USDA Agricultural Biosecurity — Bioterrorism Defense & Facility Security

The deliberate introduction of a pathogen into the U.S. food supply — foot-and-mouth disease into a cattle herd, a plant pathogen into wheat fields, toxins into food processing — is one of the scenarios that keeps security planners awake at night. Congress responded to this threat with 7 U.S.C. §§ 3351–3354, authorizing a dedicated agricultural biosecurity program that funds planning, facility security upgrades, and research at universities and food and agricultural science research facilities. The program, authorized at $30,000,000 per year (fiscal years 2019–2023), operates through USDA's National Institute of Food and Agriculture (NIFA) and the Agricultural Research Service (ARS).

Agricultural biosecurity is distinct from plant and animal disease control programs (handled by APHIS under separate authority) — it specifically addresses the intentional introduction of biological, chemical, or nuclear threats to crops, livestock, and the food supply, including bioterrorism planning, facility hardening, and rapid-response research. For the broader USDA grant framework that funds these biosecurity research programs, see USDA agricultural research grant framework.

Current Law (2026)

Legal Authority

• 7 U.S.C. § 3351 — Special authorization for biosecurity planning and response (USDA may run research, education, and extension programs for biosecurity planning and response; $30M/year FY2019–2023)
• 7 U.S.C. § 3352 — Agriculture research facility expansion and security upgrades (competitive grants to colleges and universities to expand or upgrade research facilities for protection against bioterrorism; $10M max per year per recipient; 50% non-federal match required)
• 7 U.S.C. § 3353 — Agricultural biosecurity grants (one-time grants up to $50K for food and ag science colleges to review facility security; grants up to $1M for food and agricultural science associations to assess vulnerabilities and develop protections; Secretary determines priorities and award procedures)
• 7 U.S.C. § 3354 — Agricultural bioterrorism research and development (Secretary may use existing research programs for food supply protection; may fund rapid-response research to bioterror threats; long-term university partnerships for planning, training, outreach, and response; public-private partnerships for rapid response)

How It Works

The Threat Landscape

Agricultural bioterrorism — sometimes called "agroterrorism" — represents a category of threat that is both easier to execute than attacks on physical infrastructure and potentially more damaging economically. Foot-and-mouth disease, if intentionally introduced into the U.S. cattle supply, could cost the American livestock industry hundreds of billions of dollars and trigger international trade bans on U.S. beef exports. A plant pathogen targeting wheat or corn at scale could disrupt food supplies. Contamination of food processing facilities with toxins like ricin or botulinum could kill or sicken thousands.

The USDA biosecurity program addresses this through three layers:

1. Detection and monitoring — research on rapid identification of biological threats at farms, processing plants, and in food products
2. Facility hardening — physical security upgrades at university agricultural research labs, which often hold pathogen collections and livestock research animals that could be targets or vectors
3. Response capacity — pre-positioned research capacity and university partnerships that can be activated quickly when a threat is identified

Facility Security Grants

The § 3352 competitive grant program funds universities that handle dangerous agricultural pathogens or host research animals to upgrade their physical security: better access controls, improved containment systems, enhanced surveillance, and biosafety laboratory upgrades. The program requires a 50% non-federal match — recipients must put up half the cost — and caps the federal share at $10 million per recipient per fiscal year. This keeps the grants large enough to fund meaningful facility improvements while ensuring institutional buy-in.

Security Review and Vulnerability Assessment

Even without a major facility upgrade, many agricultural research colleges haven't systematically assessed their security vulnerabilities. Section 3353 provides up to $50,000 for eligible institutions to conduct a one-time comprehensive security review — identifying physical and procedural weaknesses before they can be exploited.

For broader industry-level assessment, the law authorizes grants of up to $1 million to associations of food and agricultural scientists to conduct vulnerability assessments and develop security protocols. These broader assessments can identify systemic weaknesses across the agricultural research enterprise and recommend industry-wide protective measures.

Bioterrorism Research and Development

Section 3354 gives USDA the authority to direct existing agricultural research programs toward bioterrorism response — funding rapid-response research capacity for quick identification and containment of biological threats. The statute explicitly authorizes long-term university partnerships for biosecurity planning, training, outreach, and response capability, and public-private partnerships to enable rapid deployment of protective technologies when threats emerge.

Coordination with Other Agencies

Agricultural biosecurity sits at the intersection of USDA's agricultural mission and the homeland security mission managed by DHS and the FBI. USDA coordinates with:

• DHS — which leads overall bioterrorism response and maintains the National Biosurveillance Integration Center
• CDC/HHS — for zoonotic threats (diseases that pass from animals to humans)
• USDA APHIS — which handles foreign animal disease and plant pathogen response (including intentional introductions)
• FBI — for criminal investigation when intentional contamination is suspected

How It Affects You

If you work at a university agricultural research facility handling livestock, pathogens, or food safety organisms: The § 3352 competitive grant program (up to $10M/year per recipient, 50% non-federal match required) funds physical security upgrades — access control systems, improved containment, surveillance, and biosafety laboratory upgrades. Eligibility targets institutions that handle animals or pathogens that could be exploited for agroterrorism; track NIFA grant announcements at nifa.usda.gov for funding opportunity announcements. Separately — and more immediately operationally significant — if your institution handles any USDA or CDC Select Agents (pathogens on the restricted list, including agricultural pathogens like foot-and-mouth disease virus, Rinderpest virus, or Plum pox potyvirus), you are subject to the Select Agent Program under 7 CFR Part 331 (USDA-regulated agents) and 9 CFR Part 121 (overlap agents). Select Agent Program requirements include: annual registered facility inspections by USDA APHIS and CDC inspectors, background security risk assessment for all personnel with access, detailed inventory controls and documentation, biosafety committee oversight, and inactivation verification procedures. Violations can result in facility closure and criminal referrals. Recent USDA enforcement has focused on inventory discrepancy reports and inadequate inactivation documentation. The National Bio and Agro-Defense Facility (NBAF) in Manhattan, Kansas — now fully operational with BSL-4 capability — is the federal facility for research on dangerous foreign animal diseases; universities can explore collaborative research partnerships through USDA ARS.

If you're in livestock, poultry, dairy production, or food processing: The H5N1 highly pathogenic avian influenza outbreak in U.S. dairy cattle (2024-2025, 900+ confirmed herds, 30+ states) is the most significant real-world test of USDA agricultural biosecurity response in decades — and it revealed how quickly a novel pathogen can spread through normal animal movement practices. USDA's emergency response included mandatory H5N1 testing for cattle crossing state lines and compensation programs for affected producers. If you raise poultry: the Secure Poultry Supply (SPS) Plan is USDA's recommended preparedness framework for maintaining controlled movements during an HPAI outbreak — pre-register your flock with state animal health officials before an outbreak occurs, because SPS plan enrollment enables you to continue moving birds if an outbreak occurs nearby rather than being shut down entirely. For food manufacturers with $10M+ in annual sales: the FSMA Intentional Adulteration rule (21 CFR Part 121) requires a written food defense plan including vulnerability assessments — this is an FDA requirement parallel to USDA's biosecurity program, and both address the same underlying concern about deliberate contamination. Combined USDA-FDA food defense audit standards are increasingly coordinated. USDA APHIS's foreign animal disease updates at aphis.usda.gov are the authoritative source for tracking outbreak status.

If you're in agricultural export markets, commodity trading, or agricultural finance: The United States' foot-and-mouth disease (FMD)-free status is one of the most economically valuable agricultural attributes we maintain. A confirmed FMD outbreak would trigger immediate trade bans by virtually every major beef and pork importer — Japan, South Korea, Mexico, Canada, and others have explicit ban triggers for FMD in exporting countries. The economic modeling suggests an FMD outbreak could cost the U.S. livestock sector $15-200 billion depending on size and duration, reflecting both direct livestock losses and the collapse of $5+ billion in annual FMD-sensitive beef and pork exports. USDA's vaccine bank (maintained at NBAF and in coordination with international stockpiles) and the updated FMD response plan are the primary mitigation infrastructure. The 2024-2025 H5N1 dairy outbreak has already demonstrated the commodity market impact of a novel agricultural pathogen: egg prices, poultry supply chain disruption, and raw milk pricing have all been materially affected. For commodity traders and agricultural lenders: monitor USDA APHIS Situation Reports and the World Organisation for Animal Health (WOAH) Disease Dashboard as early warning systems for pathogen spread that could affect position values.

Implementing Regulations

The APHIS regulations governing possession and transfer of agricultural select agents live at 7 CFR Part 331 — Possession, Use, and Transfer of Select Agents and Toxins (18 sections — the biosafety and biosecurity requirements for entities handling plant and animal pathogens that could be weaponized for agroterrorism, implemented under the Agricultural Bioterrorism Protection Act of 2002):

• § 331.3 — PPQ select agents and toxins (the covered list): six plant pathogens that must be handled under strict rules — including Peronosclerospora philippinensis (Philippine downy mildew of corn), Phoma glycinicola (soybean stem blight), Ralstonia solanacearum race 3, biovar 2 (destructive potato pathogen), Rathayibacter toxicus (toxic grass endophyte), and Sclerotinia sclerotiorum (white mold affecting 400+ plant species); animal-disease-associated overlap agents (foot-and-mouth disease virus, Rinderpest virus) are regulated jointly with CDC/APHIS under 9 CFR Part 121
• § 331.5 — Exemptions: diagnostic laboratories that encounter a select agent incidentally during routine testing are temporarily exempt and must notify APHIS and/or CDC within 7 days; certain products (vaccines with inactivated pathogens, commercial products that contain select agents below certain concentrations) may be exempted by petition to APHIS; exemption does not eliminate reporting requirements if a select agent is discovered
• § 331.7 — Registration requirement: any person or entity wishing to possess, use, or transfer a covered select agent must obtain a Certificate of Registration from APHIS; registration requires: (1) a site security plan, (2) a responsible official (RO) designation, (3) background security risk assessments for all personnel who will have access, (4) a biocontainment plan, and (5) institutional biosafety committee (IBC) approval; registrations are issued for 3-year terms and may not be transferred
• § 331.9 — Responsible official (RO): each registered entity must designate an RO who is approved by APHIS to have access to select agents; the RO is personally responsible for compliance with Part 331 requirements including personnel training, incident reporting, inventory maintenance, and coordination with APHIS inspectors; the RO's personal approval by APHIS is a separate requirement from facility registration
• § 331.10 — Security risk assessments: no individual may have access to a select agent unless APHIS (or CDC for overlap agents) has conducted a background security risk assessment and determined there is no national security concern; "access" means physical presence in the same space as an uncontained agent, not just proximity to a locked storage area; assessments may be denied or conditions imposed for prior criminal history, certain immigration statuses, or risk factors identified by law enforcement; the RO may not grant access before APHIS approval
• § 331.11 — Security plan: registered entities must create and maintain a written security plan addressing physical security, access control, inventory, personnel management, and response to potential theft or unauthorized access; plans must be based on a site-specific risk assessment; for BSL-3 or higher facilities handling Tier 1 agents (the highest-risk subset), USDA-reviewed security plans are required
• § 331.12 — Biocontainment plan: a written biocontainment plan must describe the biosafety procedures, containment equipment, and practices appropriate to the risk level of the agents handled; for PPQ select agents, BSL-3 Plant (BSL-3P) or equivalent containment is typically required; containment procedures must be consistent with CDC/NIH Biosafety in Microbiological and Biomedical Laboratories (BMBL) guidelines
• § 331.13 — Restricted experiments: certain categories of experiments with select agents are prohibited without prior APHIS approval — including experiments that would increase transmissibility, virulence, drug resistance, or host range in ways that create a significant potential for causing a public health emergency; this provision implements the "gain of function" research oversight that became politically prominent during debates over COVID-19 origins
• § 331.16 — Transfer restrictions: a select agent may only be transferred to another registered entity; transfers must be pre-authorized, documented, and tracked; the sending entity must verify the receiving entity's registration status before shipment; APHIS must be notified of all transfers; carriers used for transport must be approved; international transfers require APHIS import/export permits
• § 331.19 — Theft, loss, or release notification: if a select agent is stolen, lost, or released, the entity must notify APHIS immediately upon discovery (not after investigation); unplanned releases triggering personnel exposure must be reported to APHIS within 7 days; APHIS coordinates with CDC, FBI, and law enforcement on theft or potential malicious release incidents; accidental releases must be investigated and root-cause analysis submitted to APHIS

Part 331 is jointly enforced by USDA APHIS and CDC under the federal select agent program; for overlap agents (those affecting both agriculture and human health, like foot-and-mouth disease), APHIS and CDC share regulatory jurisdiction. Annual unannounced inspections are a statutory requirement. Recent rulemakings: 82 FR 6205 (January 2017) — updated Tier 1 agent biosecurity requirements; 79 FR 26830 (May 2014) — revised personnel security and training requirements.

9 CFR Part 121 — Possession, Use, and Transfer of Select Agents and Toxins (APHIS Veterinary Services overlap agents): the APHIS VS division's regulation for overlap select agents — biological agents that pose significant threats to both animal health AND human health, jointly regulated by USDA APHIS and CDC/HHS. Part 121 structurally parallels 42 CFR Part 73 (CDC HHS select agents) and 7 CFR Part 331 (APHIS PPQ plant pathogens) but applies to veterinary/animal pathogens with dual human-animal risk:

• Overlap agents on the Part 121 list include: foot-and-mouth disease virus; Rift Valley fever virus; Japanese encephalitis virus; Venezualan equine encephalitis virus; Bacillus anthracis (anthrax); Brucella species; Burkholderia mallei (glanders); Burkholderia pseudomallei (melioidosis); and other pathogens that cause severe disease in both animals and humans; these are the agents where an animal reservoir or agricultural vector creates dual biosecurity risk

• §§ 121.10–121.16 — Security, biosafety, access restrictions, incident response, training, and transfer requirements for Part 121 overlap agents are substantively identical to the parallel requirements in 42 CFR Part 73 (§§ 73.10–73.16): FBI security risk assessment prerequisite for all personnel with access; written security and biosafety plans; Responsible Official designation; restricted experiments requiring USDA/HHS approval (including gain-of-function research with overlap agents); theft/loss notification immediately to both APHIS and appropriate law enforcement; transfers only to other registered entities; BSL-3 minimum containment for most overlap agents

• Dual-agency jurisdiction: when a facility handles both Part 121 overlap agents and CDC-regulated agents, APHIS VS and CDC inspectors conduct joint inspections; the facility must comply with the more stringent requirement where APHIS and CDC standards differ; for Tier 1 overlap agents (the highest-risk subset, including foot-and-mouth disease virus and Venezuelan equine encephalitis), enhanced security requirements apply under both agencies' rules

State Variations

This is entirely federal law — the biosecurity grants go to universities and associations, not to state governments. States have their own emergency management plans for agricultural disasters (including intentional attacks), which are coordinated with USDA APHIS and the National Animal Health Emergency Management System.

Pending Legislation

The 2025 Farm Bill (pending as of April 2026) is expected to reauthorize the agricultural biosecurity program (FY2023 authorization has lapsed) and may expand its scope in response to heightened awareness of biological threats. Following COVID-19, Congressional interest in pandemic preparedness has increased attention to agricultural biosecurity as part of the broader biosecurity infrastructure.

Recent Developments

• H5N1 HPAI in dairy cattle — unprecedented outbreak testing USDA biosecurity response: The 2024-2025 H5N1 highly pathogenic avian influenza outbreak in U.S. dairy cattle — confirmed in 900+ herds across 30+ states — is unprecedented: HPAI had never before established itself in a bovine reservoir. USDA APHIS's emergency response included mandatory testing for cattle moving across state lines, compensation programs for affected dairies, and coordination with CDC on human exposure monitoring. The outbreak exposed biosecurity gaps in the dairy sector — cattle movement between farms for breeding had spread the virus in ways that commercial poultry's more controlled biosecurity could not have. USDA's H5N1 response has been the largest agricultural biosecurity intervention since the 2015 HPAI outbreak that killed 50 million poultry.
• USDA-CDC-DHS coordination on agroterrorism — NBAF central to defense capacity: USDA's Select Agent Program (co-administered with CDC under 7 CFR Part 331 and 9 CFR Part 121) governs possession, use, and transfer of agricultural select agents — pathogens that could be used for agroterrorism. The National Bio and Agro-Defense Facility (NBAF, Manhattan, Kansas — fully operational 2023) is the primary federal research facility for dangerous foreign animal diseases. NBAF's BSL-4 capability allows research on pathogens like foot-and-mouth disease that cannot be studied elsewhere in the continental U.S. DHS and USDA intelligence units monitor for potential agroterrorism threats; the 2024 HPAI dairy outbreak prompted review of whether the spread pattern could have included deliberate introduction, though no evidence of intentional introduction has been confirmed.
• Select Agent Program enforcement — academic and commercial facility inspections: USDA and CDC inspect select agent registered facilities annually; violations can result in facility closure and criminal referrals for intentional violations. The pandemic-era shift to remote inspections revealed gaps in oversight that both agencies have worked to address. Recent enforcement actions have focused on inventory discrepancies, inadequate inactivation procedures (confirming pathogens are killed before disposal), and personnel security requirements. The Program's database of registered entities is non-public for security reasons, but USDA publishes annual enforcement statistics.
• Foreign animal disease — FMD vaccine preparedness a persistent gap: Foot-and-mouth disease (FMD) — absent from the U.S. since 1929 — remains the highest-consequence foreign animal disease biosecurity threat, with the potential to devastate U.S. livestock exports ($10+ billion annually) within days of an outbreak. USDA's FMD vaccine bank (maintained at NBAF and in coordination with international stockpiles) was significantly upgraded in the IIJA funding period. A 2024 Government Accountability Office report found that USDA's FMD response plan had improved but still lacked sufficient pre-positioned vaccine to address a large multi-state outbreak — a gap that became more politically visible after the HPAI dairy outbreak demonstrated how rapidly a novel pathogen can spread through cattle movement networks.