Contents

• Introduction to the PHS Agencies
• Sources of PHS Agency Funding
• Transfers
• PHS Program Evaluation Set-Aside
• Mandatory Funding, User Fees, and Collections
• Mandatory Appropriations
• User Fees
• Collections
• Recent Trends in PHS Agency Funding
• Impact of Budget Caps and Sequestration
• Mandatory Spending
• Discretionary Spending
• Report Roadmap
• Agency for Healthcare Research and Quality (AHRQ)
• Agency Overview
• Agency Funding Since FY2010
• Centers for Disease Control and Prevention (CDC)
• Agency Overview
• Agency Funding Since FY2010
• Food and Drug Administration (FDA)
• Agency Overview
• Agency Funding Since FY2010
• Health Resources and Services Administration (HRSA)
• Agency Overview
• Agency Funding Since FY2010
• Indian Health Service (IHS)
• Agency Overview
• Agency Funding Since FY2010
• National Institutes of Health (NIH)
• Agency Overview
• Agency Funding Since FY2010
• Substance Abuse and Mental Health Services Administration (SAMHSA)
• Agency Overview
• Agency Funding Since FY2010

Summary

Within the Department of Health and Human Services (HHS), eight agencies are designated components of the U.S. Public Health Service (PHS). The PHS agencies are funded primarily with annual discretionary appropriations. They also receive significant amounts of funding from other sources including mandatory funds from the Affordable Care Act (ACA), user fees, and third-party reimbursements (collections).

• The Agency for Healthcare Research and Quality (AHRQ) funds research on improving the quality and delivery of health care. For several years prior to FY2015, AHRQ did not receive a direct appropriation. Instead, it relied on redistributed ("set-aside") funds from other PHS agencies for most of its funding, with supplemental amounts from the ACA's Patient-Centered Outcomes Research Trust Fund (PCORTF). In FY2015, AHRQ received its own appropriation in lieu of set-aside funds. Overall, the agency's total funding rose from $403 million to $465 million between FY2010 and FY2015. That increase came despite a decrease in discretionary funding over that period, which was more than offset by increasing amounts of PCORTF funding.
• The Centers for Disease Control and Prevention (CDC) is the federal government's lead public health agency. CDC obtains its funding from multiple sources besides discretionary appropriations. The agency's funding fluctuated between FY2010 and FY2015, with the overall level increasing slightly from $10.9 billion to $11.3 billion over that period. CDC experienced a drop in its discretionary appropriations during that time, which was offset by funding from other sources, primarily the ACA's Prevention and Public Health Fund (PPHF). The Agency for Toxic Substances and Disease Registry (ATSDR) investigates the public health impact of exposure to hazardous substances. ATSDR is headed by the CDC director and included in the discussion of CDC in this report.
• The Food and Drug Administration (FDA) regulates drugs, medical devices, food, and tobacco products, among other consumer products. FDA saw its funding increase significantly between FY2010 and FY2015 from $3.1 billion to $4.5 billion. The agency is funded with annual discretionary appropriations and industry user fees. While appropriations increased modestly over the FY2010-FY2015 period, user fees more than doubled and now account for 42% of FDA's total funding.
• The Health Resources and Services Administration (HRSA) funds programs and systems that provide health care services to the uninsured and medically underserved. HRSA, like CDC, relies on funding from several different sources. The agency's funding increased from $8.1 billion in FY2010 to $10.3 billion in FY2015 despite a significant drop in its discretionary appropriation during that time. The growth in overall funding was driven largely by increasing amounts from the ACA's Community Health Center Fund (CHCF).
• The Indian Health Service (IHS) supports a health care delivery system for Native Americans. IHS's funding, which includes discretionary appropriations and collections from third-party payers of health care, increased between FY2010 and FY2015 from $5.1 billion to $5.9 billion. Appropriations and collections both increased during that period.
• The National Institutes of Health (NIH) funds basic, clinical, and translational biomedical and behavioral research. NIH gets more than 99% of its funding from discretionary appropriations. Its funding dropped from $31.2 billion in FY2010 to $30.3 billion in FY2015.
• The Substance Abuse and Mental Health Services Administration (SAMHSA) funds mental health and substance abuse prevention and treatment services. SAMHSA's funding, about 95% of which comes from discretionary appropriations, has remained at about $3.6 billion over the FY2010-FY2015 period.

Congress has yet to complete work on any of the regular appropriations bills for FY2016, which began on October 1, 2015. On September 30, the President signed the Continuing Appropriations Act, 2016 (P.L. 114-53). The measure provides continuing appropriations through December 11, 2016. It funds discretionary programs at the same rate (and under the same conditions) as in FY2015, minus an across-the-board reduction of 0.2108%. For entitlement and other mandatory spending that is funded through appropriation acts, P.L. 114-53 provides funding to maintain program levels under current law. This report will be updated with information on PHS agency funding for FY2016 once legislative action on appropriations for the new fiscal year is completed.

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Public Health Service Agencies: Overview and Funding (FY2010-FY2016)

Introduction to the PHS Agencies

The Department of Health and Human Services (HHS) has designated eight of its 11 operating divisions (agencies) as components of the U.S. Public Health Service (PHS). The PHS agencies are: (1) the Agency for Healthcare Research and Quality (AHRQ), (2) the Agency for Toxic Substances and Disease Registry (ATSDR), (3) the Centers for Disease Control and Prevention (CDC), (4) the Food and Drug Administration (FDA), (5) the Health Resources and Services Administration (HRSA), (6) the Indian Health Service (IHS), (7) the National Institutes of Health (NIH), and (8) the Substance Abuse and Mental Health Services Administration (SAMHSA).¹

While the PHS agencies all provide and support essential public health services, their specific missions vary. With the exception of FDA, the agencies have limited regulatory responsibilities. Two of them—NIH and AHRQ—are primarily research agencies. NIH conducts and supports basic, clinical, and translational medical research. AHRQ conducts and supports research on the quality and effectiveness of health care services and systems.

Three of the agencies—IHS, HRSA, and SAMHSA—provide health care services or help support systems that deliver such services. IHS supports a health care delivery system for American Indians and Alaska Natives. Health services are provided directly by the IHS, as well as through tribally contracted and operated health programs, and through services purchased from private providers. HRSA funds programs and systems to improve access to health care among low-income populations, pregnant women and children, persons living with HIV/AIDS, rural and frontier populations, and others who are medically underserved. SAMHSA funds community-based mental health and substance abuse prevention and treatment services.

CDC is a public health agency that develops and supports community-based and population-wide programs and systems to promote quality of life and prevent the leading causes of disease, injury, disability, and death. ATSDR, which is headed by the CDC director and included in the discussion of CDC in this report, is tasked with identifying potential public health effects from exposure to hazardous substances. Finally, FDA is primarily a regulatory agency, whose mission is to ensure the safety of foods, dietary supplements, and cosmetics, and the safety and effectiveness of drugs, vaccines, medical devices, and other health products. In 2009, Congress gave FDA the authority to regulate the manufacture, marketing, and distribution of tobacco products in order to protect public health.

The programs and activities of five of the PHS agencies—AHRQ, CDC, HRSA, NIH, and SAMHSA—are mostly authorized under the Public Health Service Act (PHSA).² While some of FDA's regulatory activities are also authorized under the PHSA, the agency and its programs derive most of their statutory authority from the Federal Food, Drug, and Cosmetic Act (FFDCA).³ HRSA's maternal and child health programs are authorized by the Social Security Act (SSA),⁴ and many of the IHS programs and services are authorized by the Indian Health Care Improvement Act.⁵ ATSDR was created by the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA, the "Superfund" law).⁶

Sources of PHS Agency Funding

The primary source of funding for each PHS agency is the discretionary budget authority it receives through the annual appropriations process.⁷ AHRQ, CDC, HRSA, NIH, and SAMHSA are funded through the Departments of Labor, Health and Human Services, and Education, and Related Agencies (Labor-HHS-ED) appropriations act. Funding for ATSDR and IHS is provided through the Department of the Interior, Environment, and Related Agencies (Interior/Environment) appropriations act. FDA gets its funding through the Agriculture, Rural Development, Food and Drug Administration, and Related Agencies (Agriculture) appropriations act.⁸

The economic stimulus package enacted in February 2009—the American Reinvestment and Recovery Act (ARRA)—provided a total of $15.1 billion in supplemental FY2009 discretionary appropriations to five of the PHS agencies.⁹ Details of the allocation of those funds are provided in Appendix A. Almost all of the ARRA appropriations were designated as two-year funds, available for obligation through the end of FY2010.

Transfers

The annual Labor-HHS-ED appropriations act gives the HHS Secretary limited authority to transfer funds from one budget account to another within the department. The Secretary may transfer up to 1% of the funds in any given account. However, a recipient account may not be increased by more than 3%. Congressional appropriators must be notified in advance of any transfer.¹⁰

The HHS Secretary used this transfer authority in FY2013 and again in FY2014 as part of a broader effort to provide the Centers for Medicare & Medicaid Services (CMS) with additional funding to implement the Affordable Care Act (ACA). In FY2013, for example, NIH was the primary source of transfers both to CMS for ACA implementation and to CDC and SAMHSA to help offset a loss of funding for those two agencies from the ACA's Prevention and Public Health Fund (PPHF). A significant portion of the FY2013 PPHF funds that were originally allocated to CDC and SAMHSA were reallocated to CMS for ACA implementation. In FY2014, NIH was again the primary source of transfers to CMS to support ACA implementation.¹¹

PHS Program Evaluation Set-Aside

In addition to the transfer authority provided in the annual Labor-HHS-ED appropriations act, Section 241 of the PHSA authorizes the HHS Secretary, with the approval of congressional appropriators, to use a portion of the funds appropriated for programs authorized by the PHSA to evaluate their implementation and effectiveness. This long-standing budgeting authority is known as the PHS Program Evaluation Set-Aside (set-aside), or PHS budget "tap."

Under this authority the appropriations of a number of HHS agencies and offices are subject to an assessment. Although the PHSA limits the set-aside to no more than 1% of program appropriations, in recent years the annual Labor-HHS-ED appropriations act has specified a higher amount. The FY2015 Labor-HHS-ED appropriations act capped the set-aside at 2.5%.¹² Following passage of the annual Labor-HHS-ED appropriations act, the HHS Budget Office calculates the assessment on each of the donor agencies and offices. These funds are then transferred to various recipient agencies and offices within the department for evaluation and other specified purposes, based on the amounts specified in the appropriations act.¹³

Table 1 shows the total assessments and transfers for FY2013, by HHS agency and office, and indicates whether the entity was a net donor or recipient of set-aside funds that year. NIH, whose annual discretionary appropriation exceeds that of all the other PHS agencies combined, is subject to the largest assessment of set-aside funds. NIH contributed almost $710 million (69%) of the $1.026 billion in set-aside funds in FY2013. The agency received $8 million in set-aside funding, making it a significant net donor of such funds. Similarly, HRSA contributed more set-aside funds than it received in FY2013. On the other hand, AHRQ, CDC, and SAMHSA each were net recipients of set-aside funding in FY2013. The Administration for Children and Families (ACF) and the Office of the Secretary (OS) also received set-aside funds.

The FY2013 assessments and transfers of set-aside funding shown in Table 1 are broadly representative of the distribution of such funds during each of the preceding fiscal years extending back to the mid-2000s. In FY2014, the allocation of set-aside funding was comparable to that of FY2013 but with one key difference. For the first time, CMS was a recipient of set-aside funds.¹⁴

In FY2015, congressional appropriators made substantial changes to the allocation of set-aside funds by transferring most of the funding to NIH and eliminating any transfers to AHRQ, CDC, and HRSA. As shown in Table 1, NIH went from being by far the largest net donor of set-aside funds to a net recipient of such funding in FY2015. Meanwhile, AHRQ and CDC experienced a significant net loss of set-aside funding in FY2015. The situation with AHRQ is of particular interest. From FY2003 through FY2014, AHRQ did not receive an annual discretionary appropriation. The agency was supported by set-aside funds and, in recent years, by smaller amounts from other sources. In FY2015, however, AHRQ received a discretionary appropriation for the first time in more than a decade in lieu of receiving any set-aside funding.

Mandatory Funding, User Fees, and Collections

Although the bulk of PHS agency funding is provided through annual discretionary appropriations, agencies also receive mandatory funding, user fees, and third-party collections.¹⁵ As discussed briefly below, these additional sources of funding are a substantial component of the budget of several PHS agencies.

Mandatory Appropriations

The Patient Protection and Affordable Care Act (ACA)¹⁶ included numerous appropriations that together are providing billions of dollars in mandatory spending to support new and existing grant programs and other activities.¹⁷ Some of the ACA appropriations fund specific programs and activities within the PHS agencies. These appropriations are itemized in the funding tables in this report.

The ACA also established three multibillion dollar trust funds to help support PHS agency programs and activities. First, the Community Health Center Fund (CHCF), for which the ACA provided a total of $11 billion in annual appropriations over the five-year period FY2011-FY2015, is supporting the federal health centers program and the National Health Service Corps (NHSC), both administered by HRSA.¹⁸ A table summarizing each fiscal year's CHCF appropriation and the allocation of funds appears in Appendix B.¹⁹

Second, the Prevention and Public Health Fund (PPHF), for which the ACA provided a permanent annual appropriation, is intended to support prevention, wellness, and other public health programs and activities.²⁰ To date, CDC has received the majority of PPHF funds, while AHRQ, HRSA, and SAMHSA have received smaller amounts. The HHS Secretary transferred almost half of the FY2013 PPHF funds to CMS to support ACA implementation. A broader analysis of the allocation of PPHF funding is provided in Appendix C.

The Patient-Centered Outcomes Research Trust Fund (PCORTF) is supporting comparative effectiveness research over a 10-year period (FY2010-FY2019) with a mix of appropriations—some of which are offset by revenue from a fee imposed on health insurance policies and self-insured health plans—and transfers from the Medicare Part A and Part B trust funds.²¹ A portion of the PCORTF is allocated for AHRQ. More information on the PCORTF, including the appropriation and transfer formulas, is provided in Appendix D.

In addition to the ACA funding, HRSA, CDC, and IHS each receive mandatory funds from other sources. HRSA's Family-to-Family Health Information Centers Program has been funded by a series of mandatory appropriations since FY2007; CDC receives Medicaid funding to support the Vaccines for Children program; and both IHS and NIH receive mandatory funds for diabetes programs. These and other mandatory appropriations are itemized in the agency funding tables in this report.

User Fees

Several PHS agencies assess user fees on third parties to help fund their programs and activities. User fees collected by CDC, HRSA, and SAMHSA represent a very small portion of each agency's overall budget.²² In comparison, the industry user fees that FDA collects help finance a broad range of the agency's regulatory activities and account for a substantial and growing share of the agency's budget.

It has been almost 25 years since the Prescription Drug User Fee Act (PDUFA)²³ established the first user fee program at FDA. Since PDUFA's enactment, Congress has created several other FDA user fee programs. These programs provide FDA with additional resources that allow it to hire more personnel and expedite the process of reviewing new product applications. Some user fees also pay for information technology infrastructure and post-approval regulation of safety and effectiveness. FDA's user fee programs now support the agency's regulation of prescription drugs, animal drugs, medical devices, tobacco products, and foods, among other activities. The amount of user fees that FDA collects under these programs has increased steadily since PDUFA was enacted, both in absolute terms and as a share of FDA's overall budget. In FY2015, user fees accounted for 42% of the FDA's overall budget. More discussion of user fees is provided in the FDA section of this report and in Appendix E.

Collections

IHS supplements its annual discretionary appropriation with third-party collections from public and private payers. Most of these funds come from Medicare and Medicaid, which reimburse IHS for services provided to American Indians and Alaska Natives enrolled in these programs at facilities operated by IHS and the tribes. IHS also collects reimbursements from private health insurers. IHS collections (and reimbursements) are reflected in Table 7 of this report.

Recent Trends in PHS Agency Funding

Congress has taken a number of recent steps through both the annual appropriations process and the enactment of deficit-reduction legislation to reduce the growth in federal spending. These actions, which are briefly discussed below, have helped reduce discretionary funding for several PHS agencies over the past six years (i.e., FY2010-FY2015). Among the five PHS agencies that are funded through the Labor-HHS-ED appropriations act, only SAMHSA received funding in FY2015 that was essentially level with the amount it received in FY2010. CDC, HRSA, and NIH each received a smaller discretionary appropriation in FY2015 than they had received in FY2010. Similarly, AHRQ's discretionary appropriation in FY2015 was less than the amount of set-aside funding the agency received in FY2010. With the exception of NIH, which is funded almost entirely by discretionary appropriations, the decline in discretionary funding for the other three agencies (i.e., AHRQ, CDC, and HRSA) has been offset by the receipt of mandatory ACA funds.

FDA and IHS, neither of which receives discretionary funding through the Labor-HHS-ED appropriation act, have seen their appropriations increase over the six-year period FY2010-FY2015. Both agencies have also witnessed a steady increase in funding from other sources; user fees at FDA, and third-party collections at IHS.

Impact of Budget Caps and Sequestration

In April 2011, lawmakers agreed to cuts in discretionary spending for a broad range of agencies and programs as part of negotiations to complete the FY2011 appropriations process and avert a government shutdown. Congress and the President then enacted the Budget Control Act of 2011 (BCA),²⁴ which amended the Balance Budget and Emergency Deficit Control Act of 1985 (BBEDCA).²⁵ The BCA established enforceable discretionary spending limits, or caps, for defense and nondefense spending for each of FY2012 through FY2021 and triggered annual spending reductions, equally divided between defense and nondefense spending, beginning in FY2013. Within each spending category the cuts are divided proportionately between discretionary spending and nonexempt mandatory spending. All the spending summarized in this report falls within the nondefense category.

Under the BCA, the spending reductions are achieved through a combination of sequestration (i.e., an across-the-board cancellation of budgetary resources) and lowering the BCA-imposed discretionary spending caps. The Office of Management and Budget (OMB) is responsible for calculating the percentages and amounts by which mandatory and discretionary spending are required to be reduced each year, and for applying the BBEDCA's sequestration exemptions and special rules.

Mandatory Spending

The BCA requires the mandatory spending reductions to be executed each year by a sequestration of all nonexempt accounts. Generally, the ACA and other mandatory funding discussed in this report is fully sequestrable at the applicable percentage rate for nonexempt nondefense mandatory spending (see Table 2), with the following key exceptions. First, the funds for the CDC-administered Vaccines for Children program come from Medicaid, which is exempt from sequestration. Second, funding for the Energy Employees Occupational Illness Compensation Program Act (EEOICPA) also is exempt from sequestration. Third, under the sequestration special rules, cuts in CHCF funding for community health centers and migrant health centers and the cuts in mandatory diabetes funding for IHS are capped at 2% (see Table 2).

While all the nonexempt PHS programs with mandatory funding were sequestered in FY2013 and FY2014, several of them avoided sequestration in FY2015 and/or FY2016 because there were no budgetary resources at the time the sequestration was ordered by the President. The Maternal, Infant, and Early Childhood Home Visiting program, administered by HRSA, is one example of this anomaly. The ACA authorized the Home Visiting program and funded it through FY2014 (see Table 6). Pursuant to the BCA, the President ordered the FY2015 sequestration on March 10, 2014, the day the FY2015 budget was released. But Congress and the President had yet to enact legislation extending funding for the Home Visiting program, so there were no FY2015 budgetary resources to sequester.²⁶

Discretionary Spending

Under the BCA, FY2013 discretionary spending was subject to sequestration. In general, PHS agency discretionary appropriations for that year were fully sequestrable at the applicable percentage rate for nonexempt nondefense discretionary (NDD) spending (see Table 2). As a result, each agency saw a dip in its discretionary funding for FY2013. OMB also determined that FDA user fees for FY2013 were fully sequestrable at the NDD percentage rate. But it concluded that IHS's third-party collections in FY2013 were exempt from sequestration.

For each of the remaining years (i.e., FY2014 through FY2021), the annual reductions in discretionary spending required under the BCA are achieved by lowering the discretionary spending caps by the total dollar amount of the required reduction. This means that congressional appropriators get to decide how to apportion the cuts within the lowered spending cap rather than having the cuts applied across-the-board to all nonexempt accounts through the sequestration process.

For FY2014, OMB lowered the NDD spending cap by about $37 billion. However, the Bipartisan Budget Act of 2013 (BBA)²⁷ subsequently amended the BCA by establishing new NDD spending caps for FY2014 and FY2015 and eliminating the BCA requirement that these caps be lowered. This gave congressional appropriators more funding for those two fiscal years.

The BBA set the FY2014 cap for NDD spending at $491.773 billion. That level was about $22 billion above the BCA-lowered FY2014 cap that it replaced and almost $24 billion above the FY2013 post-sequestration NDD funding level. The BBA's FY2015 NDD spending cap of $492.356 billion is only slightly higher than the FY2014 cap, but it is approximately $9 billion above the BCA-lowered FY2015 cap that it replaces.

In FY2016, discretionary spending levels are once again subject to the original requirements of the BCA. The law set the FY2016 cap for NDD spending at $530.000 billion, which OMB has lowered to $493.491 billion pursuant to the BCA.²⁸

Report Roadmap

The remainder of this report consists of seven sections, one for each PHS agency beginning with AHRQ.²⁹ Each section includes an overview of the agency's statutory authority and principal activities, and a brief summary of the agency's funding over the period FY2010-FY2015. This material is accompanied by a detailed funding table showing the FY2010-FY2015 funding levels and the FY2016 budget request for the agency. The amounts in the funding tables in this report are taken from the departmental and agency budget documents submitted to the appropriations committees, as well as agency operating plans.³⁰ Specific documents are listed in the source note under each table.

The funding tables are formatted in a similar, though not identical, manner. The formatting generally matches the way in which each agency's funding is presented in the congressional budget documents. Each table shows the funding for all the agency's budget accounts and, typically, for selected programs and activities within those accounts. These amounts are summed to give the agency's total, or program level, funding. At the bottom of the table any user fees, set-aside funds, ACA funds, and other nondiscretionary amounts are subtracted from the program level to give the agency's discretionary budget authority (i.e., annual discretionary appropriations).

The tables for AHRQ, CDC, HRSA, and SAMHSA include non-add entries—italicized and in parentheses—to indicate the contribution of funding from sources other than the agency's discretionary appropriations to specific accounts. Almost all of the CDC accounts are funded with discretionary appropriations plus amounts from multiple other sources (see Table 4).

The use of a dash in the funding tables generally means "not applicable." Either the activity or program was not authorized or there was no mandatory funding provided for that fiscal year. In contrast, a zero usually indicates that congressional appropriators had chosen not to appropriate any discretionary funds that year or, in the case of the FY2016 budget request, that no discretionary funding was requested.

It is important to keep in mind that the PHS agency funding tables that appear in budget documents and appropriations committee reports, as well as the tables in this report, show only the amount of evaluation set-aside funds received. They do not reflect the amount of funding assessed on agency accounts. As a result, the funding tables for the PHS agencies subject to an assessment (i.e., CDC, HRSA, NIH, and SAMHSA) give a somewhat distorted view of their available budgetary resources. This effect is particularly significant in the case of NIH. As mentioned earlier, NIH is assessed approximately $700 million annually, and until FY2015 the agency received $8 million each year in set-aside transfers. While the funding table for NIH shows receipt of set-aside funds, which count towards the agency's overall program level funding, the amounts shown for each agency account have not been reduced to reflect the assessment. Thus, NIH appears to have about $700 million more than is in fact the case.

Note that the funding tables show the post-sequestration amounts for the accounts that were subject to sequestration in FY2013-FY2015. The amounts shown for the FY2016 request do not reflect sequestration.

Agency for Healthcare Research and Quality (AHRQ)³¹

Agency Overview

AHRQ supports research designed to improve the quality of health care, increase the efficiency of its delivery, and broaden access to health services. Specific research efforts are aimed at reducing the costs of care, promoting patient safety, measuring the quality of health care, and improving health care services, organization, and financing. AHRQ also is required to disseminate its research findings to health care providers, payers, and consumers, among others. In addition, the agency collects data on health care expenditures and utilization through the Medical Expenditure Panel Survey (MEPS) and the Healthcare Cost and Utilization Project (HCUP).

AHRQ has evolved from a succession of agencies concerned with fostering health services research and health care technology assessment. The Omnibus Budget Reconciliation Act of 1989 (P.L. 101-239) added a new PHSA Title IX and established the Agency for Health Care Policy and Research (AHCPR), a successor agency to the former National Center for Health Services Research and Health Care Technology Assessment (NCHSR). AHCPR was reauthorized in 1992 (P.L. 102-410). On December 6, 1999, President Clinton signed the Healthcare Research and Quality Act of 1999 (P.L. 106-129), which renamed AHCPR as the Agency for Healthcare Research and Quality (AHRQ) and reauthorized appropriations for its programs and activities through FY2005.³² Congress has yet to reauthorize the agency's funding. Despite the expired authorization of appropriations, AHRQ continues to get annual funding.

The AHRQ budget is organized according to three program areas: (1) Healthcare Costs, Quality and Outcomes (HCQO) Research; (2) MEPS; and (3) program support. HCQO research focuses on six priority areas, summarized in the text box below.

From FY2003 through FY2014, AHRQ did not receive its own annual discretionary appropriation. Instead, the agency largely relied on the PHS evaluation set-aside to fund its activities and programs. In recent years AHRQ also has received mandatory funds from the PPHF and the PCORTF (see Appendix C and Appendix D). In FY2015, AHRQ received its own discretionary appropriation for the first time in more than a decade in lieu of any set-aside funding.

Agency Funding Since FY2010

AHRQ's program level has increased steadily over the past several years with decreases in discretionary funding being more than offset by transfers of ACA mandatory funds (see Table 3). Specifically, since FY2010, the agency's budget has increased by $62 million, and transfers mostly from PCORTF have more than offset decreases in PHS evaluation set-aside dollars. Although the majority of agency funding came from PHS evaluation set-aside dollars during this period—and an agency-specific discretionary appropriation in FY2015—funding from PCORTF has also grown considerably from $8 million in FY2011 to $101 million in FY2015.

Centers for Disease Control and Prevention (CDC)³³

Agency Overview

According to CDC, its mission is "to protect America from health, safety and security threats, both foreign and in the [United States]."³⁴ CDC is organized into a number of centers, institutes, and offices, some focused on specific public health challenges (e.g., injury prevention), others focused on general public health capabilities (e.g., surveillance and laboratory services).³⁵ In addition, the Agency for Toxic Substances and Disease Registry (ATSDR) is headed by the CDC Director and is discussed in this section.

Many CDC activities are not specifically authorized but are based in broad, permanent authorities in the PHSA.³⁶ Four CDC operating divisions are explicitly authorized. The National Institute for Occupational Safety and Health (NIOSH) was permanently authorized by the Occupational Safety and Health Act of 1970.³⁷ The National Center on Birth Defects and Developmental Disabilities (NCBDDD) was established in PHSA Section 317C by the Children's Health Act of 2000.³⁸ The National Center for Health Statistics (NCHS) was established in PHSA Section 306 by the Health Services Research, Health Statistics, and Medical Libraries Act of 1974.³⁹ ATSDR was established by the Comprehensive Environmental Response, Compensation and Liability Act of 1980 (CERCLA, the "Superfund" law).⁴⁰ Authorizations of appropriations for NCBDDD, NCHS, and ATSDR have expired, but the programs continue to receive annual appropriations.

CDC provides about $5 billion per year in grants to state, local, municipal, tribal, and foreign governments, and to academic and non-profit entities.⁴¹ It has few regulatory responsibilities.

Table 4 presents funding levels for CDC programs for FY2010 through the FY2016 request. In addition to annual discretionary appropriations, program level amounts for recent years include funds from the following four mandatory appropriations: (1) the Vaccines for Children (VFC) program;⁴² (2) NIOSH activities to support the Energy Employees Occupational Illness Compensation Program Act (EEOICPA);⁴³ (3) the World Trade Center (WTC) Health Program;⁴⁴ and (4) appropriations provided under ACA, principally through the PPHF.⁴⁵ CDC also receives annual set-aside funds and authorized user fees, and may also receive funding through supplemental appropriations and other transfers.

Agency Funding Since FY2010

Compared with FY2010, CDC's budget authority for FY2015 is lower, and its program level is higher (see Table 4). Two of CDC's mandatory funding sources—ACA funding, principally from the PPHF, and the WTC Health Program—have, in whole or part, replaced discretionary funding for some ongoing activities.

Both budget authority and program level reached their lowest points since FY2010 in FY2013, a result of sequestration of most mandatory and discretionary funds, and redirection of some PPHF funds to ACA implementation (see Appendix C). VFC and EEOICPA funds are exempt from sequestration. The PPHF and WTC Health Program are not, and sequestration of these mandatory funds has continued each fiscal year since FY2013.

In 2014 CDC implemented the "Working Capital Fund," a revolving fund to be used by agency programs to pay for agency-wide business services—such as procurement and human resources—that received direct appropriations in the past.⁴⁶ CDC now applies certain business services funds previously assigned to the Cross-cutting Activities and Program Support account to the programmatic accounts instead. Although this does not change the amount of funds available to the agency, it has the effect of increasing the amounts budgeted to programmatic accounts. CDC has adjusted its accounting from FY2012 forward to make budget lines comparable from year to year. Of note, Table 4 reflects this adjustment, such that amounts presented for FY2012 and later years are not necessarily comparable to amounts presented for FY2010 and FY2011.

In December 2014 Congress provided $1.771 billion in FY2015 emergency supplemental appropriations to CDC for response to the Ebola outbreak. The funds, which are available through FY2019, are to be used for both domestic and international activities. CDC has not yet presented these funds within its general budget, and they are not presented in Table 4. More information is available on the CDC website.⁴⁷

Food and Drug Administration (FDA)⁴⁸

Agency Overview

FDA regulates the safety of human foods, dietary supplements, cosmetics, and animal foods; and the safety and effectiveness of human drugs, biological products (e.g., vaccines), medical devices, radiation-emitting products, and animal drugs. In 2009, Congress gave FDA the authority to regulate the manufacture, marketing, and distribution of tobacco products in order to protect public health.

Seven centers within FDA represent the broad program areas for which the agency has responsibility: the Center for Biologics Evaluation and Research (CBER), the Center for Devices and Radiological Health (CDRH), the Center for Drug Evaluation and Research (CDER), the Center for Food Safety and Applied Nutrition (CFSAN), the Center for Veterinary Medicine (CVM), the National Center for Toxicological Research (NCTR), and the Center for Tobacco Products (CTP). Several other offices have agency-wide responsibilities.

The Federal Food, Drug, and Cosmetic Act (FFDCA) is the principal source of FDA's statutory authority.⁴⁹ FDA is also responsible for administering certain provisions in other laws, most notably the PHSA.⁵⁰ Although the FDA's authorizing committees in Congress are the committees with jurisdiction over public health issues—the Senate Committee on Health, Education, Labor, and Pensions, and the House Committee on Energy and Commerce—FDA's assignment within the appropriations committees reflects its origin as part of the Department of Agriculture. The Senate and House appropriations subcommittees on Agriculture, Rural Development, FDA, and Related Agencies have jurisdiction over FDA's budget, even though the agency has been part of various federal health agencies (HHS and its predecessors) since 1940.

FDA's budget has two funding streams: annual appropriations (i.e., discretionary budget authority, or BA) and industry user fees. In FDA's annual appropriation, Congress sets both the total amount of appropriated funds and the amount of user fees that the agency is authorized to collect and obligate for that fiscal year. Appropriated funds are largely for the Salaries and Expenses account, with a much smaller amount for the Buildings and Facilities account. The several different user fees, which account for 42% of FDA's total FY2015 program level, contribute only to the Salaries and Expenses account.

The largest and oldest FDA user fee that is linked to a specific program was first authorized by the Prescription Drug User Fee Act (PDUFA, P.L. 102-571) in 1992. Appendix E presents the authorizing legislation for current FDA user fees, sorted by the dollar amount they contribute to the agency's FY2015 budget. After PDUFA, Congress added user fee authorities regarding medical devices, animal drugs, animal generic drugs, tobacco products, priority review, food reinspection, food recall, voluntary qualified food importer, generic drugs, biosimilars, and, most recently, outsourcing facilities (related to drug compounding) and some wholesale distributors and third-party logistics providers (related to pharmaceutical supply chain security).⁵¹ Each of the medical product fee authorities requires reauthorization every five years. Several indefinite authorities apply to fees for mammography inspection, color additive certification, export certification, and priority review vouchers.⁵²

Agency Funding Since FY2010

Between FY2010 and FY2015, FDA's funding increased from $3.1 billion to $4.5 billion (see Table 5). Although congressionally provided appropriations increased 10% over that period, user fee revenue more than doubled. In FY2015, user fees account for 42% of FDA's total funding. Continuing funding issues for the agency include adequate resources to carry out food safety activities (the President's request includes a $301 million increase above the FY2015 level), the risk of user fees' being subject to subsequent sequestrations, and the ongoing challenge of performing increasing congressionally directed tasks without concomitant resources increases.

Health Resources and Services Administration (HRSA)⁵³

Agency Overview

HRSA is the federal agency charged with improving access to health care for those who are uninsured, isolated, or medically vulnerable. The agency currently awards funding to more than 3,000 grantees, including community-based organizations; colleges and universities; hospitals; state, local, and tribal governments; and private entities to support health services projects, such as training health care workers or providing specific health services.⁵⁴ HRSA also administers the health centers program, which provides grants to non-profit entities that provide primary care services to people who experience financial, geographic, cultural, or other barriers to health care.

HRSA is organized into five bureaus (see text box below) and ten offices. Some offices focus on specific populations or health care issues (e.g., Office of Women's Health, Office of Rural Health Policy), while others provide agency-wide support or technical assistance to HRSA's regional offices (e.g., Office of Planning, Analysis and Evaluation; Office of Regional Operations).⁵⁵

As noted in the text box, the majority of HRSA's programs are authorized by the PHSA or, in some cases, by the SSA. Additionally, Section 427(e) of the Federal Mine Safety and Health Amendments Act (P.L. 95-164) authorizes the Black Lung Program, which supports clinics that provide services to retired coal miners and others.

Agency Funding Since FY2010

HRSA funding increased from $8.1 billion in FY2010 to $10.3 billion in FY2015 despite a reduction in its discretionary appropriation during that time (see Table 6). Specifically, discretionary appropriations declined by about 18%; falling from $7.5 billion to $6.1 billion. Much of the decline in discretionary appropriations occurred because of the loss of discretionary appropriations for the National Health Service Corps (NHSC) and the elimination of the congressional earmark program that supported health care facility construction and renovation.

The overall growth in HRSA's funding was primarily driven by increasing amounts from the CHCF, which more than offset the decline in discretionary funding. While CHCF funding may have been intended to supplement annual discretionary appropriations for the health centers program and the NHSC, the funds have partially supplanted (i.e., replaced) discretionary health center funding and have become the sole source of funding for the NHSC program, which has not received an annual discretionary appropriation since FY2011.

With CHCF funding set to expire at the end of FY2015, Congress included two more years of CHCF funding in the Medicare Access and CHIP Reauthorization Act of 2015 (MACRA; P.L. 114-10); see Table 6 and Appendix B. MACRA also extended funding for other HRSA programs that were established and initially funded by the ACA; notably, the Maternal, Infant, and Early Childhood Home Visiting Program.

Sources: The funding amounts are from congressional budget justification documents and HHS's Budget in Brief available at http://www.hhs.gov/budget/; and from P.L. 114-10.

Indian Health Service (IHS)⁵⁶

Agency Overview

IHS provides health care for approximately 2.2 million eligible American Indians/Alaska Natives through a system of programs and facilities located on or near Indian reservations, and through contractors in certain urban areas. IHS provides services to members of 566 federally recognized tribes either directly or through facilities and programs operated by Indian Tribes or Tribal Organizations through self-determination contracts and self-governance compacts authorized in the Indian Self-Determination and Education Assistance Act (ISDEAA).⁵⁷

The Snyder Act of 1921 provides general statutory authority for IHS.⁵⁸ In addition, specific IHS programs are authorized by two acts: the Indian Sanitation Facilities Act of 1959⁵⁹ and the Indian Health Care Improvement Act (IHCIA).⁶⁰ The Indian Sanitation Facilities Act authorizes the IHS to construct sanitation facilities for Indian communities and homes, and IHCIA authorizes programs such as urban health, health professions recruitment, and substance abuse and mental health treatment, and permits IHS to receive reimbursements from Medicare, Medicaid, the State Children's Health Insurance Program (CHIP), the Department of Veterans Affairs (VA), and third-party insurers.

As discussed earlier, IHS receives its appropriations through the Interior/Environment appropriations act. IHS funding is not subject to the PHS Program Evaluation Set-Aside.

Agency Funding Since FY2010

IHS's funding, which includes discretionary appropriations and collections from third-party payers of health care, increased between FY2010 and FY2015 from $5.1 billion to $5.9 billion (see Table 7). This increase was driven both by increased discretionary appropriations, which rose from $4.1 billion to $4.6 billion, and by increased collections, which rose from $891 million to $1.1 billion. Much of the funding increase was used to support clinical services. Discretionary appropriations, in particular, have increased funding for purchased/referred care, a subset of the clinical services budget line that applies to funds used to refer patients to an outside provider when the IHS cannot provide a service within its system. Collections received from providing clinical services are also used to augment the clinical services budget.

National Institutes of Health (NIH)⁶¹

Agency Overview

NIH is the primary agency of the federal government charged with performing and supporting biomedical and behavioral research. Its activities cover a wide range of basic, clinical, and translational research, as well as research training and health information collection and dissemination. The agency is organized into 27 research institutes and centers, headed by the NIH Director. The Office of the Director (OD) sets overall policy for NIH and coordinates the programs and activities of all NIH components, particularly in areas of research that involve multiple institutes. The institutes and centers (collectively called ICs) focus on particular diseases, areas of human health and development, or aspects of research support. Each IC plans and manages its own research programs in coordination with the Office of the Director.

The bulk of NIH's budget, about 83%, goes out to the extramural research community through grants, contracts, and other awards. The funding supports research performed by more than 300,000 non-federal scientists and technical personnel who work at more than 2,500 universities, hospitals, medical schools, and other research institutions around the country and abroad.⁶² A smaller proportion of the budget, about 11%, supports the intramural research programs of the NIH institutes and centers, funding research performed by NIH scientists and non-employee trainees in the NIH laboratories and Clinical Center. The remaining 6% funds various research management, support, and facilities' needs.

NIH derives its statutory authority from the PHSA. Title III, Section 301 of the PHSA grants the Secretary of HHS broad permanent authority to conduct and sponsor research. In addition, Title IV, "National Research Institutes," authorizes in greater detail various activities, functions, and responsibilities of the NIH Director and the institutes and centers. All of the ICs are covered by specific provisions in the PHSA, but they vary considerably in the amount of detail included in the statutory language. There are few time-and-dollar authorization levels specified for individual activities. Congress mandated a significant reorganization of IC responsibilities in the FY2012 Consolidated Appropriations Act (P.L. 112-74, Division F) by creating a new National Center for Advancing Translational Sciences (NCATS) and eliminating the National Center for Research Resources (NCRR). Activities relating to translational sciences from NCRR and many other ICs were consolidated in NCATS, and NCRR's other programs were moved to several other ICs and the OD.

NIH gets almost its entire funding (99.5%) from annual discretionary appropriations. As shown in Table 8, the annual Labor-HHS-ED appropriations act provides separate appropriations to 24 of the ICs, the OD, and the Buildings and Facilities account. One of the ICs (Environmental Health Sciences) also receives funding from the Interior/Environment appropriations act. In addition, NIH receives a mandatory appropriation for type 1 diabetes research.

Agency Funding Since FY2010

NIH's funding in FY2015 is about 5% below the FY2010 level. This decline can be viewed as part of a broader funding trend that dates back to FY2003, the year Congress completed a five-year doubling of NIH's budget that resulted in the agency's funding increasing from $13.6 billion in FY1998 to $27.2 billion in FY2003.

Following the doubling period, NIH had several years of modest funding increases. Funding for the agency peaked in FY2010 at $31.2 billion before decreasing in each of the next three years. Overall, NIH's budget has failed to keep pace with the rising cost of biomedical research—as measured by the Biomedical Research and Development Price Index (BRDPI)—since the end of the doubling period. In constant (i.e., BRDPI-adjusted) 2012 dollars, NIH funding in FY2015 is 22% lower than the FY2003 level.⁶³

Substance Abuse and Mental Health Services Administration (SAMHSA)⁶⁴

Agency Overview

SAMHSA is the lead federal agency for increasing access to behavioral health services. It supports community-based mental health and substance abuse treatment and prevention services through formula grants to the states and U.S. territories and through competitive grant programs that fund states, territories, tribal organizations, local communities, and private entities. SAMHSA also engages in a range of other activities, such as technical assistance, data collection, and workforce development.

SAMHSA and most of its programs and activities are authorized under Title V of the PHSA, which organizes SAMHSA in three centers:

• Center for Substance Abuse Treatment (CSAT)⁶⁵
• Center for Substance Abuse Prevention (CSAP)⁶⁶
• Center for Mental Health Services (CMHS)⁶⁷

Each center has general statutory authority, called Programs of Regional and National Significance (PRNS), under which it has established grant programs for states and communities to address their important substance abuse and mental health needs. PHSA Title V also authorizes a number of specific grant programs, referred to as categorical grants.

SAMHSA's two largest grant programs are separately authorized under PHSA Title XIX, Part B. The Community Mental Health Services block grant falls within CMHS.⁶⁸ The full amount of the Substance Abuse Prevention and Treatment block grant falls within CSAT, although no less than 20% of each state's block grant must be used for prevention.⁶⁹

In addition to the three statutorily defined centers, SAMHSA's budget reflects a fourth category, "health surveillance and program support," for other activities such as collecting data, providing statistical and analytic support, raising public awareness, developing the behavioral health workforce, and maintaining the National Registry of Evidence-based Programs and Practices.⁷⁰

The last comprehensive reauthorization of SAMHSA and its programs occurred in 2000 as part of the Children's Health Act,⁷¹ which also added "charitable choice" provisions allowing religious organizations to receive funding for substance abuse prevention and treatment services without altering their religious character.⁷² Since 2000, Congress has expanded some of SAMHSA's programs and activities without taking up comprehensive reauthorization. Although authorizations of appropriations for most of SAMHSA's grant programs expired at the end of FY2003, many of these programs continue to receive annual discretionary appropriations.

Agency Funding Since FY2010

From FY2010 through FY2015, SAMHSA's program-level funding has generally hovered around $3.6 billion, dropping to $3.4 billion in FY2013 due to sequestration and rebounding to $3.6 billion in FY2014 (see Table 9). The current (FY2015) distribution of funding across CMHS (30%), CSAT (60%), CSAP (5%), and Health Surveillance and Program Support (5%) overstates the amount allocated to substance abuse treatment and understates the amount allocated to substance abuse prevention because CSAT's funding reflects the entire amount of the Substance Abuse Prevention and Treatment block grant, including the 20% set-aside for prevention. Relative to FY2015 funding, the FY2016 request would increase program-level funding by 1% while decreasing discretionary budget authority by 2%; it would make up the difference with increased funding from the set-aside and PPHF transfers.

American Recovery and Reinvestment Act (ARRA): FY2009 Supplemental Appropriations

Through ARRA, Congress appropriated a total of $22.4 billion in supplemental FY2009 discretionary appropriations for health and human services programs administered by HHS. Of that total amount, $15.1 billion was provided directly to, or allocated for, programs and activities administered by the PHS agencies (see text box below).⁷³ In most instances the funding was to remain available for obligation through the end of FY2010 (i.e., September 30, 2010). Essentially all the ARRA discretionary funds provided to HHS have been obligated.⁷⁴

Community Health Center Fund

ACA Section 10503 established a Community Health Center Fund (CHCF) to provide supplemental funding for community and other health centers and the National Health Service Corps (NHSC). The law provided annual appropriations to the CHCF totaling $11 billion over the five-year period FY2011 through FY2015. Of that total, $9.5 billion is for health center operations and the remaining $1.5 billion is for the NHSC.

Table B-1 shows the amounts appropriated for each fiscal year as well as the post-sequestration levels for FY2013-FY2015. CHCF funds are awarded to the various types of health centers that are supported by the federal health center program. Those include community health centers and migrant health centers, as well as facilities that serve the homeless and residents of public housing. Sequestration of CHCF funding for community health centers and migrant health centers is capped at 2%, whereas CHCF funding for the other types of facilities (i.e., health centers for the homeless and for public housing residents) and for the NHSC is fully sequestrable at the applicable rate for nonexempt nondefense mandatory spending (see Table 2).

The Medicare Access and CHIP Reauthorization Act of 2015 (MACRA; P.L. 114-10) appropriated two more years of funding to the CHCF. For both FY2016 and FY2017, MACRA provided $3.6 billion for health center operations and $310 million for the NHSC. Table B-1 shows the amounts for FY2016.

While CHCF funding may have been intended to supplement—not supplant—annual discretionary appropriations for the health center program and the NHSC, these mandatory funds have partially supplanted discretionary funding for the health center program and entirely replaced discretionary funding for the NHSC (see Table 6).

Prevention and Public Health Fund (PPHF)

ACA Section 4002 established the Prevention and Public Health Fund (PPHF), to be administered by the HHS Secretary, and provided it with a permanent annual appropriation. Under the ACA, PPHF's annual appropriation would increase from $500 million for FY2010 to $2 billion for FY2015 and each subsequent fiscal year. However, the Middle Class Tax Relief and Job Creation Act of 2012 amended the ACA by reducing the PPHF appropriation from FY2013 through FY2021 as part of a package of offsets to partly cover the costs of the law.⁷⁵ The PPHF annual appropriation is now $1 billion through FY2017, and thereafter will increase in increments to $2 billion for FY2022 and each subsequent fiscal year.

The HHS Secretary is instructed to transfer amounts from the PPHF to agencies for prevention, wellness, and public health activities. The funds are available to the Secretary at the beginning of each fiscal year. The Administration's annual budget sets out the intended distribution and use of PPHF funds for that fiscal year. The Secretary determined the distribution of PPHF funds for FY2010 through FY2013. For FY2014 and FY2015 funds, Congress explicitly directed the distribution of PPHF funds, prohibiting the Secretary from making further transfers.⁷⁶

As discussed earlier in the report, the PPHF appropriation is fully sequestrable at the applicable percentage rate for nonexempt nondefense mandatory spending (see Table 2). Sequestration is applied to the entire appropriation by the Secretary before funds are transferred to the agencies.

The distribution of PPHF funds to HHS agencies for FY2010 through the FY2016 President's budget proposal is presented in Table C-1. Further details regarding PPHF distributions to AHRQ, CDC, HRSA, and SAMHSA are provided in the respective agency budget tables in the body of this report.⁷⁷

For FY2013, the Secretary transferred almost half of available PPHF funds to CMS for ACA implementation, as shown in Table C-1. This transfer reduced the PPHF funds that had been provided to some of the PHS agencies from what they had received for FY2012. Along with the sequestration of discretionary funding in FY2013, the loss of PPHF funds that year had a significant effect on CDC's budget for FY2013.⁷⁸

In determining the transfer of PPHF funds for FY2010 through FY2013, the Secretary funded a mix of pre-existing programs and activities, and programs and activities newly authorized under the ACA. In directing the distribution of FY2014 and FY2015 PPHF funds, Congress in most cases provided PPHF funds to pre-existing programs and activities.

Patient-Centered Outcomes Research Trust Fund

Section 6301(e) of the ACA established the Patient-Centered Outcomes Research Trust Fund (PCORTF) to support comparative clinical effectiveness research at both HHS and the Patient-Centered Outcomes Research Institute (PCORI).⁷⁹ The law provided annual funding to the PCORTF over the period FY2010-FY2019 from the following three sources: (1) annual appropriations; (2) fees on health insurance and self-insured plans; and (3) transfers from the Medicare Part A and Part B Trust Funds.

Specifically, the ACA appropriated the following amounts to the PCORTF: (1) $10 million for FY2010; (2) $50 million for FY2011; and (3) $150 million for each of FY2012 through FY2019. In addition, for each of FY2013 through 2019, the ACA appropriated an amount equivalent to the net revenues from a new fee that the law imposes on health insurance policies and self-insured plans. For policy/plan years ending during FY2013, the fee equals $1 multiplied by the number of covered lives. For policy/plan years ending during each subsequent fiscal year through FY2019, the fee equals $2 multiplied by the number of covered lives. Finally, transfers to PCORTF from the Medicare Part A and Part B trust funds are calculated by multiplying the average number of individuals entitled to benefits under Medicare Part A, or enrolled in Medicare Part B, by $1 (for FY2013) or by $2 (for each of fiscal years 2014 through 2019).

For each of FY2011 through FY2019, the ACA requires 80% of the PCORTF funds to be made available to PCORI, and the remaining 20% of funds to be transferred to the HHS Secretary for carrying out PHSA Section 937.⁸⁰ Of the total amount transferred to HHS, 80% is to be distributed to AHRQ. Table D-1 shows the allocation of PCORTF funds through FY2016.

FDA User Fee Authorizations