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Factors Affecting the Microbial Quality of Shellfish

23 July 2012

Due to the build up of bacteria and viruses in bivalves from filter-feeding, bivalves can be harmful to humans when ingested. The different factors affecting the microbial quality of shellfish is therefore analysed in a study by Carlos Campos, Ron Lee, Simon Kershaw, Owen Morgan of Cefas and John Crowther, David Kay for Centre for Research into Environment and Health (CREH).


During filter-feeding, bivalves accumulate bacteria and viruses from the water column which can be pathogenic to humans. These pathogens are commonly introduced into the marine environment via runoff from land affected by livestock farming and the discharge of sewage from sewage treatment works (STWs) and intermittent discharges (IDs) (combined sewer overflows, storm overflows and emergency discharges) to watercourses within the catchment or directly to the fishery. The accumulation of microbial contaminants by shellfish is not only a human health issue but also an indication of the health status of the ecosystem as a whole.

Over recent decades, UK water companies have made substantial investments to reduce the impact of sewage discharges and diffuse pollution from agriculture on the quality of shellfish waters.

In 2009, Defra funded an investigation of the sanitary profiles of seven shellfish water catchments and a comprehensive review of site-specific factors that influence the take-up of faecal indicator organisms (FIOs) by shellfish. This review would enable Defra to improve planning of remedial action in order to ensure future protection of shellfish waters.

Reductions (% change) in total loads of faecal coliforms from all pollution sources during the summer following STW and ID improvements

Appraisal of STW improvements

Faecal indicator organism (FIO) loads (number per unit time) were quantified for seven shellfish water catchments covering different levels of sewerage improvements. In six of these catchments (the exception being the Conwy), the improvements involved installation of ultra-violet (UV) disinfection (tertiary treatment) in one or more STWs over the period 2000–2010 (AMP3/4). In five catchments (the exceptions being Conwy and Chichester Channel), the improvements also involved increase in storage capacity and installation of screens in one or more IDs. These studies were largely based on generic and modelled data and on specific assumptions made with regard to volumes of ID flow pre- and post-improvement. Results showed substantial reductions in FIO loads after sewerage improvements with the biggest estimated reductions in the Taw/Torridge and the smallest in the Yealm (Figure 1).

In the six catchments where improvements were made to key STWs, treated sewage effluents from these works now contribute <0.6% to the total FIO loads impacting on the shellfish waters.

In the five catchments where IDs have been improved, then, on the assumption of a 90% reduction in the estimated volume of ID flow following improvement, the IDs post-improvement contribute only small proportions (< 7.0%) of the total FIO fluxes. However, under a ‘worst-case scenario’ in which estimated ID flow volumes are greater pre-improvement and are reduced by only 50% following improvement, ID contributions increase to > 50%.

The impacts of sewerage and agriculturerelated sources of pollution impacting on shellfish waters were also estimated.

With the exception of Chichester Channel, (where no improvements have been made to the emergency discharges associated with the STWs at which UV-disinfection had been installed and IDs are estimated to account for 99% of the FIO loads), these studies indicated that catchments are impacted by a combination of pollution sources (Figure 2). These results support the dual focus on addressing point and diffuse sources of pollution (see Davies et al. 2010, Shellfish News 29).

Estimated source apportionment of overall faecal coliform load to seven shellfish water catchments during the summer post improvement

Factors influencing FIO accumulation by shellfish

The survival of microbial pathogens in seawater is influenced by a combination of environmental factors (Figure 3).

Factors controlling FIO survival in coastal waters

A review of the scientific literature on these effects revealed that the highest rates of bacterial elimination occur when solar radiation is high, sewage content is low, mixing conditions in the water column are high and the levels of suspended solids in the water are low.

Strong association was found between salinity and FIO levels in shellfisheries. This is because decreased salinity often indicates the presence of ‘fresh’ water which can be contaminated with sewage and also because salinity exerts a significant stress on bacterial cells. For instance, salinity could be used as a proxy for FIO contamination in the Ribble but not in Tresillian or Yealm shellfish waters presumably because of the lower complexity and the location of the sampling point in the former estuary

The review also demonstrated that rainfall is the environmental parameter most frequently cited risk factor for fluctuations in FIO contamination in shellfish. Rainfall effects depend on the magnitude of the event and the characteristics of the catchment. Using the Yealm Estuary as case study, it was discussed that rainfall-induced peak FIO concentrations could persist in shellfish flesh as much as 6 days after the rainfall event.

Different species of shellfish behave differently to these environmental factors. Usually, mussels and cockles accumulate microbial contaminants to higher level than oysters. However, site-specific differences in water:flesh FIO ratios occur because temperatures and salinities significantly higher or lower than the optimum for the species may reduce pumping action of the bivalves, with the animals ceasing filtration activity and closing at extremely high or low levels. Occasional events of water temperatures and salinities outside the minimum for shellfish growth were identified in UK estuaries.

Association between E. coli in shellfish and water

The relationship between levels of E. coli in shellfish flesh and overlying waters was studied using paired water and shellfish samples collected from 40 monitoring points within 6 production areas in England and Wales collected over the period 1991–1994. The resulting statistical models could be used to predict E. coli concentrations in the water on the basis of levels quantified in shellfish flesh as part of regulatory assessments. They could also be used to predict shellfish flesh quality in the event of a sewage discharge. However, only 35% of the variance in E. coli levels in shellfish flesh was explained by the variation of the indicator in the water. The lack of a clear linear relationship is in accordance with the past research in this field which has not produced credible mathematical relationships linking water quality and shellfish flesh concentrations. These studies would however help Defra understand the levels of water quality necessary to protect shellfish beds when the Shellfish Waters Directive is revoked by the Water Framework Directive in the UK in 2013. Further work is being undertaken by Cefas and CREH to refine the models using more up-to-date E. coli data.

Research highlights

In recent years, there has been considerable progress in reducing average levels of FIOs in shellfisheries.

In many catchments, these reductions were associated with major sewerage infrastructure improvements involving installation of UV disinfection, elimination of crude sewage discharges and reduction in the frequency of sewage spills from IDs.

Effluents from UV disinfected plants nowadays contribute with very low levels of FIOs to shellfish waters.

Currently, the main sources of FIOs are STWs that have not been improved, IDs and diffuse pollution from agricultural land.

During high-flow conditions, under the ‘worst-case scenario’ investigated, IDs may contribute over 50% of the total FIO load to shellfish waters.

Favourable conditions for FIO survival are low solar radiation, low temperature, low salinity, low density of micro-predators and high levels of organic matter.

Extreme temperatures and salinities may affect the filter-feeding activity of shellfish and alter shellfish:water FIO ratios between fisheries.

Elevated levels of FIOs may persist in shellfish flesh as much as 6 days after a rainfall event.

July 2012

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