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## # **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 toemphasize 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

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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 twopapers on epidemiological studies that were conducted in tropical climates (TrinidadTobago 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, highenergy 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

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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 andPOTW 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 moreclearly presented. Highlight what has changed and what is staying the same. This section has been edited for clarity. 1.18Justify 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). 1.20The 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. 1.24There 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** 1.27 Be transparent about the lack of NEEAR E. coli qPCR study data. EPA believes this is already stated clearly (CulturableE. coliwas not included in the NEEAR epidemiological studies, because EPA was evaluating a single indicator to be applied broadly. )4

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57 A B C 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 thatEPA 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 site-specific 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:** 

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.5

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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 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 hasbeen 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.6

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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.
3.1 **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?**  The section has been re-titled “Establishing a comparable illness rate for defining culture and qPCR thresholds"

3.2 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”. Figures 1a and 1b have been removed from the document.7

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3.3 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. EPA has address this transparently in earlier documents. This information is not necessary for the RWQC document.

3.4 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. 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 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 or2) 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. 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 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 determined that a graded approach is not possible for 304(a) CWA AWQC.

3.7 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. The suggested tables have been adapted and added to the RWQC document. Section 3.2.3 has been edited for clarity.

3.8 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. See comment 3.5.

3.9 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. 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. 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.

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

4.2 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. 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 Investigate possible incorporation of SCCWRP study results for marine waters. EPA believes this information is already adequately covered in the document.8

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4.4 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 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 Present graphical representation of qPCR data in relation to illness for freshwater and marine beaches. EPA does not believe this information is necessary for a 304(a) criteria document. 4.6 Acknowledge the similarity between CE and CCE quantification approaches in predicting health outcomes. 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 Acknowledge relationships observed with Bacteroidales qPCR. Specify potential use of Bacteroidales qPCR for future. 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. 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.
4.8 Describe range of quantification approaches for qPCR briefly. Place CCE in the context of available quantification approaches. EPA plans to publish a technical support materials. 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.

5.1 **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.**  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 Be more transparent about the fact that Virtual Beach does not work well in marine waters. EPA does not believe this reorganization is necessary.
5.3 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. 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 Section 5.2.3 needs to give examples of novel microorganisms. Text has been edited for clarity. EPA will provide more information on evaluating alternative methods in topic specific guidance. 5.5 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. Thank you for your suggestions. EPA will consider these topics as we develop topic specific guidance on sampling. 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