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UNITED STATES DEPARTMENT OF AGRICULTURE 

 ANIMAL AND PLANT HEALTH INSPECTION SERVICE 

PLANT PROTECTION AND QUARANTINE 

 CONTAINMENT FACILITY GUIDELINES 

 FOR FUNGAL PLANT PATHOGENS

[Includes fungal-like organisms: i.e., Phytophthora, Pythium, and other Oomycetes] 

(Revised Feb. 2010) (Fungal Pathogens)
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CONTAINMENT GUIDELINES FOR FUNGAL PLANT PATHOGENS 

CONTENTS 

I. PURPOSE OF THIS DOCUMENT 

II. CONSTRUCTION STANDARDS FOR THE ENTIRE CONTAINMENT STRUCTURE

A. Location and Identification 

B. Floor Plan 

C. Walls, ceilings, and floors 

D. Windows 

E. Doors 

F. HVAC system 

G. Electrical system 

H. Plumbing system 

I. Vacuum Cleaning systems 

J. Communication system 

III. CONSTRUCTION STANDARDS FOR SPECIALIZED ROOMS

A. Greenhouses

B. Vestibules

C. Showers and Restrooms

IV. EQUIPMENT STANDARDS

A. Benches, tables and other furniture

B. Sterilization or Decontamination equipment

C. Cages and Containers

D. Biosafety Cabinet

V. OPERATIONAL STANDARDS 

A. Containment Director 

B. Authorized Personnel 

C. Apparel 

D. Personal Cleanliness 

E. Facility Cleaning and disinfecting 

F. Opening and Handling packages 

G. Starting, Growing, and Storing cultures 

H. PPQ Regulatory Requirements 
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CONTAINMENT GUIDELINES FOR FUNGAL PLANT PATHOGENS 

I. PURPOSE OF THIS DOCUMENT: 

These guidelines are a reference to help you (a scientist of a state, federal, or commercial entity) design, build, 

maintain, and operate a containment facility for non-indigenous fungal plant pathogens. These guidelines are not 

intended for use with plant pathogenic bacteria, viruses, protozoa and nematodes. Widely distributed indigenous 

fungal plant pathogens may not require a containment facility. These guidelines are not intended for pathogens and 

vectors of medical and veterinary importance. If there is doubt as to the applicability of guidelines to specific 

organisms, contact Containment Facility (CF), or Pest Permit Evaluation (PPE) scientific personnel for appropriate 

guidance. 

During inspections or reinspections of your facility, USDA, APHIS, PPQ personnel will review these guidelines and 

any risk mitigation instructions that may accompany your permit. When your facility meets containment standards 

and risk mitigation instructions it will be considered "adequate" from a containment standpoint; permits may then be 

issued. 

The inspection and permitting procedures of the USDA-APHIS-PPQ are intended to prevent the release of 

nonindigenous plant pests to the environment of the United States. Accidental or purposeful release of these 

organisms is a violation of the PLANT PROTECTION ACT and is subject to civil and/or criminal penalties, loss of 

permits, and destruction of valuable cultures. 

Components of this Document: 

Your containment facility must meet the “Standards” listed in the grey, shaded boxes. To help you meet these 

standards, ask biotechnology industries, university Biosafety committees, and/or contractors for research hospitals 

and other research institutions to recommend specialized professional contractors. Professionals know state, local 

and federal laws that regulate construction, including the installation of emergency doors, incinerators, air intake and 

exhaust ducts, emergency lighting, plumbing, and many other features. PPQ’s permit specialists have little or no 

knowledge of these laws. 

N.B. Notify PPQ of any structural changes prior to implementation, the development of blueprints, signing of 

construction contracts, start of construction, etc. 

 [ Other useful containment references (non-USDA-APHIS) are: 1) "Containment Facilities and Safeguards for 

Exotic Plant Pathogens and Pests ". 1999. R. P. Kahn and S. B Mathur. (eds.) APS Press, St. Paul, MN; 2) "A 

Practical Guide to Containment (Plant Biosafety in Research Greenhouses) ". Adair, D. and R. Irwin. 2008 (revised 

edit.).Information Systems for Biotechnology, Virginia Tech, Blacksburg (http://www.isb.vt.edu); 3) "Containment 

Standards for Facilities Handling Plant Pests ". 2009. (1 st edition) Canadian Food Inspection Agency, Office of 

Biohazard Containment and Safety, (http://www.inspection.gc.ca/english/sci/bio/plaveg/placone.shtml )]. 

The “Suggestions” listed under each Standard are methods or equipment that are commonly used at this time to 

accomplish each containment standard. The design, construction and operation of your containment facility may 

vary, depending on the organisms you wish to contain, your research objectives, the functionality of your equipment 

and structural components, and your location. Again, we recommend professional advice on all design issues. 

Safety of facility personnel should not be compromised by containment requirements. Emergency exits 

should not be blocked by equipment; their operation should not be obstructed with tape or caulk. 
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We encourage Good Laboratory Practices (GLP) in all facilities; however the standards and suggestions listed here 

only cover containment. Cross contamination of cultures within the containment may or may not signify poor 

containment. 

USDA, APHIS, PPQ welcomes alternatives that are proven to meet or exceed the standards. To insure timely 

permitting, please review this document, and research design alternatives. Once design options are narrowed, call or 

fax PPQ’s Containment Facility Staff at (301) 734-5304 or FX (301) 734-5392 and continue discussions as the 

facility is planned and built. 
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II. CONSTRUCTION STANDARDS FOR THE ENTIRE STRUCTURE

CONSTRUCTION STANDARD A. Locate the facility in areas with minimal human, agricultural and 

environmental risk. Identify the facility as dedicated and secure. 

SUGGESTIONS: 

1. Locate the facility in areas relatively free of agricultural zones, high-risk microclimates (e.g.. known flood

zones) or other high-risk areas.

2. If possible design the containment facility as a separate, dedicated building. If this is not possible, design and

build to prevent pest escape.

3. Install a 15 foot- wide buffer strip of gravel and/or pavement from the foundation and around the containment

building(s). This area should not support plant growth.

4. Install a fence 6 ft or higher around the facility.

5. At the main entry to containment, post:

 Containment director/ containment officer name and contact numbers.

 A sign stating “ACCESS IS BY AUTHORIZED PERSONNEL ONLY”.

 Emergency telephone numbers.

CONSTRUCTION STANDARD B. Design the floor plan to prevent escape of the enclosed organism(s). 

SUGGESTIONS: 

1. Install one primary entry/exit.

2. Install a shower at the primary entrance.

3. If local building code allows, install vestibules for emergency exits. Install a vestibule at entries or exits

that lack a shower.

4. Build restrooms outside of containment areas. However, if restrooms must be built inside a containment

room, use the same construction standards used throughout the facility and place the restroom next to low

risk areas.

5. Build offices outside of containment areas.

6. Install self-closing doors throughout the containment structure(s). Install exterior doors that lock.

7. Install a central closet for cleaning supplies.

8. Insure negative air pressure throughout the facility.

9. Insure air moves from the least to most hazardous rooms.
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CONSTRUCTION STANDARD C. Construct walls, ceilings and floors that are impenetrable to the enclosed 

organisms, and withstand repeated cleaning and decontamination.

 

SUGGESTIONS: 

1. Construct the walls and ceilings with building materials that resist moisture and withstand repeated 

decontaminations with bleach or other caustic solutions. 

2. Paint the ceilings and walls with a light-colored, washable paint. 

3. Install floors that are impenetrable to the organism and withstand repeated cleanings. 

Monolithic (in one-piece) floors, e.g. poured concrete, asphalt tile, chemically resistant paint etc. are desirable. 

Wood floors are not acceptable. 

4. Install floor drains to collect liquid wastes for sterilization. 

5. Seal junctions, holes or penetrations of walls, ceilings, and floors with plaster, caulk, or equivalent materials. 

6. Suspended or dropped ceilings are not acceptable. 

CONSTRUCTION STANDARD D. If windows are necessary, install Windows impenetrable to the enclosed 

organisms. 

SUGGESTIONS: 

1. Install breakage resistant glazing (Plexiglas, Lexan, etc). 

2. Install windows that do not open. 

3. Seal joints between the windowsills, frames, etc. and walls with appropriate materials. 

4. Store extra transparent panels nearby for emergency use. 

CONSTRUCTION STANDARD E. Install Doors that contribute to the security of the facility. 

SUGGESTIONS: 

1. Install self-closing, steel doors with magnetic gaskets throughout the containment structure(s). 

2. Install exterior doors that lock. 

3. Install thresholds and gaskets that seal the exterior and interior doors with their frames. The space between 

seal and doorframe should not exceed 6.3mm (0.250 inch). 

4. Emergency doors 

 Post signs on the exterior and interior of emergency exits stating USDA, APHIS Containment Facility 

Emergency Exit Only. 

 Insure emergency doors are not commonly used as an entrance (remove exterior handles, use doors 

with interior or internal hinges, etc.). 

 Install audible alarms that activate when emergency exit doors are opened 

 
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CONSTRUCTION STANDARD F. Design and install an HVAC System (Heating, Ventilation and Air 

Conditioning) that prevents escape of the contained organisms. 

SUGGESTIONS: 

1. If possible, install a closed HVAC system dedicated to the containment areas. If not possible, then install 

filters to prevent organism escape from containment areas to areas or buildings outside of containment. 

2. Install tandem double HEPA filters (or their equivalent) rated at 99.97 percent efficiency for all particles 

0.3 microns and larger. 

3. Prefilters (i.e., 30% and 85% ASHRAE) can be installed ahead of HEPA filters to protect the HEPA filters. 

4. The HEPA filters must be changed annually or when the maximum level of filter’s resistance exhibited by 

an indicator (magnehelic gauge). HEPA filters should be recertified annually, and after they are changed. 

5. All filters should be sterilized before disposal when they are changed. 

6. Airflow should be from the least hazardous areas, offices and administrative area (plus 0.05 in. wg.) 

through the corridors and clean change room (zero (0) pressure) and then through the contaminated change 

room (-0.05 in. wg.) to the hallway (-0.05 in. wg.), then into the laboratories (-0.10 in. wg.) and into the 

greenhouse (-0.15 in. wg.). 

7. Air locks should be used to separate areas of different levels of potential contamination. Air locks are not 

generally ventilated, but they should be decontaminated whenever necessary. 

8. For measuring air pressure levels, differential pressure transducers may be installed in the system. The 

system is assembled to make certain that if there is a malfunction in the negative air pressure system, the 

transducers will trigger an alarm. 

9. To maintain negative air pressure in the facility, a back up source of electricity is needed to insure 

continuous power to the air handling system when the main power source is out of order. 

10. Seal connections in air ducts, plenums, etc. with caulk or an equivalent material. 

11. Seal vents to interior surfaces with caulk or an equivalent material. 

CONSTRUCTION STANDARD G. Design and install an Electrical System that maintains containment features 

under normal and emergency situations and is impenetrable to the contained organisms. 

SUGGESTIONS: 

1. Install an alarm to indicate power failure. 

2. Install an alternative power source (generator, battery bank, etc.) for use when normal power is lost or 

interrupted. 

3. Install weatherproof electrical boxes, receptacles, light fixtures, switches, etc. 

4. Seal electrical boxes, lighting, switches, wiring, conduit, etc, with appropriate materials (caulk, foam, etc,) 

that are impenetrable to the contained organisms and withstand repeated decontaminations with bleach or 

other caustic solutions. 
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CONSTRUCTION STANDARD H. Design and install a Plumbing System to contain the organisms and remove 

liquid wastes. 

SUGGESTIONS: 

1. Sewer vents should be fitted with HEPA filters to prevent escape of fungal spores.

2. Collect and sterilize effluents from sinks, floor drains, restrooms in the containment area, etc. with steam

heat or its equivalent before releasing them into the sewer system.

CONSTRUCTION STANDARD I. If Vacuum Systems are used for cleaning, Install Vacuum Systems that 

prevent the escape of the contained organisms. 

SUGGESTIONS: 

1. Use vacuum appliance only in facility.

2. Autoclave or sterilize vacuum filters and waste before disposal.

CONSTRUCTION STANDARD J. Install Communication System that allows communication between the 

interior and exterior of the facility and prevents organism escape. 

SUGGESTIONS: 

1. Install a telephone(s) or intercom system.

2. Install a computer (LAN, modem, etc.) or Fax machine to allow for communication and data transfer to and

from the facility.

III. CONSTRUCTION STANDARDS FOR SPECIALIZED ROOMS.

CONSTRUCTION STANDARDS FOR SPECIALIZED ROOMS A. Build Greenhouses with security and 

containment features. 

1. The greenhouse should not be placed on top of another building. Increases in height of the structure

increase the possibility of wind damage. Consider placing windbreaks (fences, walls, hedges, trees) if

necessary beyond the buffer area to protect against storms and high winds.

2. Construct the foundation of concrete, concrete block, brick, or similar material.

3. Extend the foundation below the soil line to insure a permanent and stable structure. Build the foundation at

least 3ft. above the soil line.

4. Construct greenhouse floors of concrete or other materials that are impervious to the contained organisms

and can withstand repeated disinfecting with caustic liquids. There should be provision for collection and

decontamination of liquid runoff.
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5. Install a frame strong enough to support the translucent walls and ceilings and resist local environmental 

conditions such as storms, snow loading, high winds, etc. 

 Install translucent wall and ceiling materials strong enough to guarantee the security of the facility. 

Plexiglas, Lucite, lexon, safety glass, and wire-reinforced glass are acceptable. Polyethylene, vinyl or 

plastic sheeting is NOT acceptable.

 Seal the translucent panels to the frame with caulk or appropriate materials on the inside and outside 

surfaces. 

 Consider the installation of screens over the roof to protect it from hail. 

 Consider the installation of an alarm system to detect broken glazing panels or other breaches of 

containment. 

6. Seal joints between the greenhouse and other containment rooms with caulk or other suitable material. 

7. If containment greenhouse is detached from the primary containment facility, install a vestibule at each 

door. (See specialized room section on Vestibules.) 

8. Install doors between the greenhouse and the rest of the facility that close completely, and seal to their 

frames. 

9. Insure the HVAC system can be turned off to allow glasshouse fumigation. 

10. The HVAC system and ducts for the greenhouse should be the designed as for the main containment 

facility with HEPA filters and negative air pressure. 

11. The greenhouse must be tested for leaks upon new construction, when repairs are performed, and on an 

annual basis. 

CONSTRUCTION STANDARDS FOR SPECIALIZED ROOMS B. Vestibules 

SUGGESTIONS: 

1. Install a vestibule in each entrance and /or exit. (Have contractor check local construction codes on 

vestibules at emergency exits, as they may be prohibited.) 

2. Shower rooms can count as a vestibule for the main entrance (see restroom construction). 

3. Design vestibule to be at least 6 feet long from door threshold to door threshold. Doors should be designed 

so that they cannot be opened at the same time. 

 

CONSTRUCTION STANDARDS FOR SPECIALIZED ROOMS C. Install Showers and Restrooms to 

prevent organism escape. 

SUGGESTIONS: 

1. Place showers/ restrooms near lowest risk rooms. 

2. Insure thresholds and gaskets of restroom doors seal to their frames. 
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IV. EQUIPMENT STANDARDS

EQUIPMENT STANDARD A. Use Benches, Tables and Other Furniture that are easy to inspect and clean. 

SUGGESTIONS: 

1. Install work surfaces and laboratory furniture (bench tops, etc.) that are seamless (or monolithic)

impervious to water, and resistant to chemicals and heat.

2. Insure spaces between benches, wall cabinets, and equipment are easy to clean and inspect.

3. Dedicate cleaning equipment (mops, brooms, buckets, etc.) for use only in the containment area, and store

it in the containment area.

EQUIPMENT STANDARD B. Use equipment to Sterilize contained organisms, soil, plant material, solid waste 

or Decontaminate solid waste and contaminated or infested articles before removing it from the facility. 

SUGGESTIONS: 

1. Install an autoclave. Double-door pass-through model is recommended. Conduct tests annually to evaluate

effectiveness of autoclave.

2. Install a gas sterilizer for articles that would be damaged by steam. Double-door pass-through model is

recommended. Conduct tests annually to evaluate effectiveness.

3. If you are considering an incinerator within the facility for waste disposal, consult your contractor about

state, local, and federal laws and ordinances.

EQUIPMENT STANDARD D. Install a Biosafety cabinet to work with organisms. 

SUGGESTION: 

1. Install a Biosafety cabinet, Class II, type A/B3, in which to open foreign source packages. The biosafety

cabinet should be tested on an annual basis by a trained professional.
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V. OPERATIONAL STANDARDS 

OPERATIONAL STANDARD A. A Containment Director is responsible for the daily operation of the facility 

and its physical integrity. 

SUGGESTIONS: 

A Containment Officer is responsible for the organisms contained in the facility. He/she also maintains a copy of 

the Standard Operating Procedures (SOP) Manual for the facility. SOPs contain directions for normal use, 

maintenance, and disinfection of the facility and it's equipment. 

SOPs also describe how to: 

 Respond to a typical emergency event (power outage, fire, glass breaks in containment area (flood,

hurricane, earthquake, tornadoes, etc.). Biosecurity for unauthorized removal of materials from

containment area.

 Replace translucent panels in greenhouse.

 Monitor visitors

Copies of SOPs should be available to workers within the containment areas. Each revision must be dated. Revisions 

should be made when operating procedures change, SOPs should be reviewed annually. 

Containment Officer: 

 Implements the SOPs and conditions listed in permits for organisms held by the facility.

 Trains employees and/or authorized personnel in the SOPs.

 Updates copies of construction records (blueprints) for the facility.

 Maintains daily, weekly and monthly maintenance records of the facility.

The Containment Officer updates these lists: 

 The names and phone numbers of those to call during emergencies as changes occur.

 The plants species in facility, as changes occur.

 Authorized personnel, as changes occur.

 Incoming and outgoing shipments of permitted organisms, including dead or destroyed incoming

organisms, and submits list to USDA, APHIS, PPQ, PRA (Permits & Risk Assessment) by January 31 of

each year (see address on last page.)

SOPs also describe procedures related to all operating standards listed below: 

OPERATIONAL STANDARD B. Only Authorized Personnel have routine access to the facility. 

Once your facility is adequate to receive plant pests, the behaviors of people who have access to your facility will 

have far more impact on the containment of the organism than any containment feature. Your selection of 
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individuals to work in this facility is critical to maintenance of plant pest containment. In addition to picking good 

personnel, please consider the suggestions below. 

SUGGESTIONS: 

1. Lock exterior doors at all times. Insure only authorized personnel have keys.

2. Train authorized personnel in the SOPs.

3. List the personnel authorized to enter the facility.

4. Require that visitors sign a logbook. Authorized personnel must accompany visitors at all times to insure

they do not bring in or carry out pests.

5. Insure emergency exit doors are not used routinely as an entrance.

OPERATIONAL STANDARD C. Wear, sterilize, and handle personal Apparel to minimize the risk of organism 

escape 

SUGGESTIONS: 

1. Insure visitors and employees wear laboratory coat in the containment area and remove it prior to leaving

the containment area. Depending on the nature of the plant pathogen to be contained head and foot covers,

coveralls and showers may be appropriate.

2. Prohibit entry of overcoats, hats, backpacks, purses, etc. into the containment areas, as these articles may

allow organisms to hide and escape.

OPERATIONAL STANDARD D. Use Personal Cleanliness to contain organisms. 

SUGGESTION: 

1. If fungal spores of contained pathogens are present in the facility, insure authorized personnel and visitors

completely shower before exiting. Use coveralls and shoes dedicated to the facility for working inside the

facility.

OPERATIONAL STANDARD E. Clean and Disinfect the interior of the facility and its equipment regularly. 

SUGGESTIONS: 

1. Clean and disinfect the facility, its furniture, and its equipment regularly with bleach or a similar

disinfectant.

2. Describe how to change air filters without contamination of containment area.

3. Eliminate undesired pests and pathogens (e.g., any arthropods which might vector contained

entomopathogens) from the facility.

4. Autoclave or sterilize solid wastes (cultures, plant materials, soil, trash, etc.) prior to disposal.

5. Laboratory coats, coveralls and other clothing should be autoclaved before being removed from the facility

for cleaning.
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OPERATIONAL STANDARD F. Open and Handle packages of permitted organisms to prevent organism 

release. 

SUGGESTIONS: 

1. Establish one enclosed area that is easy to disinfect, to open packages received from foreign sources.

2. Place foreign source packages in the biosafety cabinet before opening.

3. Autoclave or incinerate packing materials immediately after the removal of specimens and cultures.

4. Establish procedures to eliminate hitchhiking pests (insects and pathogens, fungus, bacteria, etc.)

SUGGESTIONS: 

1. List all nonindigenous plant materials used to culture plant pathogens.

2. Sterilize/destroy all packing materials from shipments and contaminants shortly after receipt.

3. Autoclave or sterilize media used to rear organisms before removing it from the facility

4. Destroy contaminated organisms as soon as detected. This may mean destroying beneficial cultures, if

pathogens are found in the culture.

5. Store tissue cultures in screw top vials or equivalent.

SUGGESTIONS: 

1. Meet all PPQ requirements or conditions as listed in permits for organisms kept in the facility. Permits

from other Federal and State Agencies may also be required for certain plant pests. Receipt of USDA Plant 

Pest Permits does not relieve applicants from the responsibility of obtaining other permits. USDA Permits 

may be withheld or revoked if other Federal and State requirement are not satisfied 

2. Send SOP and blueprints to:

Containment Facilities Program

USDA, APHIS, PPQ, PPB, CF, Unit 133

4700 River Road, Riverdale, MD 20737

Phone (301) 734-5592

FAX (301) 734-5392

3. Obtain permission from PPQ prior to shipping regulated organisms outside of the facility.

4. Maintain a list of all organisms described in PPQ permits that enter and leave the facility.

Submit the above list to USDA APHIS PPQ (at address below) by January 31 of every year to:

USDA, APHIS, PPQ, PPB, Unit 133

4700 River Road, Riverdale, MD 20737

Phone (301) 734-8896

FAX (301) 734-4300

OPERATIONAL STANDARD G. Start, grow, and store cultures with as few exotic contaminants as 

possible. Cross contamination indicates poor laboratory practice. However, it may not indicate containment 

problems.

OPERATIONAL STANDARD H. Follow all PPQ Regulatory Requirements for organisms received, 

reared in, or released from the containment facility.
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5. If the facility stops operating as a containment facility, either temporarily or permanently, notify PPQ.

Subject: Containment of Nonindigenous Fungal Plant Pathogens 

To: Prospective Permittee 

Enclosed are DRAFT CONTAINMENT GUIDELINES FOR PLANT PATHOGENS AND THEIR VECTORS.

Please review these documents and discuss specifications for your containment facility with the PPQ Containment 

Facility staff, phone (301) 851-2046, or fax (301) 734-5392 before you contract or start construction. 

Thank you, 

Containment Facility Staff