Dynamics of faecal contamination in the Waikouaiti estuary and implications for non-commercial harvest
For many New Zealand catchments, rainfall-induced faecal contamination is a primary mechanism for introducing gastro bacterial pathogens into shellfish harvesting environments. Bivalves have the ability to accumulate bacteria through filter feeding, thus putting consumers of shellfish at risk. Commercial shellfish harvesting grounds for human consumption are regulated following quantification assessments of faecal bacteria in both water and the shellfish tissue. However assessments of non-commercial areas are less stringent and only assess faecal concentrations in the water. Additionally, guidelines set by regional councils and national authorities discourage recreational harvesting for several days after a rainfall. This study assessed the impact of rainfall-induced contamination on Austrovenus stutchburyi (tuaki, cockles or littleneck clams) and Perna canaliculus (kutai, Green Lipped mussels) within the Waikouaiti Estuary, an area that is hypothesised to be impacted by faecal contamination from farming and human sources. To assess the safety of the shellfish harvesting grounds, commercial quality guidelines established by the New Zealand Food Safety Authority (NZFSA) were applied to E. coli data collected for a 13 week monitoring period with the addition of three sampling events during rainfall. Additionally the MfE/MoH (2003) guidelines were used as in recreational settings to determine the safety of the shellfish beds based on assessment of the water only. NZFSA guidelines stipulate that only 10% of all shellfish samples can exceed 700 E. coli cells per 100 grams of shellfish tissue in order to be deemed safe for human consumption. The shellfish sampling indicated a total of 3/29 (10.3% of samples) breached the NZFSA limits, resulting in borderline acceptance of this guideline. In comparing species, there was only one more contamination event identified in the cockles over the mussels. The MfE/MoH (2003) guidelines for the water specify a 10% allowable limit for exceedances over 43 colony forming units (cfu) per 100 mL and a median measuring below 14 cfu/100 mL. Overall 2/16 (12.5% of samples) of the water samplings exceeded the limit of 43 cfu/100 mL for faecal coliforms therefor surpassing the 10% threshold. On the other hand, the median was 5 cfu/100 mL, thus remaining well within the safe harvesting median limit. These breaches should be further verified with a longer sampling regime containing a larger sampling size. Both rainfall and river flow correlated with E. coli concentrations in the water, but did not provide an accurate indicator of contamination in the shellfish. Correspondingly, there was no correlation between E. coli in the water versus concentrations in the shellfish, indicating that other factors should be considered for accumulation. The conditions of the water can affect bivalve filter feeding and should be considered for future work, including: salinity, turbidity, organic content, temperature and the arrival of the contamination to the shellfish site. Microbial RNA extracts from the collected water samples were interrogated via 16S rRNA sequencing. The resulting sequences were screened for faecal taxa that could be targeted for Microbial Source tracking (MST), and secondly to identify foodborne pathogens associated with the contamination. Samples containing higher E. coli abundances and higher river flows increased in faecal and total bacterial diversities. Prospective genera that could be useful for microbial source tracking in the Waikouaiti estuary were Prevotella, Bacteroides, Enterococcus and Bacteroidales. These have previously been linked to cows, gulls, humans, and pigs as possible sources. The well-documented ruminant genera, Ruminoccocus, was absent, denoting implications with using this marker for MST, and a negative result for the confirmation of ruminant sources. Sequencing of bacteria enriched on the E. coli growth media CM1046 showed an enhanced abundance of foodborne pathogens and faecal-related genera. This media could be useful to enhance the detection of pathogens for water testing protocols. Current faecal coliform assessments do not indicate contaminant sources, which is important for defining the risk of gastro-pathogens and identifying mitigation strategies. Human sources are of particular concern as this is associated with high-risk pathogens, thus more research using MST is needed to confirm the contaminant sources. This study found that monitoring only the water of shellfish grounds is not an acceptable method for identifying breaches of microbial safety and rainfall-induced contamination in shellfish. We suggest future monitoring of non-commercial shellfish grounds should therefore include monitoring of the shellfish tissue as in commercial regimes.
Advisor: Baltar, Federico; Hepburn, Chris; Morales, Sergio
Degree Name: Master of Science
Degree Discipline: Marine Science
Publisher: University of Otago
Keywords: New Zealand; contamination; shellfish; water; estuary; Waikouaiti; customary; māori; harvesting; taiāpure; e.coli; Karitāne
Research Type: Thesis