

EPA does not believe this information is necessary for a 304(a) criteria document.

4.6 Acknowledge relationships observed with Bacteroidales qPCR. Specify 

potential use of Bacteroidales qPCR for future. 

The relationship is acknowledged in Section 3.2.3 and the Bacteriodales qPCR method 

has been added to section 5.2.3 as an alternative method.

4.7

Describe range of quantification approaches for qPCR briefly. Place CCE in 

the context of available quantification approaches.

While not specifically stated in the document, this adjustment was performed using the 

delta delta CT calculation method which has been peer reviewed and published. Since 

this was the calculation method that was used to develop the health effect relationship 

for the Enterococcus qPCR and to derive the qPCR-based criteria, the relevancy of other 

available quantification approaches to this document is not apparent to us. EPA has 

clarified that the terms CCE and CE are synonymous from our standpoint and may have 

been used interchangeably as the metric that is reported from this calculation method in 

different supporting documents. 

4.8

Since EPA did not mandate use of qPCR in the draft, EPA could promote 

use of qPCR by making the method simple, user friendly, and as rapid as 

possible. 

EPA does not disagree that there are multiple quantification approaches for qPCR. 

However, listing these approaches generally is beyond the scope of the RWQC 

document.

Charge Question 5. Please provide any other general or specific 

comments on the document, making sure to identify the section 

number/page number you are commenting on.

5.1

Be more transparent about the fact that Virtual Beach does not work well 

in marine waters.

EPA disagrees that VB does not work well in marine waters. While the multiple linear 

regression models developed by VB for freshwater beaches are somewhat better than 

for the marine beaches, the differential is not large (freshwater average adjusted R2 = 

0.5, marine average adjusted R2 = 0.39). Additionally, VB predictions at Surfside Beach 

(marine) were generally as good as those observed at the freshwater locations. 

However, EPA has not yet established the body of developmental work needed to make 

predictions of water quality in marine waters. EPA has begun work on time lag and 

transformations of variables and will make results of this work available as updates to 

the technical materials on EPA’s website as well technical guidance.

5.2

Move appropriate information from Section 3.4 about indicator pathogen 

relationship, sources of contamination, and differences in risk as a function 

of contamination source to the QMRA discussion in Section 5. 

EPA does not believe this reorganization is necessary.

5.3

Section 5.2.3 needs to give examples of novel microorganisms. An additional paragraph on indicator organisms has been added to the section. E. coli 

qPCR and Bacteroidales qPCR have been included as example novel microorganisms.

5.4

The process for evaluating new methods needs to be more clearly defined. 

Lines 2026-2029 should suggest that alternate methods be at least as 

protective rather than generating the same beach notification result.

Text has been edited for clarity. EPA will provide more information on evaluating 

alternative methods in topic specific guidance.
9

110

A B C

5.5

Suggested additional TSG

Sampling guidance for compliance purposes

-Minimum requirements

-Consideration of composite samples

-Spatial sampling frequency

-Temporal sampling frequency

-Sampling depth

-How does wet weather influence sampling requirements

-Location in relation to activity/use

-Time of day

Thank you for your suggestions. EPA will consider these topics as we develop topic 

specific guidance on sampling.