1 **Ag riculture**  **Biosafety /**  **Biocontainment Manual Table of Contents GENERA** **L** (Animal , Plants, and Aquaculture) I. Introduction a. Document Scope and intent : Wh y an Ag riculture 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 W orkshop Agreement, etc.) e. How to use the Guidance documents II. Biorisk Analysis

a. Bioh azard 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 B C Ls for agents, or just provide a few examples that highlight the disparity between the risk d rivers captured in the BMBL and risk drivers for agriculture (e.g. FMDV)) **AN IMA** **L S**  **Animal s**  **- Terrestrial**  1. Livestock (including avian species) and Wi ldlife 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.2  Facility features o Secondary containment o Ventilation Systems o Physical vs. seasonal vs. geographical containment o Enhancements for conducting arthropod - borne d isease 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, p rion 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  Wi ldlife 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 Biosecurity3  Field vs. Lab (preve ntion 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 b etween 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 W orking Group  ARS 242.1  NIH Guidelines  Reference livestock select agents and recommended containment in the BM BL  Developed countries vs. underdeveloped countries  Others N. Commissioning and Certification of Containment Facilities (make reference to readily available information, supplement as necessary) O. Decommission ing of laboratories, animal facilities, and ancillary facilities/processes (e.g., liquid and solid waste treatment facilities) **Animal s**  **- 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 practices4

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). **PLA NTS**  **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 Procedures5 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 immunocom promised) 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 health6

L. Grey Book” style document for plant diseases M. Decontamination, disinfection, and sterilization of laboratory, greenhouse and quarantine facilities  Solid vs. liquid waste  Ma intenance 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 green houses, 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 W eeds 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.7

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  Ot hers F. Commissioning and Certification of containment facilities “Guidelines for containment of Federal Noxious W eeds” G. Decommissioning of facilities **Plants -**  **Aquatic Plants** 1. Aquatic Pest Plants (19 taxa of aquatic Federal Noxious W eeds (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 standard s, In the USDA-APHIS permit website we have a document: “Guidelines for containment of Federal Noxious W eeds”.) H. Decommissioning of facilities **AP PENDICES**  I. Required Competencies, including a field skill set and lab skill set

a. Guidelines for Biosafety Laboratory Competency b. OIE Veterinary Competencies c. Other8

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 separat ion (minimum separation distances)) IV. Animal and Plant Health Services Permits