MICROBIOLOGICAL QUALITY OF SHELLFISH IN ESTUARINE AREAS JOINT AGENCY RESEARCH REPORT 2009 Forward This project was funded by New Zealand Food Safety Authority, Environment Bay of Plenty, Toi Te Ora – Public Health, Tauranga City Council, and Western Bay of Plenty District Council This report was prepared by Paul Scholes, Environment Bay of Plenty; Dr Gail Greening, Institute of Environmental Science and Research; Dr Donald Campbell & Jim Sim, New Zealand Food Safety Authority; John Gibbons-Davies, Graham Dohnt, Tauranga City Council; Kelvin Hill & Ilze Kruis, Western Bay of Plenty District Council and Dr Phil Shoemack & Annaka Davis, Toi Te Ora – Public Health. Cover photo: Anzac Bay, Tauranga Harbour: Supplied by Western Bay of Plenty District Council. DISCLAIMER None of the project organisations nor any of its employees makes any warranty, express or implied, or assumes any legal liability or responsibility for use of this Report or its contents by any other person or organisation. Microbiological Quality of Shellfish in Estuarine Areas Report 2009 2 Acknowledgements The project group gratefully acknowledges the contributions of Graham McBride – National Institute of Water & Atmospheric Research, Mark Arundel of Bethlehem Pharmacy, members of Tauranga Moana Customary Fisheries Committee in the planning and development of the project. Thanks to Tony Wood, Aquatek who collected the shellfish and water samples; and also to the Environmental Science & Research Ltd Environmental and Food Virology team for the viral analysis. Microbiological Quality of Shellfish in Estuarine Areas Report 2009 3 Executive Summary Towards the end of 2006 recreational shellfish monitoring showed an increase in elevated bacterial levels in shellfish beds within Tauranga harbour adjacent to the city of Tauranga. Recreational water quality monitoring also identified contamination events which could result in pathogenic bacteria and viruses being present at harmful levels in shellfish. Environment Bay of Plenty (EnvBOP), Tauranga City Council, Western Bay of Plenty District Council and Toi Te Ora – Public Health (TTO) agreed it was necessary to obtain better information on the pathogen levels in shellfish stocks so the public could be better informed on the risks of eating shellfish from local beds. Two estuarine areas were sampled in this study, Tauranga Harbour and Waihi Estuary. Monthly shellfish and water sampling was carried out over a 12 month period to obtain information on the usual microbiological and viral quality of shellfish. Comprehensive sampling was also carried out after two significant pollution events. This study found that enteric virus contamination of shellfish is occurring in the Tauranga Harbour and Waihi Estuary. Shellfish from a few sites - namely Tilby Point and Pilot Bay were found to be regularly contaminated with viruses. These two sites are closest to the urban area and main cities of Tauranga and Mount Maunganui. Over the study period, norovirus levels were generally low in shellfish except following the significant sewage spill. Following a sewage pollution event, high levels of norovirus were detected in shellfish located 50 m from the source. Norovirus remained detectable in shellfish 50m from the source for up to 3 months following the sewage pollution event. Low levels of norovirus were detected in shellfish from three of the six sites in the Tauranga harbour following a rainfall event. There was good correlation between the presence of norovirus and human-associated F-RNA bacteriophage in shellfish after a sewage pollution event but not after a rainfall event. This suggests that the lower level norovirus contamination was not associated with a significant quantity of human sewage being discharged. The higher levels of faecal coliforms found after this event is more likely to be animal in origin from land run-off. It can be concluded that there is no distinct relationship between the faecal indicator bacteria and positive viral results. This demonstrates that indicator bacteria may not be reliable indicators of viral contamination in shellfish collected in this survey and vice versa. This demonstrates that shellfish may not be safe to eat even when the bacterial quality is within currently accepted microbiological limits. There was repeat viral contamination found in parts of the harbour adjacent to urban areas. This supports New Zealand Food Safety Authority’s general advice not to collect shellfish near urban areas because of the ongoing impact of stormwater and sewage-related contamination. Microbiological Quality of Shellfish in Estuarine Areas Report 2009 4 Contents Forward 2 Executive Summary 4 Introduction 9 Project Goal & Objectives 10 Methodology & Sampling Sites 11 Study Area 11 Sampling Sites 11 Shellfish Species 13 Sampling Regime 14 Sample Collection & Analysis 14 Microbiological Limits 16 Supporting Information 18 Environment 18 Viral & Bacterial Indicators 18 Human Health 19 Monthly Surveillance Results 24 Indicator Bacteria Results for Shellfish 24 Viral Results for Shellfish 25 Indicator Bacteria Results for Shellfish Adjacent Water 27 Adverse Pollution Event Results 29 Sewage Overflow Event 29 Rainfall Event 33 Discussion on Sewage Overflow & Rainfall Events 39 Comparison of Results with Microbiological Limits 44 Shellfish Adjacent Water Quality 44 Shellfish Quality 44 Other Microbiological Criteria 46 Bacteria & Viral Indicators of Contamination 48 Microbiological Quality of Shellfish in Estuarine Areas Report 2009 5 Discussion 50 Sources & Pathways of Faecal Contamination 50 Longevity & Extent of Microbiological Contamination 53 Public Health Risk Assessment 54 Conclusions 56 Recommendations 57 References 58 Appendices 61 Appendix 1 Sampling Site Location Details 62 Appendix 2 Water Quality Surveillance Results 63 Appendix 3 Shellfish Quality Surveillance Results 68 Appendix 4 Sewage Overflow Adverse Pollution Event Sampling 72 Results Appendix 5 Rainfall Adverse Pollution Event Sampling Results 74 Appendix 6 Rainfall Adverse Pollution Event Data 77 Appendix 7 Total Daily Rainfall Data 81 Appendix 8 Average Daily River Flow Data 84 Appendix 9 Sewage Reticulated and Non-Reticulated Areas 86 Appendix 10 Reticulated Sewage Overflow Data 89 List of Tables Table 1 Shellfish Site Locations and Species 12 Table 2 Water Sample Site Locations 12 Table 3 Scale of Norovirus Load in Shellfish 15 Table 4 The number of trips taken by non-commercial harvesters to 20 collect shellfish, and the species of shellfish targeted by the harvesters Table 5 Estimate of annual non-commercial harvest of shellfish in 20 New Zealand, 1999-2000, and the most common harvesting methods Table 6 Outbreaks of disease notified to the Medical Officer of 22 Health, in the Bay of Plenty district from October 2007 to October 2008 Table 7 Number of cases of gastroenteritis between 1997 and 2004 23 where shellfish was suspected as being the causative agent. Table 8 Statistics for Indicator bacteria results in shellfish over the 25 12 month survey Table 9 Virus results in all shellfish sampled monthly over 12 26 months. Microbiological Quality of Shellfish in Estuarine Areas Report 2009 6 Table 10 Percent Positive Virus and FRNA Bacteriophage Results 38 over Rain Event Sampling Table 11 Presence of norovirus in shellfish samples following 40 adverse pollution events Table 12 Virus results for shellfish sampled monthly over 12 months 42 (including events) Table 13 Faecal coliform statistics for shellfish waters, October 2007 44 to September 2008 Table 14 Comparison of indicator bacteria and virus results in 48 shellfish and shellfish collecting waters based on monthly sampling over 12 months Table 15 Catchment characteristics for potential sources of faecal 52 contamination List of Figures Figure 1 Shellfish and Water Sampling Site Locations 13 Figure 2 Number of Shellfish Samples Positive for Norovirus and 26 Adenovirus Figure 3 Indicator bacteria concentrations Tauranga Harbour, 27 October 2007 to September 2008 Figure 4 Indicator bacteria concentrations Waihi Estuary, October 28 2007 to September 2008 Figure 5 Indicator bacteria concentrations in shellfish for 4 sites, 30 Tauranga Harbour Figure 6a Norovirus occurrence and levels in shellfish samples 31 following sewage overflow event Figure 6b Norovirus GI and GII levels in shellfish following sewage 32 overflow event Figure 6c Norovirus GI and GII levels in shellfish following sewage 32 overflow event Figure 7 Occurrence of norovirus (NoV) and F-RNA phage 33 genogroups in shellfish following point source sewage pollution event Figure 8 Indicator bacteria concentrations in shellfish and total daily 34 rainfall over a rainfall event, North Tauranga Harbour and Waihi Estuary Figure 9 Indicator bacteria concentrations in shellfish and total daily 35 rainfall over a rainfall event, South Tauranga Harbour Figure 10 Indicator bacteria concentrations in shellfish, Waihi Estuary 36 and total daily flow Pongakawa River Figure 11 Faecal coliform concentrations in shellfish at 5 sites, South 37 Tauranga Harbour and Wairoa River daily total flow Figure 12 Occurrence of norovirus (NoV) and F-RNA phage 39 genogroups in shellfish samples following adverse rain event Figure 13 Indicator bacteria concentrations in shellfish after a major 40 rain event and sewage contamination event, Opposite Pilot Bay Microbiological Quality of Shellfish in Estuarine Areas Report 2009 7 Figure 14 Comparison between F-RNA phage and norovirus (NoV) 41 occurrence in point source and rainfall adverse event samples Figure