Fish Health & Hygiene

Fish health and hygiene is a broad subject area that includes the following:

  • The potential risks and associated mitigation methods to prevent impacts on human health that may be associated with seafood products that are unfit for consumption;
  • The risk of disease introduction and transmission in aquaculture species and how these are monitored and managed;
  • The steps required to avoid the introduction or movement of invasive non-native species.

Harvesting Classification and Sanitary Surveys

It is a requirement under EU legislation (EC Regulation 854/2004 Annex II) for all beds from which bivalve shellfish are harvested to have a Classification according to a microbiological standard based on the presence of the bacteria Escherichia coli.    

  1. E.coli is used as an indicator organism for the presence of faecal contamination and shellfish are tested to obtain the number of colony forming units (CFUs) in 100g of flesh and intra-valvular liquid. E. coli occur naturally in the digestive tract of animals and humans and are generally considered harmless although there are strains, such as 0157:H7, which can cause illness in humans.

An application to have a shellfish bed classified can be made by contacting the Food Standards Agency (FSA) . Once an application for Classification has been made, sampling of representative shellfish is normally undertaken on behalf of the FSA by the Local Authority Environmental Health Officers (EHO).

The EHOs send the shellfish samples to an accredited testing laboratory in order to assess the levels of E. coli CFUs in 100g of flesh and intra-valvular fluid.  A provisional Classification can normally be issued after sampling fortnightly for 3 to 4 months with full Classification being achieved after a full year’s results have been obtained, normally based on monthly sampling intervals.

The processes and flowlines for establishing classification and biotoxin status of new offshore shellfish growing areas have been described in a guide that is available as here; Processes and Flowlines Guide

There is also scope under a Memorandum of Understanding between the Food Business Operator (FBO) and the FSA for the FBO to submit additional samples for inclusion in the microbiological data set for a production area. This is known as the Harvesters Own Sample Protocol.  The advantage of doing this is considered to be that a larger data set helps to identify contamination trends and may add to the stability of the Classification based on the 90% compliance.

The intention is that FBO sample results are considered alongside the FSA’s official control microbiological results dataset for the classification, closure or opening of the relevant production area.  An increase in microbiological data from a shellfish production area would increase the knowledge of the microbial contamination trends within the area and may benefit the stability of the area’s classification.

Classifications issued for shellfish harvesting beds are based on the following criteria in terms of how many CFUs are present:

Class A: A harvesting area where test results are shown to be consistently less than 230 CFUs of E. coli per 100g of flesh and intra-valvular liquid.

Class B: A harvesting area where 90% of samples have less than 4,600 CFUs of E. coli per 100g of flesh and intra-valvular liquid. The remaining 10% of samples must not exceed 46,000 E. coli per 100g.

Class C: A harvesting area where test results are shown to be less than a maximum limit of 46,000 CFUs of E. coli per 100g of flesh and intra-valvular liquid.

Prohibited Area: A harvesting area where test results are shown to be higher than 46,000 CFUs of E. coli per 100g of flesh and intra-valvular liquid.

Current Classifications for England and Wales can be found via the following web-link:

Current Classifications

Regulatory Monitoring Point results can be found on the Cefas website as follows:

shellfish Monitoring Results

Sanitary Surveys

Under EC legislation EU/854/2004, Section 6, of Annex II, if the competent authority (FSA) decides in principle to classify a new production area or re-laying area then a Sanitary Survey must be carried out. These surveys provide an inventory of the sources of pollution of human or animal origin likely to be a source of contamination for the shellfish harvesting or production area.  Information included in the surveys is as follows:

  • An examination of the quantities of organic pollutants which are released during the different periods of the year, according to the seasonal variations of both human and animal populations in the catchment area, rainfall readings, waste-water treatment etc.;
  • Determination of the characteristics of the circulation of pollutants by virtue of current patterns, bathymetry and the tidal cycle in the production area;
  • Establishment of a sampling programme of bivalve molluscs in the production area which is based on the examination of established data, and with a number of samples, a geographical distribution of the sampling points and a sampling frequency which must ensure that the results of the analysis are as representative as possible for the area considered.

Where harvesting or production beds are already classified for other shellfish species then these Sanitary Surveys are a good reference source for establishing likely points of microbial contamination.  Sanitary surveys are now in the public domain and can be accessed via:

Sanitary Surveys

Shellfish Hygiene

Bacterial Contamination of Shellfish

Improvements in public health over the last century together with more effective hygiene controls on shellfish production areas have meant that diseases such as typhoid, paratyphoid fever and other gastroenteritis caused by the Salmonella spp. bacteria found in sewage are now not so widespread.  Non-sewage related bacterial illnesses include the pathogenic Vibrio spp., especially Vibrio parahaemolyticus and Vibrio vulnificus.

Depuration of Bivalve Shellfish

The development of purification or depuration (controlled purification) as a method of eliminating bacterial contamination from shellfish dates back to the beginning of the last century when outbreaks of typhoid fever associated with the consumption of sewage contaminated shellfish occurred both in the US and Europe.  The earliest purification technique simply involved the re-laying of shellfish in clean seawater.

The chemical sterilisation of seawater was developed ~1915 at the shellfish research station at Conwy in North Wales and in the 1920’s the use of ozone for water sterilisation was introduced in France, a technique that is still widely used in many parts of Europe.

It was not until the 1950s that the use of ultraviolet sterilisation of seawater was introduced which proved popular as it did not leave residues or by-products in the seawater.  Today we normally refer to depuration as a managed or controlled process that takes place within an approved premise.  As re-laying of shellfish in cleaner water is not a controlled process then it is no longer considered to be depuration.

Operated correctly within approved premises, modern depuration systems based on UV sterilisation, ozonation or combinations of water sterilising technology (‘hybrid’ systems) have proved to be extremely effective in reducing bacterial contamination levels within shellfish and thus providing a safe food product in this respect.

For examples and technical information regarding different depuration systems, including information on the Sea Fish Industry Authority (Seafish) standard design purification systems, please refer to the publication section of the Seafish website:

Seafish publications search

Under EC Regulation EC 853/2004 the approval for shellfish purification plants to operate must be given by the Local Enforcement Authority following a technical inspection and microbiological challenge test. A purification advice service is available through Cefas:

Purification Systems Advice

Training in the correct use and operation of bivalve purification systems is available to industry through the Seafish and Royal Environmental Health Institute of Scotland (REHIS) accredited courses which are delivered in England and Wales by the Southern Shellfish Training Centre.

For a comprehensive overview of the depuration of bivalve shellfish please refer to the FAO Fisheries Technical Paper (No. 511) available via the following website:

FAO Fisheries Technical Paper

Viral Contamination of Bivalve Shellfish

In recent years it has been recognised that in Europe that viral contamination of shellfish now forms the major part of shellfish related illnesses with norovirus being the most common cause of illness. Businesses are increasingly turning to self-monitoring to protect product reputation and to limit product recalls. Unfortunately, whilst depurating shellfish is generally effective for the removal of bacterial contamination it is not effective in removing pathogenic viruses such as norovirus which are only eliminated slowly from shellfish.

Avoiding viral contamination of shellfish during production is therefore seen as key to minimising public health issues in this respect. Whilst norovirus can survive in seawater for long periods it would however seem logical that the further offshore that shellfish are cultivated the less will be the likelihood of the problems posed by norovirus contamination of shellfish.

It would seem therefore that offshore cultivation of bivalve shellfish could offer the chance to avoid the problems associated with viral contamination of shellfish, giving the offshore shellfish producer a major advantage over many of the inter-tidal producers. An alternative way of looking at this may be that shellfish grown inter-tidally could be ‘finished’ offshore i.e. held in norovirus free offshore waters until norovirus levels are considered to be at a level whereby there is no threat to the consumer.

Emerging Shellfish Hygiene Issues

There are new emerging microbial threats which have implications to both waters and bivalve shellfish of all species, and which could become problematic in the future.  V. parahaemolyticus and V. vulcanus, marine strains of Vibrio bacteria, are warm water estuarine species whose increased incidence has been linked with climate change.  These strains are becoming widely spread in the marine environment and are particularly associated with sediments.  They can cause periodic problems such as following summer storm events when conditions are optimal for growth with high temperatures and reduced salinity.  Some Vibrio species have also recently been implicated in producing toxins such as Tetrodotoxin (TTX) normally associated with puffer fish.

Antibiotic resistant E. coli are an increasing cause for concern and can be associated with waste water treatment works or with agricultural practices. As with norovirus, offshore production would be likely to remove bivalve shellfish from likely contamination sources in this respect.

Biotoxin Information & Monitoring

Toxic Algal Blooms

Phytoplankton or microalgae are simple marine plants that form the primary food source for many marine bivalve molluscs.  However, of the 5,000+ species of phytoplankton that exist worldwide about 2% are known to be harmful or toxic (Source: Wikipedia).  Where these toxin producing algae occur in large numbers then they are often referred to as harmful algal blooms or HABs. Certain species of phytoplankton are associated with producing biotoxins that can be the cause of shellfish poisonings in consumers.  Biotoxins implicated in shellfish poisonings include the following:

  • Okadaic Acid: Produced by the dinoflagellate Dinophysis, this biotoxin is responsible for causing Diarrhetic Shellfish Poisoning (DSP).
  • Saxitoxin: Produced by the dinoflagellate Alexandrium, this biotoxin is responsible for causing Paralytic Shellfish Poisoning (PSP).
  • Domoic Acid: Produced by the pennate diatom Pseudo-nitzschia, this biotoxin is responsible for causing Amnesic Shellfish Poisoning (ASP).

Due to the potentially serious health impacts that some of these toxin producing phytoplankton can have there is a monitoring programme carried out around England and Wales by Cefas on behalf of the FSA.  This monitoring programme consists of a weekly analysis of seawater samples for the presence of these phytoplankton.

Where an alert level is recorded in a shellfish production area for these biotoxin producing phytoplankton then a Temporary Closure Notice and/or Warning Notices will be issued by the Local Enforcement Authority.  These will remain in place until the waters and shellfish are found to be free of both the phytoplankton and associated biotoxins.

It should be noted that the FSA state that, whilst an official monitoring programme exists, it is the responsibility of Food Business Operators (FBOs) to ensure that the shellfish placed on the market do not contain biotoxins above permitted levels.  In practical terms, for a shellfish farm there is little that can be done whilst a HAB is present other than avoiding harvesting until the harvesting water and shellfish are given the all clear.

In terms of testing, simple test kits are now available to industry which can detect the main biotoxins associated with these types of shellfish poisoning incidents. Over time FBOs involved with shellfish production will gain experience of their production areas and will build an understanding of the times of highest risk when HABs are likely to occur.  With this knowledge FBOs can then increase testing at times of highest risk as part of their due diligence and in order to protect consumers.

For further information on the official monitoring programme see the following website:

Shellfish monitoring programme

Risk Management

End Product Standards and Testing

It is the responsibility of the FBO placing a food product on the market to ensure that it is fit for consumption and meets End Product Standards (EPS). Current EPS for live bivalve shellfish are as follows:

  1. Less than 230 CFUs of Escherichia coli in 100g of flesh and intra-valvular liquid.
  1. Must not contain Salmonella bacteria in 25g of flesh.
  1. Be alive, fresh and in good condition.
  1. Normal amounts of intra-valvular liquid at sale and adequate response of shellfish to percussive tap.
  1. Must taste fresh, no off-flavours and be free of detritus.
  1. Must not contain marine biotoxins in excess of permitted levels.

It is up to the FBO to decide how often End Product Testing (EPT) is carried out based on their own assessment of risk.  The regulator may indicate the minimum number of animals required to produce enough flesh to make a microbiological or algal biotoxin test valid but will not specify how often the FBO should carry out the test.  The reason for this is that the FBO should know their product better than anyone else and so are best placed to make an informed risk assessment of threats to human health.

FBOs can either hold the shellfish and release them only after testing, i.e. a system of positive release, or alternatively the FBO can decide on a frequency of EPT that gives them the confidence that they can observe trends and allows them to cease harvesting before critical levels of microbial or biotoxin contamination are reached.  Collaboration with other harvesters in an area on sharing results may give a better picture of the overall potential microbial or biotoxin loading to be expected.


There are many different routes by which bivalve shellfish intended for human consumption may become unfit for human consumption through microbial, chemical or physical contamination.  Pre-harvest contamination routes include waste water flow or spills and diffuse pollution which may result in biomagnification. Post-harvest recontamination routes could include cross-contamination with undepurated stock, contamination by handlers or through poor storage.

Depuration can be used to reduce low level bacterial contamination in bivalve shellfish, but it is clear from the pre and post-harvest contamination routes that this is only one aspect of ensuring food safety and minimisation of risk to consumers. Therefore, in terms of overall food safety, depuration should be viewed as part of a wider more all-encompassing system based around a Hazard Analysis Critical Control Points (HACCP) approach from production to dispatch.

The main principle behind the HACCP approach is that it focusses on identifying the ‘critical control points’ (CCP) in a food production process where food safety issues may occur, i.e. hazards, and then puts in place measures to monitor these points in order to prevent things going wrong.  HACCP also provides corrective actions where a problem occurs.

The role of HACCP in helping to ensure a standardised approach to food safety is widely recognised and is indeed a legal requirement for depuration and/or dispatch centres.  Seafish have developed a generic HACCP depuration template to help businesses comply with HACCP requirements but it is important that each FBO carries out a ‘walk through’ for their own business in order to identify the unique characteristics of their operational procedures that may be considered to be CCPs.

An overview of food hygiene legislation both national and European with particular emphasis on HACCP implementation can be found on the Seafish website as follows:

seafish legislation

There is also an online tool developed by the FSA to help small business develop HACCP. This tool is available via the following website:


Specific training courses are available through Seafish in HACCP for live bivalve production as well as many other seafood industry-based training courses and apprenticeships.  Details about this training and apprenticeships are available via The Seafood Training Academy as follows:


Active Management

Over time shellfish producers will build up experience and an understanding of the characteristics of their particular production and harvesting beds and wider catchment.  This ‘local knowledge’ should allow them to make informed decisions about their operational practises as weather conditions or other environmental parameters change.  This proactive response to changing conditions based on dynamic risk assessments by the shellfish producers is termed ‘active management’.  For example, if there had been a recent CSO spill following heavy rainfall within or near a shellfish production area then a decision might be taken to voluntarily suspend harvesting until conditions had changed. There may then be scope to modify regulatory Classification sampling to match only the times when the production beds were being harvested thus avoiding unnecessary Classification downgrades for the producer whilst still ensuring public health protection.

Ideally, a mix of historical Classifications, active management and EPT should be employed to protect both the consumer and the producer. With this approach, the Classification system gives an overview of the historic hygiene status of the beds, active management is practised by the shellfish producer to provide proactive consumer safety and EPT is used as part of the due diligence thus maximising public health protection while protecting the reputation and livelihood of the shellfish producer.

In mainland Europe there is a more pragmatic and flexible approach to Classifying production beds and in setting minimum depuration times.  Added to this, greater use of active management together with EPT means that the approach of shellfish producers in mainland Europe is closer to a HACCP-based risk management system.

Good Manufacturing Practise Guidelines

The Sea Fish Industry Authority Good Manufacturing Practise Guidelines (GMPG – June 2007) provides an excellent step-by-step guide on how to adhere to best practise when preparing live bivalve shellfish for the market including signposts to relevant legislation.

The GMPG is available for download from the publications section of the Seafish website as follows:

Seafish publications

Biosecurity & Stock Movement

This section of the website is currently being updated.

Form AAH1

Currently being updated

aquatic animal health and movements

Veterinary Medicines

The Veterinary Medicines Directorate (VMD) protects animal health, public health and the environment. They promote animal health and welfare by assuring the safety, quality and efficacy of veterinary medicines. As an executive agency of the Department of Environment, Food and Rural Affairs (Defra) the VMD contribute to their objectives to protect public health and meet high standards of animal welfare. Their work also helps the Food Standards Agency to protect and improve the safety of food people eat.

The VMD are responsible for:

  • monitoring and taking action on reports of adverse events from veterinary medicines
  • testing for residues of veterinary medicines or illegal substances in animals and animal products
  • assessing applications for and authorising companies to sell veterinary medicines
  • controlling how veterinary medicines are made and distributed
  • advising government ministers on developing veterinary medicines policy and putting it into action
  • making, updating and enforcing UK legislation on veterinary medicines

(Source: VMD website)

Veterinary Medicines Directorate

Animal and Plant Health Agency

The Animal and Plant Health Agency (APHA) work to safeguard animal and plant health for the benefit of people, the environment and the economy.

The APHA is an executive agency of the Department for Environment, Food & Rural Affairs, and works on behalf of the Scottish Government and Welsh Government.

The agency was launched on 1 October 2014. It merges the former Animal Health and Veterinary Laboratories Agency (AHVLA) with parts of the Food and Environment Research Agency (FERA) responsible for plant and bee health to create a single agency responsible for animal, plant and bee health.

The APHA are responsible for:

  • identifying and controlling endemic and exotic diseases and pests in animals, plants and bees, and surveillance of new and emerging pests and diseases
  • scientific research in areas such as bacterial, viral, prion and parasitic diseases and vaccines, and food safety; and act as an international reference laboratory for many farm animal diseases
  • facilitating international trade in animals, products of animal origin, and plants
  • protecting endangered wildlife through licensing and registration
  • managing a programme of apiary (bee) inspections, diagnostics, research and development, and training and advice
  • regulating the safe disposal of animal by-products to reduce the risk of potentially dangerous substances entering the food chain

(Source: APHA website)

Animal and Plant Health Agency
Last updated: 12 August 2021