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Agriculture Biosafety/Biocontainment Manual Table of Contents

GENERAL 

(Animal, Plants, and Aquaculture)

I. Introduction

a. Document Scope and intent: Why an Agriculture Biosafety/Biocontainment 

Guideline?

b. History of introductions/outbreaks of consequences

c. Critical definitions (e.g. Biosafety, Biosecurity, Laboratory Biosecurity and 

Biocontainment)

d. Concept of Biorisk Management with the idea of continual improvement (e.g. 

CEN Workshop Agreement, etc.)

e. How to use the Guidance documents

II. Biorisk Analysis 

a. Biohazard identification, including reverse zoonosis

b. Biorisk assessment (Human health or animal health risks from zoonotic vs. 

economic or environmental risk from GMO’s, exotic plant diseases or plant 

pests).

c. Risk Criteria for establishing ascending levels of biocontainment for veterinary 

pathogens (terrestrial and aquatic) and plant pathogens or plant pests. 

d. Integrated Risk Management process (Biosafety, Biocontainment, Biosecurity, 

other safety and security by reference to other docs (OSHA, select agents, etc.))

e. Risk Communication and Training

f. Describe difference between Individual risk vs public health risk vs. 

environmental or agricultural risk (true agricultural BCLs for agents, or just 

provide a few examples that highlight the disparity between the risk drivers 

captured in the BMBL and risk drivers for agriculture(e.g. FMDV))

ANIMALS

Animals - Terrestrial

1. Livestock (including avian species) and Wildlife

A. Laboratories (containment from lowest to highest) 

 Facility features

o Secondary containment

o Physical vs. seasonal vs. geographical containment

 Protective Equipment

o Primary containment (e.g., BSCs, flexible film isolators)

o PPE

o Other

 Standard Procedures

o Policies and procedures

o Good laboratory practices

 Special procedures

B. Animal facilities containment for both large and small species (containment from 

lowest to highest) of animal models.
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 Facility features

o Secondary containment

o Ventilation Systems

o Physical vs. seasonal vs. geographical containment

o Enhancements for conducting arthropod-borne disease work with vector 

present.

 Protective Equipment

o Primary containment (e.g., filtered animal caging, 3Ag room as primary 

barrier)

 Discussion of caging/containment needs based on different species

o PPE

o Other

 Standard Procedures

o Policies and procedures

o Good facility practices

 Special Procedures

C. Occupational Health Programs: Training, vaccinations of employees, monitoring, prepost exposure prophylaxis.

D. Animal health issues, focus on economic impacts/community risk of agents (make 

reference to human/zoonotic risk already developed in the NIH-BMBL, supplement 

as necessary)

E. Animal Care and Use issues: IACUC, APHIS, Animal Care, Attending Vet 

Responsibilities; Animal Housing and care requirements

F. Viral, bacterial, rickettsial, archaebacterial, prion and other diseases, as well as 

animal/zoonotic select agents, and their impact on agriculture

 Routes of transmission

 Arthropods as disease vectors in animal health

 Wildlife reservoirs of disease

 Persistence of agents in the environment

 Agent Summary Statements relative to species (poultry, cattle, swine, sheep, 

goats, and wildlife; supplement BMBL where necessary)

o Host factors in disease? Immunosuppression/mixed infection? Genetics?

o Production system variables (i.e., confinement housing vs. feedlot vs. 

pasture or free range)

G. Biosafety (reference NIH-BMBL where appropriate, supplement as necessary (e.g., 

enhancement checklists for certain diseases))

H. Decontamination, disinfection and sterilization of laboratory and traditional animal 

facilities, animal cadavers

 Solid vs. liquid waste disposal

 Table of decon agents adequate to each agent

 Agent stability (aerosol droplet vs. hard surface, bridge vectors (physical or 

biological), sylvatic vs. urban cycles, etc.)

I. Veterinary Biosecurity
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 Field vs. Lab (prevention fomite spread to pets/personal livestock) biosecurity

 PPE

 Decontamination, disinfection and PPE as they relate to veterinary 

biosecurity

 Integrated Pest Management Systems

J. Animal handling & restraint (chemical and physical) – highlight differences between 

field and lab; discuss needs of different species commonly used in 

research/diagnostic labs.

K. Animal surgery, necropsy & sampling methods (beyond “1cm blocks in formalin”)

L. Waste management (urine, feces, milk, eggs, tissues, etc.) and carcass disposal 

M. Design and Construction References for livestock and wildlife ABSL-2, ABSL-3, and 

BSL-3Ag

 Veterinary Containment Facilities Design & Construction Handbook 

(International Veterinary Biosafety Working Group

 ARS 242.1

 NIH Guidelines

 Reference livestock select agents and recommended containment in the 

BMBL

 Developed countries vs. underdeveloped countries

 Others

N. Commissioning and Certification of Containment Facilities (make reference to readily 

available information, supplement as necessary)

O. Decommissioning of laboratories, animal facilities, and ancillary facilities/processes 

(e.g., liquid and solid waste treatment facilities)

Animals - Aquaculture (e.g., fish, shellfish)

1. Aquaculture diseases, pests (e.g., parasites), GMOs 

A. Aquaculture health issues, focus on economic impacts, environmental risk, and 

bioaccumulation

B. Viral, bacterial, fungal, protozoa, toxins, and other organisms, and their impact on 

aquaculture

 Routes of transmission

 Disease vectors in fish and shellfish health

 Agent summary statements

o Host factors in disease

o Immunosuppression/mixed infection?

o Zoonotic agents (mostly mycobacterium species)

C. Biocontainment

 primary vs. secondary

 physical vs. seasonal vs. geographical

D. Policies and procedures; Good laboratory and facility practices
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E. Biosafety

F. Aquaculture biosecurity

 Field vs. Lab/Facility (prevention of fomite spread)

 Water quality (monitoring/treating source water and effluent)

 Decontamination and disinfection as they relate to aquaculture biosecurity 

(tank level vs. system level vs. facility level)

 Housing systems (i.e., closed, recirculating systems vs. flow-through systems 

vs. pond systems vs. net pens in open water)

 Collection (and treatment) of effluent/sewage from aquaculture systems prior 

to discharge

 Pond systems – leaching into groundwater, run-off, etc.

 Solid waste management and carcass disposal

G. Decontamination, disinfection and sterilization

 Solid vs. liquid waste disposal

 Decontamination of primary housing systems (tank, water lines, and pump) 

and potential effects on aquaculture species

 Fomite spread in waste handling system

 Table of decon agents and systems (UV radiation) adequate to each 

microbial agent.

H. Design and Construction References for Aquatic containment facilities handling 

aquatic animal pathogens

 Bailey’s Redefining Containment for Aquatic Facilities

 Canada’s Containment Standards for Facilities Handling Aquatic Animal 

Pathogens

 Others

I. Commissioning and Certification of containment systems and facilities (international 

and national standards)

J. Decommissioning of facilities (laboratories, animal facilities, decontamination or 

waste treatment facilities).

PLANTS

Plants - Terrestrial

1. Plant diseases, pests, arthropods, nematodes, and noxious weeds.

A. Laboratories (containment from lowest to highest)

 Facility features

o Secondary containment

o Physical vs. seasonal vs. geographical containment

o Biocontrol agents for plants, arthropods, and nematodes

 Protective Equipment

o Primary containment (e.g., BSCs, growth chambers, other

o PPE

o Other

 Standard Procedures
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o Policies and procedures

o Good laboratory practices

 Special procedures

B. Greenhouse and quarantine facilities (containment from lowest to highest)

 Facility features

 Secondary containment

 Ventilation Systems (particulates and aerosols)

 Physical vs. seasonal vs. geographical containment

 Biocontrol agents for plants, insects, nematodes. Enhancements for 

conducting arthropod-borne disease work with vector present.

 Protective Equipment

 Primary containment (e.g., filtered or screened insect caging)

 Discussion of caging/containment needs based on different species

 PPE

 Other

 Standard Procedures

 Policies and procedures

 Good facility practices

 Good greenhouse and/or quarantine practices

 Pesticide Policies

 Special Procedures

C. Occupational Health Programs

D. Biosafety (impact on the immunosuppressed and/or sensitive populations 

(respiratory sensitivities to plant allergens, molds) and mammalian toxins produced 

by plants as in the Laboratory Biosafety Principles and Practices book and other 

sources)

E. Training, vaccinations of employees, monitoring, pre-post exposure prophylaxis. 

(arthropod and pathogens)Plant health issues, focus on economic 

impacts/community risk (foodborne risks to consumers, impact on specific subgroups 

like the immunosuppressed or immunocompromised)

F. Viroids, virusoids, viruses, bacterial, fungal, protozoa, nematodes, insects, and 

mites, as well as plant select agents, GMOs/transgenic organisms, invasive species, 

and parasitic plants, noxious weeds and their impact on agriculture

G. Routes of transmission

H. Arthropods and nematodes as disease vectors in plant health

I. Agent summary statements

J. Host factors in disease? Immunosuppression/mixed infection?

K. Role of mycorrhizae/symbiosis in plant ecology and health
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L. Grey Book” style document for plant diseases

M. Decontamination, disinfection, and sterilization of laboratory, greenhouse and 

quarantine facilities

 Solid vs. liquid waste

 Maintenance and verification of the ventilation/air filtration system 

 Table of decon agents and chemical compatibilities

N. Plant biosecurity

 Field vs. Lab (prevention of fomite spread or arthropods “hitchhiking”

 Decontamination, disinfection and PPE as they relate to plant biosecurity.

o Agent stability – quarantine, field decon (solid turn over for sunlight 

exposure), crop rotation or spraying for pests/plant pathogens

O. Design and Construction References for screen houses, BL1-P through BL4-P, with 

or without enhancements, or greenhouses, growth rooms, fumigation chambers, and 

quarantine facilities

 ARS 242.1 (containment greenhouses, greenhouse)

 APHIS’ Containment Guidelines 9 e.g., arthropods, others)

 A Guide to Plant Containment (Dan Adair and Ruth Irwin)

 NIH Guidelines/GMO plant containment

 Containment Facilities and Safeguards for Exotic Plant Pathogens and Pests 

(American Phytopathological Society) (Out of print)

 Reference plant select agents and recommended containment

 Developed countries vs. underdeveloped countries. Food security issues 

related to biosecurity

 Others

P. Commissioning and Certification of Containment systems and Facilities (make 

reference to readily available information, supplement as necessary.

Q. Decommissioning of laboratories, greenhouses and quarantine facilities, and 

ancillary facilities/processes (e.g., liquid and solid waste treatment facilities).

Plants - Terrestrial Pest Plants (Parasitic)

1. Five genera (excepting native or widespread spp.) are currently regulated as Federal 

Noxious Weeds Others may be regulated as plant pests (7 CFR 330) whether or not listed 

as FNWs

A. Policies and procedures; Good laboratory and facility practices.

B. Biosafety

C. Biosecurity

 Field vs. Lab/Facility (prevention of spread)

 Decontamination and disinfection as they relate to biosecurity

D. Decontamination, disinfection and sterilization

 Solid vs. liquid waste disposal

 Table of decontamination agents adequate to each plant taxa.
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E. Design and Construction References for Aquatic containment facilities handling aquatic 

pest plants

 Parts of Bailey’s Redefining Containment for Aquatic Facilities applicable to 

aquatic plants

 Others

F. Commissioning and Certification of containment facilities “Guidelines for containment of 

Federal Noxious Weeds”

G. Decommissioning of facilities

Plants - Aquatic Plants 

1. Aquatic Pest Plants (19 taxa of aquatic Federal Noxious Weeds (FNW))

A. Health issues, potential propagules, contaminants or toxins in the water.

 Focus on economic impacts/environmental risk 

B. Biocontainment

 primary vs. secondary

 physical vs. seasonal vs. geographical

C. Policies and procedures; Good laboratory and facility practices

D. Biosafety

E. Biosecurity

 Field vs. Lab/Facility (prevention of spread)

 Decontamination and disinfection as they relate to biosecurity

F. Decontamination, disinfection and sterilization

 Solid vs. liquid waste disposal

 Table of decontamination agents 

 Design and Construction References for Aquatic containment facilities 

 Parts of Bailey’s Redefining Containment for Aquatic Facilities applicable to 

aquatic plants

 Others

G. Commissioning and Certification of containment facilities (International and national 

standards, In the USDA-APHIS permit website we have a document: “Guidelines for 

containment of Federal Noxious Weeds”.)

H. Decommissioning of facilities

APPENDICES

I. Required Competencies, including a field skill set and lab skill set

a. Guidelines for Biosafety Laboratory Competency

b. OIE Veterinary Competencies

c. Other
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II. Pest Control and Management (for laboratory, animal rooms, growth chambers, and 

greenhouse facilities).

III. Fieldwork Practices (animal vs. plant, use of biocontrol agents, netting, physical 

separation (minimum separation distances))

IV. Animal and Plant Health Services Permits