

This book brings together information often difficult to find, joining the worlds of aquaculture science and industry production, through the leveraging of their synergies and dependencies. It contains a wealth of scientific knowledge which can only be traced in a fragmented manner in specialised journals.
Chapter 2

Designing a Biosecurity Plan at the facility level: Criteria, Steps and Obstacles
Victoria Alday-Sanz

One of the advantages of being the editor `in chief` of this book is that one can add a chapter at the last minute. Not only that, but add a chapter that puts forth learning from personal experience rather than a simple review of other publications. Thus, few references are listed to support the statements in this document. Rather, references have been selected to provide access to more detailed information. As an excuse for the lack of formality, one could say that when the target audience is shrimp producers, achieving a document that is easy to read is more important than being scientifically fashionable.

The objective of this chapter is to provide farmers with some knowledge and guidance on how to design and implement biosecurity plans in their facilities. It is doubtful that a neighbour’s biosecurity plan will be effective your farm. Each facility and each farming system needs its own biosecurity plan that identifies the points of risk and defines the mitigation measures to minimize those risks.

Unfortunately, there are no fixed rules or recipe-book guidelines. This document simply provides some principles to understand health and disease issues that will allow producers to develop their own biosecurity plans.

First, we need to state that too little is known about shrimp pathogen transmission and disease expression or the immune system of shrimp. Although this chapter summarizes the currently available knowledge, one must keep in mind that what we know today is not written in stone and that knowledge regarding various issues will change over time. For example, pathogens that are currently thought to be transmitted only horizontally may eventually be shown to also be transmitted vertically. However, we need to move forward and make decisions, as informed as possible, based on the best currently available knowledge.

1. The purpose of biosecurity

The literal translation of biosecurity is, from Greek, “safe life”. However, different definitions have been created and adapted to suit particular needs. FAO has defined biosecurity as a strategic and integrated approach that encompasses the policy and regulatory frameworks for analysing and managing relevant risks to human, animal and plant life and health, and associated risks to the environment.

In simpler terms, and applying it to the purpose of this chapter, we can say that biosecurity refers to the activities that aim to prevent, control and eradicate risks to life and health. Biosecurity, in this context, applies to the control of infectious diseases. In order to control the risks, we need to find the appropriate level of protection for each particular case. This will depend on the consequences of that risk, with severe consequences requiring a higher level of protection. It is often impossible to achieve zero risk within an economically viable operation and, thus, it is necessary to reach a trade-off between the cost of minimizing risk and the possible economic impact of that risk.

The primary aim of commercial shrimp farming is not to rear healthy shrimp but to make money. Therefore, it should be properly understood that the goal of biosecurity is to reduce the economic impact of diseases. In other words, biosecurity should be regarded as a tool toward the sustainability of a company. There are, of course, companies whose market product is SPF animals. In that case biosecurity is not only a sustainability tool but also a necessary way of operating.

2. Health and disease

Diseases are a constant, if not altogether routine, aspect of livestock rearing. Animals, including humans, get diseased even under, so called, good husbandry conditions. However, health and disease are not black and white issues. The area between the two is, in fact, various shades of grey. For instance: average survival rates of 50-60% in shrimp hatcheries or 60-70% in grow-out ponds are considered to be reasonably good for certain production systems. In such cases, no investigation is carried out to find out the cause of death of a significant part of the stock, and it is usually unknown whether an infectious disease process has played a role in the loss. In fact, a disease that does not cause unexpected losses is not considered a disease.

It is necessary to make a difference between infection and disease. An infected animal is not necessarily diseased. It may not present mortality or clinical signs, but it may have an impact on the animal’s performance. For example, Penaeus vannamei infected with IHHNV exhibits growth and deformity syndrome while the same virus causes high mortality in Penaeus stylirostris and has no affect on Penaeus modonon. On the other hand, it is possible that IHHNV infections may have an effect on P. monodon that we are currently unaware of and therefore do not measure. It is difficult to know, but it is reasonable to assume than an active viral infection may have an impact on shrimp physiology. This is one of the reasons behind the industry’s switch towards SPF (specific pathogen free) animals.

In animal production, health is a measure of productivity. Put another way, disease is a production cost to a farmer. Since shrimp viruses do not infect humans or other vertebrates, they do not represent a public health concern, and the major impacts of shrimp diseases are negative economic consequences and danger to indigenous crustaceans species.

Understanding disease processes in a population of interdependent individuals is not an easy task. Moreover, in the case of shrimp, it is a population that can only be observed with difficulty until the time of harvest. In addition to that, one needs to consider more recent knowledge indicating that diseases often have multifactorial aetiology. Thus, pathogens that were formerly considered to be the primary causes of disease are now known to be only necessary factors that must be combined with other determinant factors to trigger the disease process. A clear example is WSSV infected shrimp that develop white spot disease only if the water temperature falls below 30-32oC or rises above 15 oC.

When one analyzes an epidemic curve, several stages can be described. The first stage (1) Is the endemic level, where animals are infected but disease is not expressed (disease implies clinical signs as well as mortality) Next (2) is an ascending stage with clinical signs and/or mortality, the steepness of which can vary and give some indication of the rates of disease transmission and incubation (i.e., steeper ascention for higher rates). The next (3) is the variable disease peak and plateau, followed by the descending stage (4). The duration of the latter two stages will depend on the virulence of the pathogen, efficacy of transmission, stocking densities, environmental conditions, etc. A final state (5) consists of secondary disease peaks that are often related to the introduction of new susceptible animals or to changes in transmission or environmental conditions that may have temporarily suppressed replication of the pathogen or the expression of disease.

Each of these stages will vary in duration and rate of change depending on the characteristics of the pathogen and existing environmental conditions. Understanding this process will help in developing sensible and effective biosecurity measures.


In order to control the spread of infectious diseases in a facility, we need to act as soon as possible, that is in stage 1 where we already have infection but no signs of disease. This would be equivalent to obtaining a positive nested PCR result in the absence of clinical signs (including mortality). Detection of PCR+ animals implies that an active monitoring of the stock must be practiced. This will be discussed in detail in section 4.2.1. If we ignore stage 1 and wait for stage 2 to react (i.e., until there are clinical signs with or without mortality), we have lost precious time and it is likely that, in the meantime, we have been spreading the pathogen throughout the facility.

3.SPF, SPR and SPT status

In recent years, the terms SPF and resistance have been used widely in the shrimp industry. These terms are often allocated incorrect meanings. Additionally, the term resistance is, in itself, confusing as there are two types of resistance: resistance to infection and resistance to disease expression (tolerance). Using the proper terminology is useful in order to avoid misunderstandings.

Animal health status and susceptibility to infection or disease can be defined using the terms: specific pathogen-free (SPF), specific pathogen-resistant (SPR), and specific pathogen-tolerant (SPT). Note that each term refers to “specific pathogens,” not to every known pathogen. In each situation, reference to the specific pathogen(s) involved is needed in order to understand the animal’s true health characteristics.

Specific Pathogen-Free

SPF status is obtained through specific management conditions where pathogens are excluded from the rearing facilities. This is a common strategy in domestication programs. SPF animals are free of one or more specific pathogens, but this health status does not refer to their susceptibility to infection or disease. In addition to being SPF, animals may or may not also be resistant or tolerant to the same or other pathogens. True SPF animals have not been exposed to pathogens, and their SPF status is a transient one. Once these animals are exposed to an environment where a range of pathogens – especially those for which their SPF status is designated – is present, their SPF status is lost. They would not continue to be SPF, even if they tested negative by polymerase chain reaction or other diagnostic tests, as they might be infected at a level below the test’s detection threshold.

Regarding trade, SPF animals are safer than any other group of animals in avoiding the transboundary movement of pathogens. However, unknown pathogens or pathogens not included in the screening for SPF status can still be present and/or undetected. It is also, becoming clear that different strains of certain pathogens may not be detected by some of the commonly used tests. These undetected strains of pathogens pose a risk of pathogen movement through uncontrolled traffic in aquatic animal stocks.

Specific Pathogen-Resistant

Animals gain “resistant” status because of their genetic background. They can be resistant to infection (SPR) or resistant to disease, as in being tolerant to a pathogen (SPT). As with SPF, resistance is specific for a particular pathogen. SPR animals are not susceptible to infection and do not represent a transmission risk for that specific pathogen, provided there is no “mechanical” contamination through any viable pathogen adhering to the gills or any other surface. If these animals have not been exposed to pathogens, they can also have SPF status. Pathogen resistance is a qualitative characteristic. An animal is either resistant or it is not, and the status is permanent. SPR status for a particular pathogen is not lost due to management practices, although it can be lost in subsequent generations through poor animal-breeding and selection strategies.

Specific Pathogen-Tolerant

SPT animals either do not develop disease when infected with a specific pathogen or that pathogen has a lower impact on them than on normal animals. Tolerance is a quantitative characteristic. For example, there might be different degrees of tolerance to the pathogen or environmental factors may have less influence on the development of the disease condition. If SPT animals have not been exposed to pathogens, they can also have SPF status, but being susceptible to infection, they cannot be SPR for that same pathogen. Unless these animals are also SPF, they are potential carriers of pathogens and therefore represent a risk for disease spread.

4. Designing a biosecurity plan

As mentioned in the introduction, each facility needs to develop its own biosecurity plan. This will require full understanding of the design and operations of the facility, knowledge of the animal’s health status and the pathogen’s transmission mode in order to be able to identify the risks and to develop meaningful biosecurity measures.

4.1. Criteria

When evaluating and defining biosecurity measure>s there are three rules that need to be kept in mind. Measures should be:

  • Justifiable. They should be scientifically sound. Company policy or personnel sanitation measures should not be included under the biosecurity umbrella but should stand on their own.
  • Practical. They should not impede routine farming practices. Staff commitment and engagement is necessary for the plan’s implementation and their participation in optimizing the mitigation measures is desirable.
  • Economically viable. A balance should be found between the costs and benefits of the biosecurity measures.
4.2. Steps to be followed

In order to design a biosecurity plan a series of steps >must be followed. These include acquiring knowledge of the stock’s current health status, the design and implementation of surveillance programs, selection of those pathogens which will be targeted for control, identification of risk points and definition of control measures, development of diagnostic capacity or access to it,definition of a contingency strategy and planning for a staff awareness building campaign.

4.2.1. Health status of the shrimp

The starting point is d>etermining accurately the health and infectious status of the facility stocks. Some of the pathogens present may be known. This will probably be the case with the pathogens causing high mortalities. It is possible that other pathogens will be present that may have been given less attention or even ignored due to their low impact on survival.However, these may affect growth and performance and therefore cause significant production losses.

Surveillance and monitoring

Surveillance and monitoring are mechanisms applied to collect and interpret data on the animal populations’ health to accurately describe their health status with respect to specific diseases (Subasinghe et al., 2004).

There are two main purposes for surveillance programs. In the case of diseases that are already present, the aim is to detect their prevalence and distribution and any changes in the same. In this case, the term used is monitoring. The term surveillance is used for the detection of new or exotic diseases where the aim is to have an early detection system where sensitivity is important (e.g., PCR methods are recommended). The final objective of surveillance and monitoring is preparedness.It is a tool that provides warnings, as soon as possible, of any sanitary risks that the stock is facing.

One of the basic purposes of surveillance is to generate cost-effective information for assessing and managing risks. Therefore surveillance (and monitoring) programs need to be designed to minimize the number of samples collected but maximize the information generated. They require trained expertise, suitably equipped laboratories, good knowledge of susceptible-carrier species in the local environment, knowledge of transmission mechanisms and suitable infrastructure.

When designing such type of studies, one should take into account that:

  • Both wild and farmed animals are susceptible to infections,
  • Many pathogens are carried by apparently healthy animals,
  • The health/disease situation is never static, and is often linked to environmental factors,
  • Prevalence of infection might be highly variable seasonably,
  • An appropriate sample size is necessary to generate reliable information and specific sampling requirements need to be tailor-made for each individual disease (please refer to Cameron, 2002, for more detail on sample size),
  • They need to be carried out at least twice a year in different seasons,
  • Detection of exotic pathogens must be confirmed by more than one diagnostic technique such as PCR, histology or in situ hybridization,
  • Many viral diseases have a broad host range so that all crustaceans should generally be regarded as potential carriers of shrimp viruses, unless it has been demonstrated that particular species are refractory to infection,
  • A negative result has two possible meanings, one that the pathogen is not present the other that it is below the detectable level,
  • Many pathogens can be transmitted vertically via gametes or spawning fluids and tissues or via contaminated feces.

record keeping of results for disease surveillance and monitoring is extremely important for learning about disease patterns and risk factors. These should be generated and integrated into the production data.

In addition, daily stock health inspections for mortality, sick animals and abnormal external signs (e.g., changes in color, shape, feeding behavior or poor growth) are extremely important in order to detect disease processes before severe mortality occurs or infection becomes widespread.

4.2.2. Listed pathogens

Shrimp, as any other production animal,are affected by a range of pathogens. These can be viruses, bacteria, fungi or parasites. Pathogens with the most severe economic impact on shrimp farming are viruses followed by intracellular bacteria Most shrimp viruses are known by their acronyms (Table 1).

Table 1: Complete names of the main shrimp pathogens and their acronyms.
Pathogens Acronyms
White spot syndrome virus WSSV
Yellow head virus YHV
Gill-associated virus GAV
Taura syndrome virus TSV
Infectious myonecrosis virus IMNV
Baculovirus penaei BP
Monodon baculovirus
New name: Penaeus monodon polyhedrovirus (PemoNPV)
Infectious hypodermal and haemotopoietic necrosis virus
New name: Penaeus stylirostris densovirus (PstDNV)
Hepatopancreatic parvovirus
New name: Penaeus monodon densovirus (PmDNV)
Necrotizing hepatopancreatitis NHP

The pathogens listed are the ones that are usually targeted to be screened out of production systems or that will be targeted for control measures. This list can only include diseases where the aetiology is properly identified and where there are diagnostic methods available. Depending on the initial health status of the stock and the surrounding environment, the listed pathogens may refer exclusively to those that are associated with severe mortality and major economic impacts or may affect growth and performance. This list should only include primary pathogens and avoid the inclusion of secondary ones. For instance, Vibrio species in most cases behave as secondary pathogens and are part of the normal microflora of the shrimp environment. Trying to target these microorganisms is a useless and costly exercise.

Transmission of listed pathogens

Understanding the transmission of the listed pathogens is crucial in order to implement effective biosecurity measures. There are two general pathways that are important for shrimp pathogens: horizontal and vertical. Horizontal transmission is from one shrimp to a neighboring shrimp whether it is directly via cannibalism, via water (cohabitation) or ingestion of contaminated feces. Horizontal transmission also takes place through contact with other susceptible or carrier species in the environment or through ingestion of contaminated or infected fresh food. From epidemiological studies, transmission via ingestion of infected or contaminated tissue appears to be far more efficient than through cohabitation.

Vertical transmission, on the other hand, is the transmission of infection from the broodstock to their offspring. In the strict sense, vertical transmission refers to the pathogen being carried within the egg (intra ovum) so that cleaning or disinfection of eggs or larvae will not prevent transmission. Intra ovum transmission has not been verified for any shrimp pathogen but is suspected for WSSV and IHHNV. Although, this pathway is only suspected, it is important to take it into account for development of breeding stocks. In this case, the exclusion of the pathogen can only be achieved by the removal of infected broodstock. Another possible way of vertical transmission is contamination of the egg surface due to infection of the ovary stroma or sperm (per ovum). Every systemic pathogen is suspected of per ovum transmission. In this case, cleaning and disinfection of eggs is an option to break the transmission pathway. However, not much success has been achieved by this means. In most cases, exclusion of per ovum pathogens requires the rejection of infected broodstock. Contaminated water or the ingestion of sloughed tissue or feces from pathogen containing broodstock also represent infection vehicles during early larval stages. In these cases, it is possible to prevent transmission through the removal and cleaning or disinfection of eggs prior to hatching. While disease expression may vary with the stage of development, susceptibility to infection is suspected to be possible at all stages. A summary of the disease expression stage, tissue distribution and type of vertical transmission of the main shrimp pathogens is included in Table 2.

Table 2: Main shrimp pathogens
Pathogen Stage of disease expression Tissue distribution Verticaltransmission
Intra ovum (inside the egg) Per ovum (around the egg) Via ingestion of particles in faeces
WSSV Juvenile to adult Systemic reproductive track Suspected Yes No
YHV Juvenile to adult Systemic No Yes No
GAV Systemic/reproductive track No Yes >No
TSV Juvenile to adult Systemic No Yes No
IMNV Juvenile to adult Systemic No Yes No
BP Larvae to early juvenile Enteric No No Yes
MBV Larvae to early juvenile Enteric No No Yes
HPV Juvenile to adult Enteric No No Yes
IHHNV Larvae to early juvenile Systemic/ reproductive track Suspected Yes No
NHP Juvenile to adult Enteric No No Yes
Strepto-coccus Juvenile to adult Systemic No Suspected Yes

*Considering that GAV is closely related to YHV, it is believed that YHV is also present in the reproductive track although it has not yet been demonstrated.

In addition, viral transmission from wild crustaceans other than shrimp has been reported for most shrimp viruses. Special attention must be given to WSSV due to its broad range of potential hosts, a fact that has led to the official OIE declaration that all decapods are susceptible to infection from WSSV.

In terms of health management, shrimp viruses should be considered to cause persistent infections. Once animals have been infected, they remain infected for life. Similarly with intracellular bacteria: NPH and >Streptococcus. Streptococcus is responsible for extracellular infections; however, it has a component of intracellular infection in haemocytes. In these cases, antibiotic treatment is only partially successful as the intracellular space is difficult to reach. Often relapses of disease outbreaks, not necessarily re-infections, are observed.>

Pathogen and disease > description and the suitability of different diagnostic techniques are described in Cuellar-Anjel >et al>. (this volume). Another source of information is the Aquatic Animal Health Manual of the OIE (World Animal Health Organization) which is reviewed every few years and can be downloaded for free >


4.2.3. Risk Identification

A biosecurity program >is consistent with HACCP (Hazard Analysis, Critical Control Points) principles. These can be used as a guide for implementation

Principle 1. Hazard analysis: to identify >the infectious hazards, at each step of the process.

Principle 2. Critical control points: actions are taken to reduce or eliminate the hazard.

Principle 3. Critical limits: the limits to which the hazard must be reduced (for instance the level of filtration).

Principle 4. Monitoring: observation and measurement of cleaning and disinfecting to ensure the critical limits are met at each step.

Principle 5. Correction: action must be taken if the critical limits are not met at each step.

Principle 6. Recording: records must be kept to show that the biosecurity program is in place and being implemented correctly and continuously.

Principle 7. Verification: tests and procedures to ensure that the HACCP system is working properly.

Risk identification (critical control points) and prioritization are the bases for the development of mitigation measures. These can be divided into major groups. Measures targeting the control of pathogen introduction into the facilities will be dealt with by the external biosecurity. The other group is comprised of those measures targeting the control of the spread of the pathogen within the facility that will be dealt with by the internal biosecurity. These mitigation measures need to be defined through a participative process with the production staff who would know the most efficient and practical solutions to decrease risks.

Often, due to economic reasons, not all mitigation measures can be implemented simultaneously. In those cases, priority should be given to those that tackle the highest biosecurity risks rather than those that are easier or less costly to implement.

External biosecurity:

External biosecurity deals with bioexclusion, the prevention of pathogen introduction from outside the farming facilities. The ideal biosecure facility is a covered rearing facility using recycled water, but this is rather unusual in the shrimp industry. >The first step in definining external biosecurity is to identify of all the possible sources of pathogen introduction and to define the appropriate procedures to control or reduce risk.

In the case of shrimp pathogens, the possible sources and a list of possible mitigation measures to decrease the risk are summarized in Table 3. The manner of implementation of the measures needs to be discussed and optimized together with the staff that will implement them.

Table 3: Possible sources of shrimp pathogens and risk mitigation measures.
Source Mitigation measures
Shrimp for stocking New broodstock
  • Use of SPF animals (the SPF pathogen list should include at least all listed pathogens)
  • PCR testing after cold stress before stocking, if at risk of WSSV
  • PCR testing after spawning for WSSV and systemic viruses
  • Washing and disinfection of eggs and nauplii for both systemic and enteric viruses.
Wild crustaceans
  • Use of crab fences to prevent their access to ponds, mainly close to mangrove areas
  • Filtration of water (down to 300-microns) to prevent the introduction of wild infected animals or carriers.
  • Preventing the introduction of crustaceans for domestic consumption and for use as bait for fishing.
  • Systematic fishing of crustaceans and fish from the incoming water canals in order to reduce their presence as they may act as carriers or amplify the pathogen if they are susceptible to infection
  • Treatment with pesticide of the pond bottom populations when ghost shrimps and related crustaceans are abundant in a pond.
Fresh feed
  • Stop the use of crustaceans as feed in maturation.
  • Eviscerate and clean fresh feed before feeding.
  • Avoid the purchase of Artemia biomass unless it is certified free of the listed pathogens.
  • In case of severe epidemics, water may act as a direct carrier of viruses. Disinfection of water prior to introduction into the pond is recommended but often not feasible.
  • Water is filtered to remove carriers of the virus (300microns and storage of the water for 4 days before stocking).
Non-host biological carriers (birds and insects)
  • These may have a relevant role in the case of epidemics.
  • Difficult to control (use bird nets, ultrasound, small ponds can be covered with mosquito nets, avoid lightening at night, etc…)
Fomites (inanimate objects contaminated with pathogens)
  • Washing and disinfection routines need to be established for vehicles and farm/sampling equipment.
  • Shower and cloth changing before entering the facilities is needed particularly if entering a space of higher biosecurity level (i.e. maturation) or after visiting another shrimp farm.
Effluents and waste from processing plants Treatment of effluents and collection and safe disposal of solid wastes is crucial to prevent the spread and increase in prevalence of pathogens into the wild.
Spread to wild populations

In the event of a disease outbreak, direct disposal of infected/disease populations (at any stage) or waste products derived from them (i.e. from the processing plants) into the water should be avoided in order to minimize the prevalence of the pathogen in wild animals surrounding the facility as this will become an external biosecurity problem in the near future. In these cases, when the decision is made to stamp out the stock in the tank or pond, shrimp should be harvested or killed in the tank or pond. If possible the water in the tank or pond should be disinfected and held for 2-3 days prior to discharge.

External visitors

External visitors present a relative risk to biosecurity. If any visitor has entered a shrimp farming area within the last week they need to report it and make sure the visitor has showered and changed clothes and shoes since visiting the area. Once inside the facilities, they need to comply with the biosecurity rules. In some cases it is necessary to point out to the visitors that no live, fresh or frozen crustaceans are allowed in the facility.

Internal biosecurity:

Internal biosecurity deals with biocontainment: preventing the release or spread of pathogens. Again, the first step is the identification of all possible means of pathogen dissemination and the definition of the appropriate procedures to control or reduce risk. Once more, procedures need to be defined in a participative process with the production staff included in the process as they would know the most efficient and practical solution to reduce risks.

When considering the risk of spreading a pathogen, there are two parameters to consider. One is the possibility of an item (equipment, clothes, shoes, vehicles, etc…) carrying infectious viral particles and the other is the possibility for those viral particles to reach a susceptible host. Based on the combination of the two, we can determine the level of risk.

Standard Operating Procedures (SOPs)

It is not possible to list all possible actions and activities that imply a risk in the spread of pathogens. The following matrix (Table 4) can help identify the possible ways of spreading pathogens during working operations. Each individual would need to critically analyze his/her own work and identify the different risks that are involved in his/her activities. Any circumstance in which shrimp come in contact with people, vehicles, equipment and surfaces represents a certain degree of risk. This also applies to contact with water and pond soil/mud but at a lower level of risk.


Once the different risk activities have been identified, risk mitigation measures need to be defined. Most of these mitigation measures will require cleaning and disinfection procedures. Such measures should be incorporated in the SOP´s for routine application.

Special emphasis should be given to harvest operations. These represent a particularly high risk as they require that a large volume of shrimp and water come into contact with people, vehicles, equipment and surfaces. Harvesting should always be considered as a high risk activity, even if no disease condition has been identified since an unidentified infection or disease process may be present. Cleaning and washing with strong detergent and soaking of all surfaces of equipment and vehicles including wheels, wheel arches, mudguards and exposed chassis, allowing at least 10 minutes contact period before rinsing at high pressure with clean water is required to be done at the site of harvest. It is crucial to avoid water spillage during transport of harvested shrimp to the processing plant through the use of sealed plastic bags within the tubs. This will restrict the area of sanitary risk to the harvested pond.

There are some tools in animal production that could facilitate internal biosecurity. These are: fallowing, an all-in-all-out growing strategy, zoning and compartmentalization, use of uniforms and restrictions in vehicle movement.


This is an ancient practice in agriculture. Basically, it refers to land that is plowed and tilled but left unseeded during a growing season. Gaps in aquaculture production at the same location is of great value in health management as dry out periods can break re-infection cycles. This should be performed regularly, ideally after every crop and before re-stocking with a new population of animals into a previously used site and especially after stamping out a diseased population. Obviously, the economic cost of fallowing should be proportional to the benefit obtained. Although benefits are only noticed in the long term and in comparison with ponds that have not undergone the fallowing procedure.

Fallowing should start after removing all susceptible and carrier species, water where the stocks have been held and contaminated equipment and materials. Disinfection should proceed the fallowing period. The fallowing period length will depend on the previous sanitary conditions, whether fallowing follows a normal crop or has been triggered by a sanitary emergency. It should be taken into account that often earthen ponds have a very rich ecosystem under the soil that retracts underground during dry out periods and emerges again when the pond is filled. Pond bottom ploughing and liming is highly beneficial and, in certain occasions, a short-life pesticide (carbamate or trichlorphon) might be necessary.


All-in-all-out strategies are regularly used in terrestrial animal production. It is a system that keeps animals together in groups by age and size. Animals of different ages do not mix within a section of the facility. These groups are moved together into the different phases of production. When a group moves forward, the section it occupied is completely emptied cleaned and disinfected. This strategy reduces disease transmission, by minimizing the risk of infection from older animals to younger animals. All animals within the group will have a similar sanitary record and level of immune system development.

Zoning and Compartmentalization

Zoning is the process of delineating infected and uninfected populations within a country or group of countries with respect to specific diseases. If we apply this concept at the facility level, the term compartmentalization should be used and it could be defined as the process to define areas that can be kept at a different sanitary status from the surrounding areas. The objective is to reduce the risk of spread of a pathogen by increasing the chances of control and to be able to maintain areas that are free of a particular pathogen. These compartments should be as small as functionally possible and each of them may have different degrees of biosecurity (i.e. maturation facilities versus grow out ponds). Each of them could be regarded as epidemiological units and the risk of contamination from one to another should be negligible.

The challenge lies in the farming operations respecting the same structure of compartmentalization while still carrying out their duties efficiently. The complicity and enthusiasm of the staff is crucial to do this successfully.

In the presence of an infected compartment, buffer compartments should be created around it where the pathogen will be monitored to have a clear understanding of the spread of the disease. In infected compartments, minimal monitoring is required except for monitoring recurrent outbreaks that require management intervention to minimise losses.

Use of uniforms

Personnel movement from compartment to compartment implies a risk as their clothes, shoes and themselves can act as viral carriers. In order to keep the highest staff movement control levels as well as providing a higher degree of freedom for the staff, a color uniform system, including shoes can be implemented. The color coded system permits spotting at a glance if everyone is in their allocated area. The use of the appropriate uniforms should be compulsory during on site work and uniforms should be removed at the time of duty completion.Staff carrying out activities within different compartments would have to change into the specific uniform allocated to each compartment.

While the risk represented by contaminated clothes and shoes might not the highest, the main role of the uniforms in biosecurity might be considered that of mind setter.

Restrictions in vehicle movement

It seems unlikely for viable viral particles present on vehicles to be able to reach a susceptible host. However, the possibility exists, and vehicle movement should be restricted to specific areas of concern.

In the event of a sanitary emergency, vehicles should be thoroughly cleaned and disinfected in order to minimize potential pathogen transfer between compartments. It is important that excess organic matter and dirt be removed prior to disinfection as most disinfectants are inactivated in the presence of organic matter.


Disinfection is one of the main health management tools in animal rearing and a part of routine practice in biosecurity programmes. Disinfection programs need to be designed for specific purposes. They can be designed to eradicate and exclude specific pathogens or to decrease pathogen load.

The use of chemical products entails the implementation of measures for protection of personnel (skin, eyes and respiratory tract) and cultured animals and for mitigation of negative environmental effects. Disinfectants need to be tested for different applications, particularly if they are to be used with live animals, since their toxicity and efficacy may vary depending on a range of environmental factors (pH, organic matter, salinity, temperatures, etc...). As a general rule, disinfection action is faster at high temperatures, as long as the disinfectant is not decomposed. At low temperatures, the biocidal effect of most disinfectants decreases. For most disinfectants the optimum pH is reported and this should be taken into account when choosing a disinfectant. For instance, quaternary ammonia is more efficient at alkaline pH while iodine and iodophores are more efficient at neutral to acid pH. The presence of organic matter or grease will inactivate most disinfectants. Therefore, cleaning of surfaces before disinfection is critical. Some of the most commonly used disinfectants in aquaculture are listed in Table 5.


As a general rule, manufacturer´s instructions should be strictly followed for the effective use of a disinfectant. These include the concentration and contact time recommended. Not all active ingredients are suitable for every pathogen and all environmental conditions. Particular care should be taken when used for disinfection or treatment of live shrimp at any stage. Trials at different concentrations should be carried out at the recommended doses to evaluate possible toxicity of the product.

One of the most effective disinfection procedures is desiccation. Many bacteria and viruses can not withstand drying. In order to clean a contaminated facility, drying of buildings and ponds may be very cost effective and should always be done between crops as a routine procedure. UV light is a very effective disinfectant particularly when combined with drying. Drying plus direct sunlight (not through a glass window) result in very strong disinfection

Chlorine and iodine are the main disinfectants used in shrimp farming. Both are highly toxic for aquatic animals and, in order to prevent serious accidents that could result from a handling error, it is recommended to neutralize these products with sodium thiosulfate. In order to inactivate chlorine, the amount of thiosulfate should be 2.85 times the amount of chlorine in grams. For iodine, the amount of thiosulfate should be 0.78 times the amount of iodine in grams.

Contrary to fish viruses, there is not much information available on the specific concentrations to deactivate the different shrimp viruses. This is due to the lack of shrimp cell lines where the viability of the virus could easily be evaluated after a disinfecting treatment.

A good review on disinfectants can be found in Danner and Merril, 2006.

4.2.6. Diagnostics

Adequate facilities, equipment and skills or access to them are required to ensure correct diagnosis. Special attention should be given to the diagnostic laboratory capabilities with continuous training and upgrading, validation of techniques and participation in ring tests.

There are two main methodologies required to support a biosecurity program. These are histology and PCR. Histology permits the examination of the tissues and the lesions caused by pathogens. Pathogens cannot be detected prior to the appearance of lesions; therefore it is a low sensitivity technique. Histology is the most suitable method for disease diagnosis in the case of most pathogens. PCR detects the presence of the genome of a specific pathogen. This method is highly sensitive and is most suitable for the screening of clinically healthy animals. Both techniques are necessary and should be used for their specific purposes.

4.2.7. Contingency plans

Sanitary emergencies are likely to occur in any facility and the staff needs to be ready to react to them. For this purpose, a contingency plan that will describe the steps and timing that the staff needs to follow has to be included in the biosecurity strategy. Every biosecurity plan needs to have a contingency plan in recovery order to achieve production in the minimum time possible, at the minimum cost and with minimum disruption. The efficiency of this contingency plan is linked to a rapid initial response and a rapid, effective implementation of biosecurity measures.

The contingency plan will depend on whether the pathogen or the disease detected is exotic or endemic to the facilities, its potential economic impact and whether there is the intention to eradicate the pathogen from the facility or not. The three options in the case of a sanitary emergency are: treatment (only applicable in the case of bacterial or fungal infections), slaughtering of the population (in the case of severe exotic pathogens) or continued production under strict internal biosecurity control (in the case of endemic diseases).

If we refer again to Figure 1 (section 2), we can understand that an epidemic takes time to build up. It starts with infection of the population (segment 1), followed by appearance of clinical signs/mortality (segment 2), that reach a plateau (segment 3) and then a period when clinical signs/mortality decline (segment 4). The earlier an epidemic can be detected, the more efficiently it can be controlled in sanitary and economic terms. Detecting it during segment 1, when there is only infection but no clinical signs, including mortality, would require that a monitoring or surveillance program be running in the facilities.

Clinical signs have to be understood as a warning sign. These are signs of a disease process. This process may be infectious or not (i.e., low oxygen level is not infectious). That can only be discovered later. These clinical signs can range from changes in colour, deformities, slow growth, poor feed conversion rate, low hatching rate, etc... Clinical signs should always be investigated.

The contingency plan should also specify:

  • Diagnostic procedures and, in case of an exotic disease, the diagnostic confirmation,
  • Reporting procedures,
  • Instructions for sanitary slaughtering
  • Instructions for shrimp handling and disposal in case of mortality or sanitary slaughtering,
  • Instructions on the movement of staff, vehicles and animals
  • Instructions for establishment of positive and buffer compartments
  • Disinfection procedures
  • Fallowing procedures

Flagging system

One of the first stages in a sanitary emergency is to create awareness. Staff should be informed of the situation and act in accordance with the contingency plan. In order to provide awareness, a flag system could be established at the affected site. This flag system could use three different colours. Green to report normal operations, yellow to indicate detection of pathogens and red to indicate the presence of clinical signs/mortality. This flag code and its implications are summarized in Table 6.


Every member of the staff needs to be well aware of the appropriate actions that need to be followed when problems are identified. This should be done before emergencies occur. Training personnel during a sanitary emergency is not the most suitable time.

Decision making

As mentioned before, there are three options regarding affected stocks during sanitary emergencies: treatment (only applicable in the case of bacterial and fungal infections), slaughter of the population (in case of severe exotic pathogens) or continued production under strict internal biosecurity control (in case of endemic diseases). Some parameters that need to be evaluated prior to making decisions are the status of historical records and records of the current sanitary situation, whether the emergency is due to the detection of a pathogen or the expression of disease by that pathogen, the potential severity of the disease, shrimp size, mortality pattern and, economic situation of the company and shrimp market value at the time.

Table 7 presents an example of the decision recommended in the case of detection or expression of disease by an exotic pathogen or a pathogen that would affect broodstock. The presence of most of the systemic pathogens causing high mortality would require stamping out of the population. Detection of IHHNV in broodstock would require screening infected animals out of the system, while if detected in the ponds, waiting to see shrimp performance would be the recommended option. However, it should be kept in mind that rearing infected animals may perpetuate infection within a facility. Enteric viruses can be screened out with washing and disinfection of eggs and nauplii. These are likely to affect growth but unlikely to cause a disease outbreak.


When the sanitary background situation is different and the pathogen is endemic to the facility or the stocks are going through an epidemic situation, the arguments for a decision to be made are mostly short term. In these cases, decisions to harvest, continue production or slaughter are the options available.

Criteria for deciding to harvest or slaughter will depend on shrimp size and mortality pattern. These can be analyzed using the matrix in Table 8. Doubt arises when mortality is light in small animals or mortality is heavy in large animals. The decision will need to take into account the climate forecast, pond bottom conditions, the health situation of the rest of the farm, etc….


As mentioned before, harvesting is a high risk activity regardless of the health status of the shrimp in the pond, even more so in the case of an emergency harvest. During an emergency harvest, the harvesting procedure is the same as under normal conditions, but the harvest should be closely supervised by biosecurity personnel in order to confirm its full implementation. Special emphasis should be placed on the collection of organisms at the pond’s discharge point (i.e. using a mesh bag), thorough disinfection of the harvest site and equipment and safe transportation of the product to the processing plant.

Depending on the severity of the disease, soil ponds could be partially filled with water and treated with a short life pesticide (carbamate or trichlorphon) for 1 week before discharging the water. Similarly, in the case of sanitary slaughter of shrimp, water can be treated with a short life pesticide (carbamate or trichlorphon) for 1 week before discharging the water. Dead shrimp should be collected and disposed of at an appropriate site without endangering the environment. If the epidemic is expanding throughout the farm, it might be possible to stamp out infections at not only the affected ponds but also at ones in the buffer compartment in an attempt to stop the pathogen from spreading.

Chain of reporting

Reporting of mortality, clinical signs, abnormal behavior or positive laboratory results needs to be as efficient as possible. This requires a chain of reporting as short as possible with immediate communication. Waiting to see the evolution before reporting should be avoided. Actually, a bonus (incentive) system to encourage close observation of animals and rapid reporting could be established in order to detect disease problems as early as possible.

Case scenarios

The contingency plan section has described general lines of action in the case of a disease outbreak. They should not be taken literally without analyzing the ¨bigger picture¨ such as future weather conditions, health status of the rest of the farm, economic cost of the decision and sustainability of the company. The preparation of a series of case scenarios can help in the sequence of thinking and in the decision making process. However, it should be noted, that the final decision should not be made solely from a sanitary perspective, it should be an economic decision taking into account the present health status and economic situation of the company an well as its long term sustainability.

Simulation exercise

A simulation exercise of the contingency plan should be organized if there has been no need to test it. Periodic testing exercises of a disease outbreak alarm should be carried out in order to test the efficacy of the response. It is suitable to test the system bi-annually if no real alarms occur during that period. Alerts of a supposed disease outbreak can be triggered at different times of day or night to determine the time taken to organize the response and diagnosis.

Some related information will need to be collected, for instance:

  • Previous diagnostic results available for the particular pond or section,
  • Time to deliver diagnostic results,
  • Tracking up and down the shrimp source and
  • Pond conditions during the whole culture cycle: water quality parameters, feeding requirements
4.2.8. Awareness strategy

A biosecurity program is only as good as the staff implementation.

No matter how brilliant a biosecurity plan may be, if not properly implemented, it will fail. The application of biosecurity is a shared responsibility where each individual involved plays a different but critical role in the implementation of the overall program. Successful implementation requires allocating responsibility even at the lower level of workers. Making them understand the purpose and the reasoning behind the different mitigation measures and the consequences of failing to implement them will help workers to carry out their duties.

The importance of training cannot be overemphasized. Adequate staff training staff with special emphasis on workers is crucial for successful implementation. In addition, periodic refresher courses to facilitate disease recognition and understanding of disease transmission and spread would be required. Training through continuous learning rather than a one off exercise can be more efficient.

5. Obstacles

The introduction or enhancement of biosecurity in a facility will surely face some constraints. These need to be identified and explored in detail for later correction.

From personal experience, there are two main constraint levels in the process. One is at the management level and relates to the economic cost of such programs and the other is closer to the worker level and relates to the mentality of the staff.

The economic cost

Unfortunately, biosecurity is frequently seen as an expense rather than an investment. It should be regarded as one more input in the production chain such as the cost of feed, staff or animals.

The objective of a biosecurity plan is to minimize the economic impact of diseases. One of the fundamental rules when developing a biosecurity strategy is that it needs to be economically viable. The benefit of a properly designed and implemented biosecurity plan is to increase production in a sustainable way. The control of acute diseases in order to minimize mortality and the reduction of the impact of chronic diseases that affect shrimp growth are targeted by biosecurity. A producer can always think: why should I invest in biosecurity when I have been able to make a profit growing shrimp until today? That is a fair question but there is a certain degree of risk in this attitude. The degree of success of such a gamble will not be assessed by scientists, pathologists or veterinarians, but by accountants and bankers (P. Smith, personal communication).

Sometimes the need arises to better demonstrate additional proof of efficacy and/or potential economic benefits of the proposed biosecurity plan. The cost of implementing preventive measures or the cost of a therapeutic intervention may be quantifiable in advance. On the other hand, a precise prediction of whether a disease will occur, the extent of the consequent losses, if it does, and the efficiency of any preventive or therapeutic measures can rarely be made. In fact, it is virtually impossible to demonstrate the economic benefits of investing in biosecurity until a real disease outbreak occurs.

Staff mentality

One of the main constraints of implementing a biosecurity plan is the different attitudes workers and managers have towards biosecurity. It is important to understand these different attitudes, as there might be a significant level of resistance to implementation. Mitigation measures often demand additional efforts such as making routine practices more difficult to perform or slaughtering animals that were required to stock ponds or reach production targets. Unless the staff has a clear vision of the risks faced and the need for sustainability of the business, such resistance is expected to be encountered.

Basically, the staff’s attitude towards biosecurity will depend on their personal beliefs, the attitude they perceive from their colleagues, their assessment of the potential consequences and their perception of the benefits. This attitude can be best influenced by education and incentives, although understanding these attitudes and modifying staff behavior can represent an important challenge.

Gunn et al., (2008) carried out an interesting study about people’s attitudes towards biosecurity applied to livestock rearing. Detailed reading of their analysis provides ideas on how to work on improving staff attitude. According to the theory of reasoned action, voluntary behavior is an outcome of two variables: a person’s attitude regarding a particular behavior (personal beliefs and their assessment of the potential consequences) and understanding a “subjective norm” (Figure 2). There are a series of feedback loops from any given behavior to the beliefs regarding the behavior e.g. consequences and normative beliefs.


1. Outcome perceptions. Both positive and negative perceptions can be identified:

  • positive: improved profit, better health, better welfare, professional pride, good husbandry, elimination of “bad” farmers
  • negative: desired outcomes not achievable in the absence of action by others, too costly, too much work, increased bureaucracy, decreased freedom.

2. Importance of outcome:

  • positive: responsibility, only way to have a future in farming, farmers have to take action to maintain control
  • negative: outcome impossible/not achievable, farming has no future.

3. The referents are the main sources of information regarding biosecurity issues: managers, consultants, QC, diagnostic laboratory staff, R&D, scientific literature, media, etc.

4. All referents can have both a positive and a negative influence. One of the most common sources of negative influence is the media

5. The behavioural intent can be modified by penalties imposed for non compliance with norms. However, this is the last and least successful approach to change attitudes.

6. Last remarks

Almost every aquaculture facility has its own set of biosecurity measures as part of its own SOPs. Not that many, have a properly thought out biosecurity strategy. Writing such a plan, critically, analyzing the risks of introduction and spread of pathogens and alternative mitigation measures is an interesting and useful exercise. Much can be learnt by doing so. Once the plan is written, it must be made available to the staff with detailed, comprehensive and practical descriptions of all the actions, procedures, instructions and control measures to be employed.

Once you have designed and implemented a biosecurity plan, it is not the end….. it is not over!! Biosecurity is a work in progress that needs to be reviewed regularly in order to be effective. These reviews (i.e. annual) should incorporate physical, biological and operational changes as well as new knowledge related to the pathogens or diseases.

In our efforts to maintain good health status, one should understand that health is not only the absence of pathogens. Health can only be achieved through the combination of a good rearing environment, good nutrition, good genetic background (no inbreeding, development of resistance or tolerance) and pathogen control through biosecurity. There are no shortcuts or ¨magic bullets¨ to achieve and maintain health or to eliminate health problems.

The author is very grateful to Prof. Tim Flegel and Ms. Camila Parra for their edition and corrections.

7. References

Gunn, G.J., Heffernan, C., Hall, M., Mc Leod, A. And Hovi, M., 2008. Measuring and comparing constraints to improved biosecurity amongst GB farmers, veterinarians and the auxiliary industries. Preventive Veterinary Medicine 84, 310-323.

Cameron, A., 2002. Survey toolbox for Aquatic Animal Diseases-A practical Manual and Software package. Australian Centre for International Agricultural Research, Canberra, 375pp.

Subasinghe, R., McGladderry, S. and Hill, B., 2004. Surveillance and zooning for aquatic animal diseases. FAO technical Paper. No.451. Rome 73p.

OIE, 2006. Aquatic Animal Health Code and Aquatic Animal Health Manual. World Organization for Animal Health. Paris, France, 202p. (Free download at

Danner, G.R., and Merril, P., 2006. Disinfectants, disinfection and biosecurity in aquaculture. In. Aquaculture Biosecurity, prevention, control and eradication of aquatic animal diseases. Scarfe, A.D., Lee, C. and O´Bryen, P. J. Blackwell Publishing. USA. 182p.

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