Recent Troubles at the FDA and Their Impact on Transparency

The FDA’s long-standing commitment to transparency faces unprecedented challenges in 2025 following a series of organizational disruptions that threaten to undermine the agency’s ability to share critical regulatory information with stakeholders and the public. These developments represent a significant departure from the agency’s historical transparency trajectory and raise serious concerns about the future accessibility of regulatory data and decision-making processes.

Mass Workforce Reductions and Organizational Disruption

The most significant challenge facing FDA transparency stems from the massive reduction in force implemented in April 2025. The Department of Health and Human Services terminated approximately 3,500 FDA employees on April 1, 2025, representing nearly 20% of the agency’s workforce. This dramatic downsizing followed an earlier reduction in February 2025 that eliminated approximately 700 workers, creating a cumulative impact that has fundamentally altered the agency’s operational capacity.

While HHS officials emphasized that the cuts would not directly impact medical product reviewers, food reviewers, or inspectors, the layoffs eliminated critical support staff across multiple areas essential to transparency operations. The reduction in force targeted employees in policy development, communications, information technology, procurement, and project management—all functions that are integral to maintaining the agency’s transparency infrastructure.

Former FDA Commissioner Robert Califf captured the gravity of the situation in a LinkedIn post stating, “The FDA as we’ve known it is finished”. This assessment reflects the widespread concern that the agency’s foundational capabilities for information sharing and public communication have been irreparably damaged.

Communication Infrastructure Breakdown

Press Releases and Public Information Systems

The workforce reductions have created significant gaps in the FDA’s ability to communicate with the public and industry stakeholders. Communications staff responsible for issuing press releases, updating the FDA’s website, and informing consumers about health risks and new product approvals were among those eliminated. This has resulted in delays and inconsistencies in the dissemination of critical safety information and regulatory updates.

The impact on communication capabilities became evident through reports of delayed updates to key databases and reduced responsiveness to routine inquiries from industry participants. Even before the April layoffs, industry observers had noted a decline in FDA’s responsiveness, particularly to non-essential or routine questions, suggesting that the communication infrastructure was already under strain.

Website and Database Management Issues

The FDA’s digital transparency infrastructure has suffered significant disruptions due to the loss of IT support staff. Key databases that physicians and public health experts rely on for drug safety and manufacturing information have been neglected, leaving health professionals without access to basic information about medications they prescribe. An FDA official described the situation as “really a nightmare,” noting that “things that used to function are no longer functioning”.

Specific database problems include missing labeling information in the FDA’s drug database, which provides critical information about drug approvals, labeling changes, and market withdrawals. Most entries since the April 1 job cuts are missing essential labeling information that tells doctors what drugs are approved for, contraindications, dosing instructions, and side effects. Additionally, the National Drug Code Directory, which provides identification codes for pharmaceutical products, has experienced delayed updates due to staff cuts.

Drug Safety Information Delays

One of the most concerning transparency impacts involves delays in drug safety reporting. The FDA’s Drug Safety-Related Labeling Changes (SrLC) database, which typically receives updates every four days, had gone extended periods without updates. This database contains critical information about newly identified risks or side effects of medications already on the market.

Inspection and Compliance Reporting

The FDA’s ability to maintain its extensive inspection and compliance reporting systems faces significant challenges due to support staff reductions. While inspectors themselves were reportedly not affected by the layoffs, inspection support staff responsible for booking travel, securing translators, and managing administrative functions were eliminated.

The impact on inspection transparency is particularly concerning given the FDA’s existing challenges with inspection backlogs. Prior to the workforce reductions, the agency faced criticism for failing to meet pre-pandemic inspection levels, with roughly 2,000 pharmaceutical manufacturers not inspected since before COVID-19. The additional strain from reduced support staff threatens to further compromise the agency’s ability to maintain transparency about facility compliance and inspection outcomes..

Long-term Transparency Implications

Institutional Knowledge Loss

The elimination of thousands of experienced FDA employees represents a significant loss of institutional knowledge that has traditionally supported the agency’s transparency initiatives. Scientists who developed regulatory science standards, policy staff who interpreted regulations, and communications professionals who translated complex regulatory information for public consumption have been removed from the agency.

This knowledge loss threatens the continuity of transparency practices and may result in inconsistent application of disclosure policies as remaining staff struggle to maintain established processes with reduced resources and experience.

Stakeholder Confidence and Trust

The disruption to FDA transparency systems has undermined stakeholder confidence in the agency’s ability to maintain its historical commitment to open government and regulatory clarity. Over 200 biotech leaders signed a letter to the Senate Health, Education, Labor, and Pensions Committee urging the government to “quickly preserve and restore” the FDA’s core functions and avoid delays to promised drug-approval decision dates.

The breakdown of communication systems and delays in critical safety information sharing have created an environment of uncertainty that challenges the trust-based relationship between the FDA and the industries it regulates. This erosion of confidence may have long-term implications for voluntary compliance and cooperative regulatory relationships that have traditionally supported the agency’s transparency objectives.

Conclusion

The recent troubles at the FDA represent the most significant threat to regulatory transparency in decades. The massive workforce reductions, communication infrastructure breakdown, database management failures, and operational disruptions have created a perfect storm that undermines the agency’s ability to maintain its historical commitment to open government and stakeholder engagement.

While the full impact of these changes continues to unfold, early evidence suggests that the FDA’s capacity for transparent regulatory oversight has been fundamentally compromised. The loss of critical support staff, breakdown of communication systems, and delays in safety information sharing represent a dramatic departure from the agency’s transparency trajectory and raise serious questions about the future accessibility of regulatory information.

The implications extend far beyond administrative efficiency, as transparency failures can impact patient safety, undermine industry confidence, and compromise the integrity of the regulatory system. Restoring the FDA’s transparency capabilities will require not only addressing immediate staffing needs but also rebuilding the institutional infrastructure that has traditionally supported the agency’s commitment to open government and regulatory clarity.

Sources

Quality Unit Oversight Failures: A Critical Analysis of Recent FDA Warning Letters

The continued trend in FDA warning letters citing Quality Unit (QU) deficiencies highlights a concerning reality across pharmaceutical manufacturing operations worldwide. Three warning letters recently issued to pharmaceutical companies in China, India, and Malaysia reveal fundamental weaknesses in Quality Unit oversight that extend beyond isolated procedural failures to indicate systemic quality management deficiencies. These regulatory actions demonstrate the FDA’s continued emphasis on the Quality Unit as the cornerstone of pharmaceutical quality systems, with expectations that these units function as independent guardians of product quality with sufficient authority, resources, and expertise. This analysis examines the specific deficiencies identified across recent warning letters, identifies patterns of Quality Unit organizational failures, explores regulatory expectations, and provides strategic guidance for building robust quality oversight capabilities that meet evolving compliance standards.

Recent FDA Warning Letters Highlighting Critical Quality Unit Deficiencies

Multiple Geographic Regions Under Scrutiny

The FDA has continues to provide an intense focus on Quality Unit oversight through a series of warning letters targeting pharmaceutical operations across Asia. As highlighted in a May 19, 2025 GMP Compliance article, three notable warning letters targeted specific Quality Unit failures across multiple regions. The Chinese manufacturer failed to establish an adequate Quality Unit with proper authority to oversee manufacturing operations, particularly in implementing change control procedures and conducting required periodic product reviews. Similarly, the Indian manufacturer’s Quality Unit failed to implement controls ensuring data integrity, resulting in unacceptable documentation practices including torn batch records, damaged testing chromatograms, and improperly completed forms. The Malaysian facility, producing OTC products, showed failures in establishing adequate training programs and performing appropriate product reviews, further demonstrating systemic quality oversight weaknesses. These geographically diverse cases indicate that Quality Unit deficiencies represent a global challenge rather than isolated regional issues.

Historical Context of Regulatory Concerns

FDA’s focus on Quality Unit responsibilities isn’t new. A warning letter to a Thai pharmaceutical company earlier in 2024 cited Quality Unit deficiencies including lack of control over manufacturing operations, inadequate documentation of laboratory preparation, and insufficient review of raw analytical data. These issues allowed concerning practices such as production staff altering master batch records and using erasable markers on laminated sheets for production records. Another notable case involved Henan Kangdi Medical Devices, where in January 2020 the FDA stated explicitly that “significant findings in this letter indicate that your quality unit is not fully exercising its authority and/or responsibilities”. The consistent regulatory focus across multiple years suggests pharmaceutical manufacturers continue to struggle with properly empowering and positioning Quality Units within their organizational structures.

Geographic Analysis of Quality Unit Failures: Emerging vs. Mature Regulatory Markets

These FDA warning letters highlighting Quality Unit (QU) deficiencies reveal significant disparities between pharmaceutical manufacturing practices in emerging markets (e.g., China, India, Malaysia, Thailand) and mature regulatory jurisdictions (e.g., the U.S., EU, Japan). These geographic differences reflect systemic challenges tied to regulatory infrastructure, economic priorities, and technological adoption.

In emerging markets, structural weaknesses in regulatory oversight and quality culture dominate QU failures. For example, Chinese manufacturers like Linghai ZhanWang Biotechnology (2025) and Henan Kangdi (2019) faced FDA action because their Quality Units lacked the authority to enforce CGMP standards, with production teams frequently overriding quality decisions. Similarly, Indian facilities cited in 2025 warnings struggled with basic data integrity controls, including torn paper records and unreviewed raw data—issues exacerbated by domestic regulatory bodies like India’s CDSCO, which inspects fewer than 2% of facilities annually. These regions often prioritize production quotas over compliance, leading to under-resourced Quality Units and inadequate training programs, as seen in a 2025 warning letter to a Malaysian OTC manufacturer whose QU staff lacked GMP training. Supply chain fragmentation further complicates oversight, particularly in contract manufacturing hubs like Thailand, where a 2024 warning letter noted no QU review of outsourced laboratory testing.

By contrast, mature markets face more nuanced QU challenges tied to technological complexity and evolving regulatory expectations. In the U.S. and EU, recent warnings highlight gaps in Quality Units’ understanding of advanced manufacturing technologies, such as continuous manufacturing processes or AI-driven analytics. A 2024 EU warning letter to a German API manufacturer, for instance, cited cybersecurity vulnerabilities in electronic batch records—a stark contrast to emerging markets’ struggles with paper-based systems. While data integrity remains a global concern, mature markets grapple with sophisticated gaps like inadequate audit trails in cloud-based laboratory systems, whereas emerging economies face foundational issues like erased entries or unreviewed chromatograms. Regulatory scrutiny also differs: FDA inspection data from 2023 shows QU-related citations in just 6.2% of U.S. facilities versus 23.1% in Asian operations, reflecting stronger baseline compliance in mature jurisdictions.

Case comparisons illustrate these divergences. At an Indian facility warned in 2025, production staff routinely overruled QU decisions to meet output targets, while a 2024 U.S. warning letter described a Quality Unit delaying batch releases due to inadequate validation of a new AI-powered inventory system. Training gaps also differ qualitatively: emerging-market QUs often lack basic GMP knowledge, whereas mature-market teams may struggle with advanced tools like machine learning algorithms.

These geographic trends have strategic implications. Emerging markets require foundational investments in QU independence, such as direct reporting lines to executive leadership, and adoption of centralized digital systems to mitigate paper-record risks. Partnerships with mature-market firms could accelerate quality culture development. Meanwhile, mature jurisdictions must modernize QU training programs to address rapidly changing technologies and strengthen oversight of decentralized production models.

Data Integrity as a Critical Quality Unit Responsibility

Data integrity issues feature prominently in recent enforcement actions, reflecting the Quality Unit’s crucial role as guardian of trustworthy information. The FDA frequently requires manufacturers with data integrity deficiencies to engage third-party consultants to conduct comprehensive investigations into record inaccuracies across all laboratories, manufacturing operations, and relevant systems. These remediation efforts must identify numerous potential issues including omissions, alterations, deletions, record destruction, non-contemporaneous record completion, and other deficiencies that undermine data reliability. Thorough risk assessments must evaluate potential impacts on product quality, with companies required to implement both interim protective measures and comprehensive long-term corrective actions. These requirements underscore the fundamental importance of the Quality Unit in ensuring that product decisions are based on accurate, complete, and trustworthy data.

Patterns of Quality Unit Organizational Failures

Insufficient Authority and Resources

A recurring theme across warning letters is Quality Units lacking adequate authority or resources to fulfill their responsibilities effectively. The FDA’s warning letter to Linghai ZhanWang Biotechnology Co. in February 2025 cited violations that demonstrated the company’s Quality Unit couldn’t effectively ensure compliance with CGMP regulations. Similarly, Lex Inc. faced regulatory action when its “quality system was inadequate” because the Quality Unit “did not provide adequate oversight for the manufacture of over-the-counter (OTC) drug products”.

These cases reflect a fundamental organizational failure to empower Quality Units with sufficient authority and resources to perform their essential functions. Without proper positioning within the organizational hierarchy, Quality Units cannot effectively challenge manufacturing decisions that might compromise product quality or regulatory compliance, creating systemic vulnerabilities.

Documentation and Data Management Deficiencies

Quality Units frequently demonstrate inadequate oversight of documentation and data management processes, allowing significant compliance risks to emerge. According to FDA warning letters, these issues include torn batch records, incompletely documented laboratory preparation, inadequate retention of weight printouts, and insufficient review of raw analytical data. One particularly concerning practice involved “production records on laminated sheets using erasable markers that could be easily altered or lost,” representing a fundamental breakdown of documentation control. These examples demonstrate how Quality Unit failures in documentation oversight directly enable data integrity issues that can undermine the reliability of manufacturing records, ultimately calling product quality into question. Effective Quality Units must establish robust systems for ensuring complete, accurate, and contemporaneous documentation throughout the manufacturing process.

Inadequate Change Control and Risk Assessment

Change control deficiencies represent another significant pattern in Quality Unit failures. Warning letters frequently cite the Quality Unit’s failure to ensure appropriate change control procedures, highlighting inadequate risk assessments as a particular area of concern. FDA inspectors have found that inadequate change control practices present significant compliance risks, with change control appearing among the top ten FDA 483 violations. These deficiencies often involve failure to evaluate the potential impact of changes on product quality, incomplete documentation of changes, and improper execution of change implementation. Effective Quality Units must establish robust change control processes that include thorough risk assessments, appropriate approvals, and verification that changes have not adversely affected product quality.

Insufficient Batch Release and Production Record Review

Quality Units regularly fail to conduct adequate reviews of production records and properly execute batch release procedures. A frequent citation in warning letters involves the Quality Unit’s failure to “review production records to assure that no errors have occurred or, if errors have occurred, that they have been fully investigated”. In several cases, the Quality Unit reviewed only analytical results entered into enterprise systems without examining the underlying raw analytical data, creating significant blind spots in quality oversight. This pattern demonstrates a superficial approach to batch review and release decisions that fails to fulfill the Quality Unit’s fundamental responsibility to ensure each batch meets all established specifications before distribution. Comprehensive batch record review is essential for detecting anomalies that might indicate quality or compliance issues requiring investigation.

Regulatory Expectations for Effective Quality Units

Core Quality Unit Responsibilities

The FDA has clearly defined the essential responsibilities of the Quality Unit through regulations, guidance documents, and enforcement actions. According to 21 CFR 211.22, the Quality Unit must “have the responsibility and authority to approve or reject all components, drug product containers, closures, in-process materials, packaging material, labeling, and drug products”. Additionally, the unit must “review production records to assure that no errors have occurred or, if errors have occurred, that they have been fully investigated”. FDA guidance elaborates that the Quality Unit’s duties include “ensuring that controls are implemented and completed satisfactorily during manufacturing operations” and “ensuring that developed procedures and specifications are appropriate and followed”. These expectations establish the Quality Unit as both guardian and arbiter of quality throughout the manufacturing process, with authority to make critical decisions regarding product acceptability.

Independence and Organizational Structure

Regulatory authorities expect Quality Units to maintain appropriate independence from production units to prevent conflicts of interest. FDA guidance specifically states that “under a quality system, it is normally expected that the product and process development units, the manufacturing units, and the QU will remain independent”. This separation ensures that quality decisions remain objective and focused on product quality rather than production metrics or efficiency considerations. While the FDA acknowledges that “in very limited circumstances, a single individual can perform both production and quality functions,” such arrangements require additional safeguards including “another qualified individual, not involved in the production operation, conduct[ing] an additional, periodic review of QU activities”. This guidance underscores the critical importance of maintaining appropriate separation between quality and production responsibilities.

Quality System Integration

Regulatory authorities increasingly view the Quality Unit as the central coordinator of a comprehensive quality system. The FDA’s guidance document “Quality Systems Approach to Pharmaceutical CGMP Regulations” positions the Quality Unit as responsible for creating, monitoring, and implementing the entire quality system. This expanded view recognizes that while the Quality Unit doesn’t assume responsibilities belonging to other organizational units, it plays a crucial role in ensuring that all departments understand and fulfill their quality-related responsibilities. The Quality Unit must therefore establish appropriate communication channels and collaborative mechanisms with other functional areas while maintaining the independence necessary to make objective quality decisions. This integrated approach recognizes that quality management extends beyond a single department to encompass all activities affecting product quality.

Strategic Approaches to Strengthening Quality Unit Effectiveness

Comprehensive Quality System Assessment

Organizations facing Quality Unit deficiencies should begin remediation with a thorough assessment of their entire pharmaceutical quality system. Warning letters frequently require companies to conduct “a comprehensive assessment and remediation plan to ensure your QU is given the authority and resources to effectively function”. This assessment should examine whether procedures are “robust and appropriate,” how the Quality Unit provides oversight “throughout operations to evaluate adherence to appropriate practices,” the effectiveness of batch review processes, and the Quality Unit’s investigational capabilities. A thorough gap analysis should compare current practices against regulatory requirements and industry best practices to identify specific areas requiring improvement. This comprehensive assessment provides the foundation for developing targeted remediation strategies that address the root causes of Quality Unit deficiencies.

Establishing Clear Roles and Adequate Resources

Effective remediation requires clearly defining Quality Unit roles and ensuring adequate resources to fulfill regulatory responsibilities. FDA warning letters frequently cite the absence of “written procedures for QU roles and responsibilities” as a significant deficiency. Organizations must develop detailed written procedures that clearly articulate the Quality Unit’s authority and responsibilities, including approval or rejection authority for components and drug products, review of production records, and oversight of quality-impacting procedures and specifications. Additionally, companies must assess whether Quality Units have sufficient staffing with appropriate qualifications and training to effectively execute these responsibilities. This assessment should consider both the number of personnel and their technical capabilities relative to the complexity of manufacturing operations and product portfolio.

Implementing Robust Data Integrity Controls

Data integrity represents a critical area requiring focused attention from Quality Units. Companies must implement comprehensive data governance systems that ensure records are attributable, legible, contemporaneous, original, and accurate (ALCOA principles). Quality Units should establish oversight mechanisms for all quality-critical data, including laboratory results, manufacturing records, and investigation documentation. These systems must include appropriate controls for paper records and electronic data, with verification processes to ensure consistency between different data sources. Quality Units should also implement risk-based audit programs that regularly evaluate data integrity practices across all manufacturing and laboratory operations. These controls provide the foundation for trustworthy data that supports sound quality decisions and regulatory compliance.

Developing Management Support and Quality Culture

Sustainable improvements in Quality Unit effectiveness require strong management support and a positive quality culture throughout the organization. FDA warning letters specifically call for “demonstration of top management support for quality assurance and reliable operations, including timely provision of resources to address emerging manufacturing and quality issues”. Executive leadership must visibly champion quality as an organizational priority and empower the Quality Unit with appropriate authority to fulfill its responsibilities effectively. Organizations should implement programs that promote quality awareness at all levels, with particular emphasis on the shared responsibility for quality across all departments. Performance metrics and incentive structures should align with quality objectives to reinforce desired behaviors and decision-making patterns. This culture change requires consistent messaging, appropriate resource allocation, and leadership accountability for quality outcomes.

Conclusion

FDA warning letters reveal persistent Quality Unit deficiencies across global pharmaceutical operations, with significant implications for product quality and regulatory compliance. The patterns identified—including insufficient authority and resources, documentation and data management weaknesses, inadequate change control, and ineffective batch review processes—highlight the need for fundamental improvements in how Quality Units are structured, resourced, and empowered within pharmaceutical organizations. Regulatory expectations clearly position the Quality Unit as the cornerstone of effective pharmaceutical quality systems, with responsibility for ensuring that all operations meet established quality standards through appropriate oversight, review, and decision-making processes.

Addressing these challenges requires a strategic approach that begins with comprehensive assessment of current practices, establishment of clear roles and responsibilities, implementation of robust data governance systems, and development of a supportive quality culture. Organizations that successfully strengthen their Quality Units can not only avoid regulatory action but also realize significant operational benefits through more consistent product quality, reduced manufacturing deviations, and more efficient operations. As regulatory scrutiny of Quality Unit effectiveness continues to intensify, pharmaceutical manufacturers must prioritize these improvements to ensure sustainable compliance and protect patient safety in an increasingly complex manufacturing environment.

Key Warning Letters Discussed

Linghai ZhanWang Biotechnology Co., Ltd. (China) — February 25, 2025
- (For the original FDA letter, search the FDA Warning Letters database for “Linghai ZhanWang Biotechnology Co” and the date “02/25/2025”)
Henan Kangdi Medical Devices Co. Ltd. (China) — December 3, 2019
- (For the original FDA letter, search the FDA Warning Letters database for “Henan Kangdi Medical Devices” and the date “12/03/2019”)
Drug Manufacturing Facility in Thailand — February 27, 2024
- (For the original FDA letter, search the FDA Warning Letters database for “Thailand” and the date “02/27/2024”)
BioAsia Worldwide (Malaysia) — February 2025
- (For the original FDA letter, search the FDA Warning Letters database for “BioAsia Worldwide” and the date “02/2025”)

For the most authoritative and up-to-date versions, always use the FDA Warning Letters database and search by company name and date.

FDA Under Fire: The Troubling Impacts of Trump’s First 100 Days

The first 100 days of President Trump’s second term have been nothing short of seismic for the Food and Drug Administration (FDA). Sweeping layoffs, high-profile firings, and a mass exodus of experienced staff have left the agency reeling, raising urgent questions about the safety of drugs, devices, and food in the United States.

Unprecedented Layoffs and Firings

Mass Layoffs and Restructuring

On April 1, 2025, the Department of Health and Human Services (HHS) executed a reduction in force that eliminated 3,500 FDA employees. This was part of a larger federal downsizing that saw at least 121,000 federal workers dismissed across 30 agencies in Trump’s first 100 days, with health agencies like the FDA, CDC, and NIH particularly hard hit. Security guards barred entry to some FDA staff just hours after they received termination notices, underscoring the abruptness and scale of the cuts.

The layoffs were not limited to support staff. Policy experts, project managers, regulatory scientists, and communications professionals were let go, gutting the agency’s capacity to write guidance documents, manage application reviews, test product safety, and communicate risks to the public. Even before the April layoffs, industry had noticed a sharp decline in FDA responsiveness to routine and nonessential queries-a problem now set to worsen.

High-Profile Departures and Forced Resignations

The leadership vacuum is equally alarming. Key figures forced out or resigning under pressure include:

Dr. Peter Marks, CBER Director and the nation’s top vaccine official, dismissed after opposing the administration’s vaccine safety stance.
Dr. Robert Temple, a 52-year FDA veteran and regulatory pioneer, retired amidst the turmoil.
Dr. Namandjé N. Bumpus, Deputy Commissioner; Dr. Doug Throckmorton, Deputy Director for regulatory programs; Celia Witten, CBER Deputy Director; Peter Stein, Director of the Office of Drugs; and Brian King, head of the Center for Tobacco Products, all departed-some resigning when faced with termination.
Communications, compliance, and policy offices were decimated, with all FDA communications now centralized under HHS, ending decades of agency independence.

The new FDA Commissioner, Martin “Marty” Makary, inherits an agency stripped of much of its institutional memory and scientific expertise. Add to this very real questions about about Makary’s capabilities and approach:

1. Lack of FDA Institutional Memory and Support: Makary steps into the role just as the FDA’s deep bench of experienced scientists, regulators, and administrators has been depleted. The departure of key leaders and thousands of staff means Makary cannot rely on the usual institutional memory or internal expertise that historically guided complex regulatory decisions. The agency’s diminished capacity raises concerns about whether Makary can maintain the rigorous review standards and enforcement practices needed to protect public health.

2. Unconventional Background and Public Persona: While Makary is an accomplished surgeon and health policy researcher, his career has been marked by a willingness to challenge medical orthodoxy and criticize federal health agencies, including the FDA itself. His public rhetoric-often sharply critical and sometimes inflammatory-contrasts with the FDA’s traditionally cautious, evidence-based communication style. For example, Makary has accused government agencies of “lying” about COVID-19 boosters and has called the U.S. food supply “poison,” positions that have worried many in the scientific and public health communities.

3. Alignment with Political Leadership and Potential Conflicts: Makary’s views align closely with those of HHS Secretary Robert F. Kennedy Jr., particularly in their skepticism of certain mainstream public health measures and their focus on food additives, pesticides, and environmental contributors to chronic disease. This alignment raises questions about the degree to which Makary will prioritize political directives over established scientific consensus, especially in controversial areas like vaccine policy, food safety, and chemical regulation.

4. Contrarianism and a Tendency Towards Conspiracy: Makary’s recent writings, such as his book Blind Spots, emphasize his distrust of medical consensus and advocacy for challenging “groupthink” in health policy. Critics worry this may lead to the dismissal of well-established scientific standards in favor of less-tested or more ideologically driven policies. As Harvard’s Dr. Aaron Kesselheim notes, Makary will need to make decisions based on evolving evidence, even if that means occasionally being wrong-a process that requires humility and openness to expert input, both of which could be hampered by the loss of institutional expertise.

5. Immediate Regulatory and Ethical Challenges: Makary inherits unresolved, high-stakes regulatory issues, such as the controversy over compounded GLP-1 drugs and the agency’s approach to ultra-processed foods and food additives. His prior involvement with telehealth companies and outspoken positions on food chemicals could present conflicts of interest or at least the appearance of bias, further complicating his ability to act as an impartial regulator.

Impact on Patient Health and Safety

Reduced Oversight and Enforcement

The loss of thousands of staff-including scientists and specialists-means fewer eyes on the safety of drugs, devices, and food. Despite HHS assurances that product reviewers and inspectors were spared, the reality is that critical support staff who enable and assist reviews and inspections were let go. This has already resulted in:

Delays and unpredictability in drug and device approvals, as fewer project managers are available to coordinate and communicate with industry.
A likely reduction in inspections, as administrative staff who book travel and provide translation for inspectors are gone, forcing inspectors to take on additional tasks and leading to bottlenecks.
The pausing of FDA’s unannounced foreign inspection pilot program, raising the risk of substandard or adulterated imported products entering the U.S. market.

Diminished Public Communication

With the elimination of FDA’s communications staff and the centralization of messaging under HHS, the agency’s ability to quickly inform the public about recalls, safety alerts, and emerging health threats is severely compromised. This loss of transparency and direct communication could delay critical warnings about unsafe products or outbreaks.

Loss of Scientific Capacity

The departure of regulatory scientists and the decimation of the National Center for Toxicological Research threaten the FDA’s ability to conduct the regulatory science that underpins product safety and efficacy standards. As former Commissioner Robert Califf warned, “The FDA as we’ve known it is over, with most leaders who possess knowledge and deep understanding product development safety no longer in their positions… I believe that history will regard this as a grave error”.

Impact on Clinical Studies

Oversight and Ethical Safeguards Eroded

FDA oversight of clinical trials has plummeted. During Trump’s previous term, the agency sent far fewer warning letters for clinical trial violations than under Obama (just 12 in Trump’s first three years, compared to 99 in Obama’s first three), a trend likely to worsen with the latest staff cuts. The loss of experienced reviewers and compliance staff means less scrutiny of trial protocols, informed consent, and data integrity, potentially exposing participants to greater risk and undermining the credibility of U.S. clinical research.

Delays and Uncertainty for Sponsors

With fewer staff to provide guidance, answer questions, and manage applications, sponsors of clinical trials and new product applications face longer wait times and less predictable review timelines. The loss of informal dispute resolution mechanisms and scientific advisory capacity further complicates the regulatory landscape, making the U.S. a less attractive environment for innovation.

Impact on Good Manufacturing Practices (GMPs)

Inspections and Compliance at Risk

While HHS claims inspectors were not cut, the loss of support staff and administrative personnel is already affecting the FDA’s inspection regime. Inspectors now must handle both investigative and administrative tasks, increasing the risk of missed deficiencies and delayed responses to manufacturing problems. The FDA may increasingly rely on remote, paper-based inspections, which proved less effective during the COVID-19 pandemic and could allow GMP violations to go undetected.

Global Supply Chain Vulnerabilities

The rollback of foreign inspection programs and diminished regulatory science capacity further expose the U.S. to risks from overseas manufacturers, particularly in countries with less robust regulatory oversight. This could lead to more recalls, shortages, and public health emergencies.

A Historic Setback for Public Health

The Trump administration’s first 100 days have left the FDA a shell of its former self. The mass layoffs, firings, and resignations have gutted the agency’s scientific, regulatory, and communications capacity, with immediate and long-term consequences for patient safety, clinical research, and the integrity of the U.S. medical supply. The loss of institutional knowledge, the erosion of oversight, and the retreat from global leadership represent a profound setback for public health-one that will take years, if not decades, to repair.

As former FDA Commissioner Califf put it, “No segment of FDA is untouched. No one knows what the plan is”. The nation-and the world-are watching to see if the agency can recover from this unprecedented upheaval.

Citations:

Engineering Runs in the ASTM E2500 Validation Lifecycle

Engineering runs (ERs) represent a critical yet often underappreciated component of modern biopharmaceutical validation strategies. Defined as non-GMP-scale trials that simulate production processes to identify risks and optimize parameters, Engineering Runs bridge the gap between theoretical process design and manufacturing. Their integration into the ASTM E2500 verification framework creates a powerful synergy – combining Good Engineering Practice (GEP) with Quality Risk Management (QRM) to meet evolving regulatory expectations.

When aligned with ICH Q10’s pharmaceutical quality system (PQS) and the ASTM E2500 lifecycle approach, ERs transform from operational exercises into strategic tools for:

Design space verification per ICH Q8
Scale-up risk mitigation during technology transfer
Preparing for operational stability
Continuous process verification in commercial manufacturing

ASTM E2500 Framework Primer: The Four Pillars of Modern Verification

ASTM E2500 offers an iterative lifecycle approach to validation:

Requirements Definition
Subject Matter Experts (SMEs) collaboratively identify critical aspects impacting product quality using QRM tools. This phase emphasizes:
- Process understanding over checklist compliance
- Supplier quality systems evaluation
- Risk-based testing prioritization
Specification & Design
The standard mandates “right-sized” documentation – detailed enough to ensure product quality without unnecessary bureaucracy.
Verification
This phase provides a unified verification approach focusing on:
- Critical process parameters (CPPs)
- Worst-case scenario testing
- Leveraging vendor testing data
Acceptance & Release
Final review incorporates ICH Q10’s management responsibilities, ensuring traceability from initial risk assessments to verification outcomes.

Engineering runs serve as a critical bridge between design verification and formal Process Performance Qualification (PPQ). ERs validate critical aspects of manufacturing systems by confirming:

Equipment functionality under simulated GMP conditions
Process parameter boundaries for Critical Process Parameters (CPPs)
Facility readiness through stress-testing utilities, workflows, and contamination controls

	Demonstration/ Training Run prior to GMP area	Shakedown. Demonstration/Training Run in GMP area	Engineering Run	cGMP Manufacturing
Room and Equipment
Room	N/A	IOQ Post-Approval	Released and Active
Process Gas			Generation and Distribution Released Point of use assembly PQ complete
Process utility
Process Equipment		Functionally verified or calibrated as required (commissioned)	IOQ Approved	Full released
Analytical Equipment			Released
Alarms		N/A	Alarm ranges and plan defined	Alarms qualified
Raw Materials
Bill of Materials	RM in progress		Approved
Suppliers	Approval in Progress		Approved
Specifications	In Draft		Effective
Release	Non-GMP Usage decision		Released
Process Documentation
Source Documentation	To be defined in Tech Transfer Plan		Engineering Run Protocol	Tech Transfer closed
Batch Records and product specific Work Instructions	Draft		Reviewed Draft	Approved
Process and Equipment SOPs	N/A	Draft	Effective
Product Labels	N/A		Draft Labels	Approved Labels
QC Testing and Documentation
BSC and Personnel Environmental Monitoring	N/A		Effective
Analytical Methods	Suitable for use		Phase Appropriate Validation
Stability	N/A		In place
Certificate of Analysis	N/A		Defined in Engineering Protocol	Effective
Sampling Plan	Draft		Draft use as defined in engineering protocol	Effective
Operations/Execution
Operator Training	Observe and perform operations to gain hands on experience with SME observation		Process specific equipment OJT Gown qualifiedBSC OJT Aseptic OJT Material Transfer OJT (All training in eQMS)	Training in Use
Process Lock	As defined in Tech Transfer Plan		6-week prior to execution	Approved Process Description
Deviations	N/A	N/A	Process – Per Engineering Run protocol FUSE – per SOP	Per SOP
Final Disposition	N/A	N/A	Not for Human Use	Per SOP
Oversite	PP&D		MS&T	QA on the floor and MS&T as necessary

U.S. Pharmacopeia’s draft chapter〈1110〉Microbial Contamination Control Strategy Considerations

The pharmaceutical industry is navigating a transformative period in contamination control, driven by the convergence of updated international standards. The U.S. Pharmacopeia’s draft chapter〈1110〉 Microbial Contamination Control Strategy Considerations (March 2025) joins EU GMP Annex 1 (2022) in emphasizing risk-based strategies but differ in technical requirements and classification systems.

USP〈1110〉: A Lifecycle-Oriented Microbial Control Framework

The draft USP chapter introduces a comprehensive contamination control strategy (CCS) that spans the entire product lifecycle, from facility design to post-market surveillance. It emphasizes microbial, endotoxin, and pyrogen risks, requiring manufacturers to integrate quality risk management (QRM) into every operational phase. Facilities must adopt ISO 14644-1 cleanroom classifications, with ISO Class 5 (≤3,520 particles ≥0.5 µm/m³) mandated for aseptic processing areas. Environmental monitoring programs must include both viable (microbial) and nonviable particles, with data trends analyzed quarterly to refine alert/action levels. Unlike Annex 1, USP allows flexibility in risk assessment methodologies but mandates documented justifications for control measures, such as the use of closed systems or isolators to minimize human intervention.

The Challenge of Cleanroom Classification Harmonization

EU GMP Annex 1: Granular Cleanroom and Sterilization Requirements

Annex 1 builds on ISO 14644-1 cleanroom standards but introduces pharmaceutical-specific adaptations through its Grade A–D system. Grade A zones (critical processing areas) require ISO Class 5 conditions during both “at-rest” and “in-operation” states, with continuous particle monitoring and microbial limits of <1 CFU/m³. Annex 1 also mandates smoke studies to validate unidirectional airflow patterns in Grade A areas, a requirement absent in ISO 14644-1. Sterilization processes, such as autoclaving and vaporized hydrogen peroxide (VHP) treatments, require pre- and post-use integrity testing, aligning with its focus on sterility assurance.

Reconciling Annex 1 and ISO 14644-1 Cleanroom Classifications

While both frameworks reference ISO 14644-1, Annex 1 overlays additional pharmaceutical requirements:

Aspect	EU GMP Annex 1	ISO 14644-1
Classification System	Grades A–D mapped to ISO classes	ISO Class 1–9 based on particle counts
Particle Size	≥0.5 µm and ≥5.0 µm monitoring for Grades A–B	≥0.1 µm to ≥5.0 µm, depending on class
Microbial Limits	Explicit CFU/m³ limits for each grade	No microbial criteria; focuses on particles
Operational States	Qualification required for “at-rest” and “in-operation” states	Single-state classification permitted
Airflow Validation	Smoke studies mandatory for Grade A	Airflow pattern testing optional

For example, a Grade B cleanroom (ISO Class 7 at rest) must maintain ISO Class 7 particle counts during production but adheres to stricter microbial limits (≤10 CFU/m³) than ISO 14644-1 alone. Manufacturers must design monitoring programs that satisfy both standards, such as deploying continuous particle counters for Annex 1 compliance while maintaining ISO certification reports.

Classification	Description
Grade A	Critical area for high-risk and aseptic operations that corresponds to ISO 5 at rest/static and ISO 4.8 (in-operation/dynamic). Grade A areas apply to aseptic operations where the sterile product, product primary packaging components and product-contact surfaces are exposed to the environment. Normally Grade A conditions are provided by localized air flow protection, such as unidirectional airflow workstations within a Restricted Access Barrier System (RABS) or isolator. Direct intervention (e.g., without the protection of barrier and glove port protection) into the Grade A area by operators must be minimized by premises, equipment, process, or procedural design.
Grade B	For aseptic preparation and filling, this is the background area for Grade A (where it is not an isolator) and corresponds to ISO 5 at rest/static and ISO 7 in-operation/dynamic. Air pressure differences must be continuously monitored. Classified spaces of lower grade can be considered with the appropriate risk assessment and technical justification.
Grade C	Used for carrying out less critical steps in the manufacture of aseptically filled sterile products or as a background for isolators. They can also be used for the preparation/filling of terminally sterilized products. Grade C correspond to ISO 7 at rest/static and ISO 8 in-operation/dynamic.
Grade D	Used to carry out non-sterile operations and corresponds to ISO 8 at rest/static and in-operation/dynamic.

Risk Management: Divergent Philosophies, Shared Objectives

Both frameworks require Quality Risk Management. USP〈1110〉advocates for a flexible, science-driven approach, allowing tools like HACCP (Hazard Analysis Critical Control Points) or FMEA (Failure Modes Effects Analysis) to identify critical control points. For instance, a biologics manufacturer might use HACCP to prioritize endotoxin controls during cell culture harvesting. USP also emphasizes lifecycle risk reviews, requiring CCS updates after facility modifications or adverse trend detections.

Annex 1 mandates formal QRM processes with documented risk assessments for all sterilization and aseptic processes. Its Annex 1.25 clause requires FMEA for media fill simulations, ensuring worst-case scenarios (e.g., maximum personnel presence) are tested. Risk assessments must also justify cleanroom recovery times after interventions, linking airflow validation data to contamination probability.

A harmonized approach involves:

Baseline Risk Identification: Use HACCP to map contamination risks across product stages, aligning with USP’s lifecycle focus.
Control Measure Integration: Apply Annex 1’s sterilization and airflow requirements to critical risks identified in USP’s CCS.
Continuous Monitoring: Combine USP’s trend analysis with continuous monitoring for real-time risk mitigation.

Strategic Implementation Considerations

Reconciling these standards requires a multi-layered strategy. Facilities must first achieve ISO 14644-1 certification for particle counts, then overlay Annex 1’s microbial and operational requirements. For example, an ISO Class 7 cleanroom used for vial filling would need Grade B microbial monitoring (≤10 CFU/m³) and quarterly smoke studies to validate airflow. Risk management documentation should cross-reference USP’s CCS objectives with Annex 1’s sterilization validations, creating a unified audit trail. Training programs must blend USP’s aseptic technique modules with Annex 1’s cleanroom behavior protocols, ensuring personnel understand both particle control and microbial hygiene.

Toward Global Harmonization

The draft USP〈1110〉and Annex 1 represent complementary pillars of modern contamination control. By anchoring cleanroom designs to ISO 14644-1 and layering region-specific requirements, manufacturers can streamline compliance across jurisdictions. Proactive risk management—combining USP’s flexibility with Annex 1’s rigor—will be pivotal in navigating this evolving landscape. As regulatory expectations converge, firms that invest in integrated CCS platforms will gain agility in an increasingly complex global market.