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Guidelines for Use of Funds

USDA APHIS Veterinary Services

Antimicrobial Resistance Dashboard

Cooperative Agreements

This guidance describes costs allowed or unallowed for reimbursement through an APHIS Veterinary 

Services (VS) Cooperative Agreement funded via Antimicrobial Resistance Dashboard (AMR Dashboard) 

funding. Additional program-specific cost guidance is included in the AMR Dashboard Funding 

Opportunity Announcement. 

The Office of Management and Budget (OMB) cost principles (2 CFR Subpart E) must be used to 

determine whether a cost can be charged to the project and, if so, the extent to which it can be charged. 

A review of the detailed Financial Plan will focus on reasonable requests for expenses that support the 

accomplishment of Work Plan objectives. 

Allowable Costs 

Allowable costs must be reasonable, allocable, and necessary for project completion. 

When identifying the resources needed, the Applicant must comply with Federal and State policy and 

should include the following details. 

1. Personnel: VS will allow costs for salary and wages for personnel who are essential to complete the 

activities described in the Work Plan. The total compensation per individual employee must be 

reasonable for the work performed, conform to the established policy of the organization, and be 

consistently applied to Government and nongovernmental activities. Applicants must: 

• List all personnel needed to accomplish the project, including position titles, number of hours, 

hourly rate (or percentage of staff year), and the total amount needed for each employee 

position 

• Identify employee’s appointment type, e.g., full-time, temporary, or part-time workers. 

• Explain how employee compensation was calculated. 

• Identify any compensation increases projected during the award period. 

2. Fringe Benefits: List the benefits rate. 

• Benefits may include health and life insurance, unemployment insurance, workers’ 

compensation, retirement, social security, pensions, etc. 

• Identify benefits included in the wages or salaries (e.g., vacation and sick leave). 

3. Travel: Funds may be requested for field work, training, attendance of meetings and conferences, and 

other travel costs (excluding international travel) associated with the proposed work. Recipients should 

follow their State written travel policies when calculating travel costs. If there is no State travel policy, 

Federal per diem rates should be used. Federal per diem rates can be found on GSA. Reference 2 CFR 

Part 200.474. Travel rates can’t exceed the Federal GSA Per Diem Rates for lodging and M&IE.

• Local travel: Identify any local travel to project work sites as outlined in proposed activities. 

Indicate, by position type, who will be traveling, total projected mileage, and rate per mile. 

Include number of days and per diem rates for extended or overnight travel. Indicate the 

number of trips per day/week/month, as appropriate. 
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• Out of State travel: Identify the number of travelers, meeting/conference/training title, and 

destination. Provide the cost of transportation, lodging, subsistence and related items, number 

of days, rate per day, and the total. Registration fees should be included in the “Other” category. 

• Foreign travel: Identify any travel outside of Canada and the United States and its territories and 

possessions. However, for a recipient located outside Canada and the United States and its 

territories and possessions, foreign travel means travel outside that country. Prior approval is 

required for all foreign travel which is accomplished by reference to it in the Work Plan and 

financial plan. 

4. Equipment: The Federal definition of equipment is tangible personal property (including information 

technology systems) having a useful life of more than 1 year and a unit value of $5,000 or more unless 

the Recipient definition of equipment is more restrictive. Provide a description of the equipment to be 

purchased or leased, including unit cost, and total purchase or leasing costs. The purpose of each 

equipment item and how it will benefit or be used for the project must be provided in the project Work 

Plan. 

5. Supplies: Provide a general description of the supplies required to perform the proposed activities. 

Provide an itemized breakdown of the types of supplies and total estimated cost per type when the 

cumulative value of supplies exceeds $5,000. 

6. Contractual: Applicants must describe, in the narrative of the Work Plan, what the subaward/contract 

will accomplish. Applicants should include the total “contract” cost, by contractor or subrecipient, in the 

project budget. Provide a separate budget with cost breakdowns for each contractor or subrecipient, for 

all applicable cost categories and totals. Make sure to describe in the narrative of the Work Plan how 

the subaward/contract will be accomplished: competitive or sole source. Sole source requires a 

justification with the package. 

Consulting contract applicants must include: 1) name(s) of consultant(s) to be engaged; 2) daily fees to 

be paid to each consultant; 3) number of estimated days of continuing services; 4) scope of work to be 

performed (deliverables); 5) other incidental data supporting the proposed costs; and 6) a description of 

how the consultant(s) will be selected: competitive or sole source (sole source requires a justification 

with the package). 

7. Other: Identify any direct costs which were not itemized elsewhere, such as conference registration 

fees, communications, printing, publication charges, computer time or usage, Recipient laboratory 

testing, etc. 

8. Information Technology: Work Plans that include a cumulative request for Information Technology of 

$25,000 or more require additional USDA IT review. Information Technology is any equipment, 

interconnected system(s), or subsystem(s) of equipment that is used in the automatic acquisition, 

storage, manipulation, management, movement, control, display, switching, interchange, transmission, 

or reception of data or information by an Agency. The term “information technology” includes, but is 

not limited to, computers, network and ancillary equipment, software, firmware, and similar 

procedures, services (including support services), and related resources. Refer to 2 CFR Part 200.1 for 

additional information. 

9. Outreach Materials: Program funds may be used for outreach materials, as needed to complete 

approved projects that support the program priorities. This may include developing, distributing, and 
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delivering educational materials or content such as training curricula, videos, websites, pamphlets, fliers, 

fact sheets, publications, and other print and media. An applicant who receives funding for a project 

that includes the production, purchase, or distribution of materials is not obligated to put the USDA logo 

on the materials they produce or purchase under a cooperative agreement. However, APHIS has the 

option of reviewing all materials to be produced and may request acknowledgement of funding from the 

USDA APHIS AMR Dashboard if we determine it is in our collective best interest. Refer to the General 

Terms and Conditions for APHIS Cooperative Agreements Grants, Publications and Audiovisuals article 

for additional information. 

VS’ total share of the project must be a whole dollar amount, no cents.

Unallowable Costs 

The items below are costs that will not be funded through AMR Dashboard Cooperative Agreements: 

• Costs incurred prior to the effective date of the agreement (unless a pre-award has been

signed). 

• Construction of a new building or facility, or the acquisition or expansion of an existing building 

or facility, including site grading, improvement, and architect fees. 

• Land acquisition. 

• Projects or activities associated with VS-State-industry cooperative programs that are typically 

supported through appropriated funds, including activities typically funded via APHIS VS annual 

umbrella agreements and Animal Disease Traceability agreements. AMR Dashboard funds may 

be used to build on AMR activities associated with other VS cooperative programs. 

• Promotional or thank-you materials, incentives to encourage participation, or similar costs 

unallowable by OMB cost principles (2 CFR Subpart E – Cost Principles General Provisions for 

Selected Items of Cost). 

• Food and beverage for meetings, trainings, or workshops. 

• Bonuses or commissions. 

• Fundraising. 

• Meeting, conference, symposia, or workshop honoraria which is payment to individuals or 

guests other than for documented professional services. 

• Compensation of Federal Employees. Salary payments, consulting fees, or other remuneration 

of full-time Federal employees are unallowable costs. 

Cost Sharing 

Cost sharing and matching, defined in 2 CFR Part 200.306, is “the portion of the project costs not paid by 

Federal funds (unless otherwise authorized by Federal statute).” There is no required cost share/match 

for AMR Dashboard cooperative agreements. If an Applicant includes contributions as part of a cost 

share in their budget proposal and it is accepted by APHIS VS, the commitment of funds becomes legally 

binding, must be reported on the SF-425, and is subject to audit. Third-party in-kind contributions are 

non-cash contributions that have value that will benefit the project and are contributed by a nonFederal third-party without charge. These contributions should also be reflected in the budget proposal 

as part of a cost share. 

Neither Applicant costs nor the value of third-party, in-kind contributions may count towards satisfying a 

cost sharing or matching requirement if they have been or will be counted towards satisfying the cost 

sharing or cost matching requirement of another Federal assistance award, a Federal procurement 

contract, or any other award of Federal funds. 
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If the Applicant does not meet its cost share ratio or cost-match requirement as stipulated in the 

cooperative agreement, action can be taken to (1) reduce the next cooperative agreement, (2) reduce 

VS’ share proportionately, or (3) allow the reduced cost share when it is in the best interest of the 

Federal Government. After the cooperative agreement has expired, adjustments to a cost share cannot 

be approved. Refer to 2 CFR Part 200.306 for additional information. 

Subawards 

Subawards are defined as an award provided by the applicant to a subrecipient who will be performing 

tasks or providing deliverables that adhere to the work as identified in the applicants Work Plan. If an 

applicant desires to use a subaward, the subrecipient selected must undergo risk assessment reviews as 

detailed in 2 CFR Part 200.205 in order to receive the subaward. Recipient procurements shall be in 

accordance with 2 CFR Part 200.317 or .318, as applicable. Other types of subawards must be approved 

per 2 CFR Part 200.308 (c) (6). 

Indirect Costs 

Indirect costs are negotiated by the Recipient and their cognizant agency for indirect costs (2 CFR Part 

200.1). The cognizant agency is the Federal agency that provides the most Federal funds to the 

Recipient. The result of this negotiation is a Negotiated Indirect Cost Rate Agreement (NICRA). A signed 

NICRA needs to be attached to the application in eFG if indirect costs are assessed. When a Cooperative 

Agreement budget/funding period does not coincide with the same period for which the rate was 

established, it may be necessary to use two different rates in computing the amount of indirect costs 

applicable to the Cooperative Agreement budget. If a new rate has been negotiated, then attach a copy 

of the signed NICRA to the applicable Financial Report submission. If indirect costs were previously 

claimed based on the use of a “provisional” rate and a “final” or a “fixed” rate is determined prior to the 

end of the Cooperative Agreement period of performance, then adjustments to the claims are required 

to reflect the establishment of the final or fixed rates. 

The Agricultural Appropriations bill places a statutory cap of 10 percent on indirect costs that can be 

claimed on Cooperative Agreements with nonprofit organizations. This does not apply to Grants. When 

the statutory cap applies, APHIS cannot pay indirect costs in excess of 10 percent of the total direct costs 

of the Cooperative Agreement. If the Recipient’s NICRA rate when applied is less than 10 percent of total 

direct costs, then the Recipient NICRA applies. 

When discussing indirect costs, the definition for nonprofit institutions differs from the definition given 

in the cost principles. Nonprofit institutions include both private and public organizations including 

colleges, universities, schools, hospitals, and others. State, local, and Tribal governmental entities are 

not considered nonprofit institutions. Below are two examples which illustrate the proper application of 

the indirect cost rate, considering the statutory cap. 

Example 1: 

Yellowstone Fish and Wildlife Society (an IRS classified Nonprofit) Cooperative Agreement with total 

direct costs of $100,000. The Society has an indirect cost rate of 30% and the base for application is 

salaries, wages, and fringe benefits. 
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The Society’s SF-424A states that $70,000 will be spent on salaries, wages, and fringe benefits. The 

remaining $30,000 is for travel, contracts, and equipment. 

In this case, if the 10% statutory cap was applied, the indirect costs would be 10% x $100,000 = $10,000. 

If their 30% rate was applied to the base of $70,000 (salaries, wages, and fringe benefits), the indirect 

costs would be 30% x $70,000 = $21,000. In this scenario, the statutory cap would apply, and they could 

only claim $10,000 in indirect costs. 

Example 2: 

Kansas State University (KSU) Cooperative Agreement with total direct costs of $100,000. KSU has an 

indirect cost rate of 15% and the base for application is exclusively salaries and wages. 

KSU’s SF-424A states that $50,000 will be spent on salaries and wages. The remaining $50,000 is for 

fringe benefits, travel, supplies, and training. 

In this case, if the 10% statutory cap was applied, the indirect costs would be 10% x $100,000 = $10,000. 

If their 15% rate was applied to the base of $50,000 (salaries and wages), the indirect costs would be 

15% x $50,000 = $7,500. In this scenario, KSU’s rate would apply since it is less than the statutory cap

Recipients, except for state and local government entities that receive more than $35 million in direct 

Federal funding each year, that have an expired NICRA or who have never had an approved rate, can use 

a de minimis rate of 10 percent of modified total direct costs pursuant to 2 CFR Part 200.414 (f). 

No documentation is required to justify this rate. Modified total direct costs is the sum of these costs:

• all direct salaries and wages

• applicable fringe benefits

• materials and supplies

• services

• travel

• subawards and subcontracts up to the first $25,000 of each subaward and subcontract

Definitions 

The eCFR :: 2 CFR Part 200 -- Uniform Administrative Requirements, Cost Principles, and Audit 

Requirements for Federal Awards includes a comprehensive list of definitions. Below are some common 

definitions along with definitions for terms that are not listed in the eCFR :: 2 CFR Part 200 -- Uniform 

Administrative Requirements, Cost Principles, and Audit Requirements for Federal Awards. 

1. Allowable costs: costs that are reasonable, allocable, and necessary to the project and comply 

with funding statute requirements. 

2. Contract: Contract means a legal instrument by which a non-Federal entity purchases property 

or services needed to carry out the project or program under a Federal award. The term as used 

in this part does not include a legal instrument, even if the non-Federal entity considers it a 

contract, when the substance of the transaction meets the definition of a Federal award or 

subaward. 

3. Cooperative agreement: a legal instrument of financial assistance between a Federal awarding 

agency or pass-through entity and a non-Federal entity when substantial involvement is 

anticipated. 

4. Cost sharing or cost matching: the portion of project costs not paid by Federal funds (unless 

otherwise authorized by Federal statute). Cost sharing refers to the portion of project not borne 
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by the Federal Government, i.e., a recipient’s participation on the total cost of the project. For 

example, if the Recipient “cost-sharing” is 33 1⁄4 percent, then the Federal share is 66 3⁄4 percent 

of the recipient’s total project costs. Cost matching refers to the portion of the project not 

borne by the Federal Government, and it directly compares Federal and non-Federal 

participation dollar for dollar. For example – a 50 percent match of Federal funds means that 

the recipient must provide 50 cents for every Federal dollar. A 100 percent match means one 

recipient dollar (or dollar value) for every Federal dollar. 

5. Disallowed costs: those charges to a Federal award that the Federal awarding agency or passthrough entity determines to be unallowable, in accordance with the applicable Federal 

statutes, regulations, or the terms and conditions of the Federal award. 

6. Equipment: tangible personal property (including information technology systems) having a 

useful life of more than 1 year and a per unit value of $5,000 or more. 

7. Grant: a legal instrument of financial assistance between a Federal awarding agency or passthrough entity and a non-Federal entity which does not provide for substantial involvement. 

8. Indirect (facilities & administrative (F&A)) costs: costs incurred for a common or joint purpose 

benefitting more than one cost objective, and not readily assignable to the cost objectives 

specifically benefitted, without effort disproportionate to the results achieved. 

9. Information technology systems: computing devices, ancillary equipment, software, firmware, 

and similar procedures, services (including support services), and related resources. 

10. Non-Federal entity: A State, local government, Indian tribe, institution of higher education (IHE), 

or nonprofit organization that carries out a Federal award as a recipient or subrecipient. 

11. Pass-through Entity: a non-Federal entity that provides a subaward to a subrecipient to carry 

out part of a Federal program. 

12. Recipient: a non-Federal entity that receives a Federal award directly from a Federal awarding 

agency to carry out an activity under a Federal program. 

13. Restricted costs: those charges to a Federal award that the Federal awarding agency or passthrough entity determines to be unallowable, in accordance with the applicable Federal 

statutes, regulations, or the terms and conditions of the Federal award.

14. Subaward: an award provided by a pass-through entity to a subrecipient for the subrecipient to 

carry out part of a Federal award received by the pass-through entity. It does not include 

payments to a contractor or payments to an individual that is a beneficiary of a Federal 

program. A subaward may be provided through any form of legal agreement, including an 

agreement that the pass-through entity considers a contract. 

15. Subrecipient: a non-Federal entity that receives a subaward from a pass-through entity to carry 

out part of a Federal program. 

16. Substantial involvement: when the Federal awarding agency provides collaboration, 

participation, or intervention. The Federal awarding agency is substantially involved when it acts 

as a partner with the Recipient. 

17. Unliquidated obligations: on a cash basis, unliquidated obligations are obligations incurred but 

not yet paid. On an accrual basis, they are obligations incurred but for which an expenditure has 

not yet been recorded. 

18. Unobligated balance: the amount of funding that has been authorized on a Federal award but 

remains uncommitted by the Recipient. 

Common Cost Types 

2 CFR – Subpart E – Cost Principles General Provisions for Selected Items of Cost 

Type of Cost 2 CFR Part Classification of Costs 
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Advertising and public 

relations costs 200.421 Restricted – refer to CFR 

Advisory councils 200.422 Unallowable – unless authorized by statute, the Federal agency, 

or as an indirect cost where allocable to Federal awards 

Alcoholic beverages 200.423 Unallowable 

Alumni/ae activities 200.424 Unallowable 

Audit services 200.425 Restricted – refer to CFR 

Bad debts 200.426 Unallowable 

Bonding costs 200.427 Restricted – refer to CFR 

Collections of 

improper payments 200.428 Refer to CFR 

Commencement and 

convocation costs 200.429 

Unallowable except as provided for in Appendix III to Part 200-

Indirect (F&A) Costs Identification and Assignment, and Rate 

Determination for Institutions of Higher Education, paragraph 

(B)(9) Student Administration and Services, as student activity 

costs 

Compensation - fringe 

benefits 200.431 

Allowable – provided that the benefits are reasonable and are 

required by law, non-Federal entity-employment agreement, or 

an established policy of the non-Federal entity 

Compensation -

personal services 200.430 Refer to CFR 

Conferences 200.432 Refer to CFR 

Contingency 

Provisions 200.433 Restricted – refer to CFR 

Contributions and 

donations 200.434 Unallowable 

Defense and 

prosecution of 

criminal and civil 

proceedings, claims, 

appeals, and patent 

infringements 

200.435 Restricted – refer to CFR 

Depreciation 200.436 Restricted – refer to CFR 

Employee health and 

welfare costs 200.437 Refer to CFR 

Entertainment costs 200.438 Unallowable 

Equipment and 

other capital 

expenditures 

200.439 Restricted –refer to CFR 

Exchange rates 200.440 Allowable – prior approval of agency required – refer to CFR 

Fines, penalties, 

damages, and other 

settlements 

200.441 Unallowable – prior approval of agency required – refer to CFR 

Fund raising and 

investment 

management costs 

200.442 Restricted – refer to CFR 
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Gains and losses on 

disposition of 

depreciable assets 

200.443 Restricted – refer to CFR 

General costs of 

government 

200.444 Unallowable 

Goods or services for 

personal use 200.445 Restricted – refer to CFR 

Idle facilities and idle 

capacity 200.446 Restricted – refer to CFR 

Insurance and 

indemnification 200.447 Restricted – prior approval of agency required – refer to CFR 

Intellectual property 200.448 Restricted – refer to CFR 

Interest 200.449 Restricted – refer to CFR 

Lobbying 200.450 Unallowable – refer to CFR 

Losses on other 

awards or contracts 200.451 Unallowable 

Maintenance and 

repair costs 200.452 Allowable 

Materials and supplies 

costs, including costs 

of computing devices 

200.453 Allowable 

Memberships, 

subscriptions, and 

professional activity 

costs 

200.454 Restricted – refer to CFR 

Organization costs 200.455 Unallowable – prior approval of agency required – refer to CFR 

Participant support 

costs 

200.456 Allowable – prior approval of agency required – refer to CFR 

Plant and security 

costs 

200.457 Allowable 

Pre-award costs 200.458 Restricted – refer to CFR 

Professional service 

costs 

200.459 Restricted – refer to CFR 

Proposal costs 200.460 Restricted – refer to CFR 

Publication and 

printing costs 200.461 Refer to CFR 

Rearrangement and 

reconversion costs 200.462 Allowable 

Recruiting costs 200.463 Refer to CFR 

Relocation costs of 

employees 200.464 Restricted – refer to CFR 

Rental costs of real 

property 

and equipment 

200.465 Allowable – refer to CFR 

Scholarships and 

student aid costs 200.466 Restricted – prior approval of agency required – refer to CFR 
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Selling and marketing 

costs 

200.467 Unallowable – prior approval of agency required – refer to CFR 

Specialized service 

facilities 200.468 Allowable – refer to CFR 

Student activity costs 200.469 Unallowable 

Taxes 

(including Value 

Added Tax) 

200.470 Restricted – refer to CFR 

Termination costs 200.471 Restricted – refer to CFR 

Training and 

education costs 200.472 Allowable 

Transportation costs 200.473 Allowable 

Travel costs 200.474 Refer to CFR 

Trustees 200.475 Refer to CFR