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Criteria for Establishing Premises Freedom for Pathogens of 

Concern in Aquaculture Settings

[National Aquaculture Health Plan & Standards (NAHP&S) Health Inspection Option] 

I. Authority 

II. Definitions

III. Steps to Establishing Premises Freedom 

IV. Maintaining Premises Freedom

V. Additional Guidance on Premises Freedom 

I. Authority 

APHIS is the Competent Authority for protecting and promoting the health of farm-raised aquatic 

animals. APHIS oversees this premises freedom definition and the designation of facilities that 

meet these premises freedom requirements. Additionally, under the National Aquaculture Health 

Plan & Standards (NAHP&S), APHIS provides official health inspection options to certify the 

health of farm-raised aquatic livestock and support the safe and secure movement of aquatic 

animals, one of which is premises freedom from pathogens of concern. 

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II. Definitions 

• Approved laboratory: A laboratory with oversight from APHIS for conducting pathogen testing 

for the purposes of official surveillance, testing, and export requirements.

• Approved assay: A laboratory procedure which has been reviewed and approved by APHIS to 

test for the presence of a specific pathogen for the purposes of official surveillance, testing, and

export requirements.

• Farm-raised: Aquatic animals reared in controlled environments with intentional interventions to 

enhance animal production through feeding, husbandry, and protection from predators with an 

implied ownership throughout the rearing period. Farm-raised animals may include animals 

reared for the purposes of enhancing wild stocks, restoring declining wild species or populations, 

or recovering wild threatened and endangered species and those animals are privately owned until 

purchased and legally released by public or private entities.

• Premises: Includes a tract of land or water, and all its buildings, maintained by a single set of 

services and personnel for aquaculture. 

• Pathogen of concern: Any infectious pathogen that causes significant impact to aquaculture, 

aquatic animal production, and/or trade or movement. This typically includes, but is not limited 

to, pathogens listed by the National List of Reportable Animal Diseases (NLRAD), World 

Organisation for Animal Health (OIE), and emerging pathogens.

• Risk pathway: A route by which pathogens of concern might be introduced onto a premises.

These typically include animals, water, feed, vectors, and fomites. 
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• Surveillance: A systematic series of evaluations to determine the health status of a population or 

region using observational, passive, and targeted approaches in conjunction with test results. 

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III. Steps to Establishing Premises Freedom

For a premises to establish premises freedom for a specific pathogen of concern, it must complete 

steps 1-5 over two consecutive years as described below. Recognition of premises freedom will 

be determined by APHIS and a letter will be issued.

1. Identify the pathogens of concern to the premises and decide whether premises freedom is 

needed. 

a. A premises may decide that establishing and maintaining premises freedom for a given 

pathogen of concern will support their business needs. For example, premises freedom 

may be required for some international export markets including the APHIS Registered 

Aquaculture Export Facility (RAEF) inspection program, and/or as part of an APHIS 

program such as the Comprehensive Aquaculture Health Program Standards (CAHPS). 

b. The pathogen(s) of concern may vary based on the business needs. 

i. For APHIS programs (such as CAHPS) or as part of a facility’s aquatic animal 

health program, the pathogens of concern may be facility dependent. 

ii. For international export markets, the pathogens of concern may vary by the 

destination country. The export requirements to a given country are posted on 

APHIS’ IRegs for Live Animals resource page. 

2. Verify if a certain type of testing laboratory must be used, and whether sampling must be 

conducted by an accredited veterinarian (AV). 

a. The type of testing laboratory depends on the purpose for establishing premises freedom. 

i. For enrollment in an APHIS program such as CAHPS, testing must be done at an 

APHIS-Approved laboratory (see live aquatic animal export testing guidance). 

ii. For international export, the testing laboratory type depends on the destination 

country. The guidance for live aquatic animal export testing is posted here (live 

aquatic animal export testing guidance). 

b. Whether sampling must be conducted by an accredited veterinarian depends on the 

purpose for establishing premises freedom. 

i. For enrollment in an APHIS program such as CAHPS, sampling must be 

conducted by or under the supervision of an accredited veterinarian or other 

APHIS approved collector. 

ii. For international export, sampling must be conducted by or under the supervision 

of an accredited veterinarian or other APHIS approved collector. 

iii. Use the APHIS National Veterinary Accreditation Program (NVAP) self-search 

tool to find a local accredited veterinarian. 

3. The premises must have a written biosecurity plan that addresses all the potential pathways 

of introduction for the pathogens of concern. 

a. A risk evaluation should be conducted by the facility in consultation with APHIS to 

determine the potential pathways of introduction based on the type of animals, the 

production method used, and their end use. 
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b. Once these pathways are identified, the written biosecurity plan must address the 

biosecurity practices in place to mitigate pathogen introduction through these routes. At a 

minimum, the written biosecurity plan must address the following pathways (see i.

through iv. below), with associated activity logs, available for review (e.g., annual 

inspections and upon request), ensuring that biosecurity practices are implemented and 

followed. 

i. Animals

1. Only animals of equal or higher health status are allowed onto the farm

(e.g., animals are sourced from other premises that meet APHIS’ 

premises freedom for at least the same diseases of concern as the

receiving farm).

2. Animals must be separated by life stage on the farm and/or adhere to allin all-out management practices.

ii. Water

1. Incoming water originates from a secure water source free from 

pathogens of concern, such as well or ground water, OR

2. Incoming water is treated and/or managed in a manner to prevent the 

introduction of pathogens of concern.

iii. Feed

1. Feed ingredients DO NOT contain pathogen(s) of concern for susceptible 

or vector species.

iv. Vectors/Fomites

1. Cleaning and disinfection protocols are appropriate for pathogens of 

concern.

2. Fallowing is instituted for “hard breaks” between year classes/life stages, 

as appropriate for pathogens of concern. 

3. Parasite, pest, and predator management as appropriate for pathogens of 

concern. 

c. The biosecurity plan must be reviewed and approved by APHIS on an annual basis.

4. Identify the number of distinct populations that exist on the premises.

a. Before testing can begin, it is important to know if there is more than 1 population on the 

premises. 

i. Most premises contain a single population of animals. While there may be 

different parts of the premises (e.g., tanks, grow out ponds, etc.) there is contact 

between the animals such as shared waters, structures, environment, aerosols, 

personnel, or equipment.

ii. In some cases, there may be more than one population on the premises because 

they are epidemiologically distinct. This means that the independent populations 

do not co-mingle with others via direct or indirect means such as shared water, as 

above. 

b. Testing must be conducted separately for each distinct population for all pathogens of 

concern. 
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5. Develop an annual surveillance plan (i.e., annual testing of the pathogens of concern) for 

each distinct population (see #4 above). 

If the purpose of establishing premises freedom is for enrollment in an APHIS program such as 

CAHPS, or international export, then the official health surveillance sampling plan must be 

reviewed and approved by APHIS prior to sample collection. 

a. Sample size: a proper surveillance plan begins with calculating the number of animals to 

sample from each population on the premises. 

i. There are several pieces of information that need to be gathered for the sample 

size calculation. These include the diagnostic sensitivity of the assay being used, 

the desired confidence level of detecting an infected animal, and the desired 

pathogen prevalence detection threshold for the population. 

1. Testing laboratories should provide the diagnostic sensitivity (as a 

percentage) of the assay if known. If unknown, and the assay is APHIS 

approved, assume the diagnostic sensitivity is 85%.

2. The confidence level of detecting an infected animal should be 95%.

3. The pathogen prevalence detection threshold should be 2% or lower.

4. This information is then entered into the “Animal Sample Size 

Calculator” posted here under “Open the Animal Size Calculator.”

a) Enter the diagnostic sensitivity value (percentage) of the assay 

into the “Diagnostic Test Sensitivity” box in the top left corner. 

b) Enter 95% into the “Confidence Level” box in the top left 

corner. 

c) Locate the 2.00% “Prevalence of Disease” column in the table 

and locate the “Herd or Flock Size” row in the table which 

corresponds with the population size. Where that column and 

row intersect equals the minimum number of animals to sample. 

2. If animals will be pooled for testing, the sample size will need to be 

revised (see point c below).

b. Animals for sampling: certain animals should be sampled to increase the likelihood of 

detecting the pathogens of concern (if present). 

i. Sampling should represent the entire population. In general, the collected 

samples should include a mixture of all life stages in the population. Special 

consideration should be given to sick (moribund) animals when available, and 

sampling certain life stages or during seasons when environmental conditions 

offer the best opportunity to detect the pathogen. 

ii. If the whole animal is not being sampled, then the tissue which is most likely to 

contain the pathogen of concern should be collected. 

c. Pooling of samples: in some cases, pooling of samples prior to testing is allowed as 

described below. 

i. Pooling of samples should consider the specific pathogen assay, species, and 

purpose of testing. If pooling was performed, it should be noted on the laboratory 

report. 

1. For international export, pooling requirements may depend on the 

destination country. 

ii. If pooling is allowed, it should be performed by the testing laboratory and 

the criteria listed below must be followed:

1. Most adult animals (or their target tissues) may be pooled in sets of up to 

five animals/tissues per pool. 

2. Smaller animals may be pooled in larger quantities if needed to meet 

minimum tissue weights for laboratory processing; however, the 

laboratory should aim to pool the fewest number of animals as possible 
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to obtain the required amount of tissue needed for initial and 

confirmatory testing. 

3. For shrimp pooling procedures, please request information using the 

following email: VSAquacultureHealth@usda.gov. 

d. Frequency of sampling: sampling as part of the surveillance plan must occur regularly to 

assure the premises is free of the pathogens of concern.

i. Annual surveillance plan may consist of either: 

1. At least two surveys per year with a minimum of three or more months 

apart, or 

2. More frequent (e.g., monthly) surveys equating to the same annual 

number of tests if approved by APHIS in advance (e.g., through 

CAHPS). 

ii. This sampling plan must be conducted over at least two consecutive years to 

establish premises freedom for the pathogens of concern. All test results must be 

negative for the pathogens of concern. 

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IV. Maintaining Premises Freedom 

For a premises to maintain premises freedom for a pathogen of concern, it must meet all the “Steps to 

Establishing Premises Freedom” in Section III above, as well as ongoing testing, health checks, and 

reporting as described below. 

1. Once premises freedom is established for a given pathogen, the sampling plan must continue 

without any breaks in sampling frequency to maintain premises freedom. 

2. Recognition of premises freedom will be determined by APHIS and a letter will be issued. 

3. All test results must be negative for the specific pathogen(s) of concern for which premises 

freedom is being sought. 

4. The health status of the population must be continually monitored. If morbidity or mortality rates 

exceed the thresholds, then disease investigations must be initiated through the facilities’ 

accredited veterinarian to determine what level of response is required. 

a. If there is a suspicion or a detection (i.e., positive test result) of a pathogen of concern, 

then it must be immediately reported to APHIS (see Section V. below). Pathogens of 

concern include those listed by the NLRAD, OIE, and emerging pathogens. 

5. All documents related to premises freedom must be maintained for at least 3 years and available 

to APHIS upon request. 

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V. Additional Guidance on Premises Freedom

Specific questions regarding the establishment and/or maintenance of premises freedom should be 

emailed directly to: VSAquacultureHealth@usda.gov. 

 In the event of a suspect or positive detection of a pathogen of concern, contact APHIS immediately 

(VSAquacultureHealth@usda.gov). APHIS will then work with the premises to conduct a disease 

investigation and determine if there is a breach in premises freedom status.