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  1. Risk and Safety Assessments (Food)

Review of Microbiology Laboratory Capacity, Efficiency and Management

February 2016

The U.S. Food and Drug Administration’s (FDA or the Agency) Foods and Veterinary Medicine (FVM) program has completed a “Review of Microbiology Laboratory Capacity, Efficiency and Management” as part of a larger effort to strengthen internal processes and ensure that the FVM program is making the best use of its available resources.

The microbiology review is a strategic review conducted under the direction of the FDA’s Office of Foods and Veterinary Medicine (OFVM). The FVM program did a similar review in 2014 on the safety of chemicals in foods and other products.

Achieving the FVM program public health goals depends not only on the quality of research that the program carries out, but also on its organizational effectiveness. Microbiology research within the program is structured across five divisions within the Agency’s Center for Food Safety and Applied Nutrition (CFSAN), and one division within the Center for Veterinary Medicine (CVM). As the review report states, “Enhanced success of FVM’s research microbiology program will require improved integration and coordination of research activities, effective and efficient use of laboratory staff and resources and the development of a unified research vision that supports and aligns with the needs of the Agency’s regulatory mission.”

To accomplish its objectives, and provide continued national and international scientific leadership, OFVM, aided by the consulting firm (Versar), reviewed its research microbiology program across CFSAN and CVM. The review included:

  • Anonymous and confidential interviews of employees involved in all the elements of FVM’s research microbiology program; and
  • Independent review by three outside consultants, who met with FVM program senior leadership to brief and discuss the materials and provided separate recommendations.

After receiving the consultants’ review and recommendations, the FVM program leadership formed a working group that included representatives of the offices and divisions surveyed as part of the review. The working group then considered the review documents and developed a report that identified the most significant challenges and opportunities for improvement, and presented a series of recommendations in four broad categories: science; organizational management; communication and collaboration; training and expertise. An implementation group has already addressed several of the recommendations, including hiring permanent CFSAN directors for the Office of Applied Research and Safety Assessment (OARSA) and the Office of Regulatory Science (ORS), along with improved communications including regular, scheduled meetings with research and program management.

The review report, and its two appendices, are available below.

Foods and Veterinary Medicine Program Review of Microbiology Laboratory Capacity, Efficiency and Management  

Executive Summary

OFVM, encompasses CFSAN and CVM. Within the FVM program, microbiology research is structured across 5 divisions within CFSAN (across 3 offices) and 1 division within CVM. Enhanced success of FVM’s research microbiology program depends on improved integration and coordination of research activities, effective and efficient use of laboratory staff and resources and the development of a unified research vision that supports and aligns with the needs of the Agency’s regulatory mission.

The FVM program is taking the necessary steps to ensure that its science/research program continues to provide national and international scientific leadership and makes best use of current Agency resources, while at the same time assessing where additional investments need to be made based on the principles of prevention and risk-based priority setting. To accomplish these goals, OFVM with the assistance of a consulting firm (Versar), initiated a review of its research microbiology program, focusing on the laboratory capacity, efficiency and management of the program’s multiple elements across CFSAN and CVM. The review included:

  • Anonymous and confidential interviews of employees involved in all the elements of FVM’s research microbiology program
  • Independent review by three outside consultants, who met with FVM program senior leadership to brief and discuss the materials and provided separate recommendations

Following completion of the review and consultant recommendations (see Appendices), FVM program senior leadership formed an internal microbiology working group with representatives from offices and research divisions that were surveyed in the report. The working group was tasked with reviewing the documents and developing a report which not only identified the most significant challenges and opportunities for improvements, but also presented plausible recommendations for strengthening FVM’s research microbiology program. For greater detail of particular aspects of the review, see the expanded reports attached as appendices.


OFVM (encompassing CFSAN and CVM) was created in 2009 to lead a functionally-unified foods and veterinary medicine program and enhance the Agency’s ability to meet today’s great challenges and opportunities in food and feed safety, veterinary medicine, nutrition, and other critical areas.  The FVM microbiology research program portfolio also includes laboratory activities which are coordinated with the Office of Regulatory Affairs (ORA) and, where appropriate, utilizes the specialized capabilities of the National Center for Toxicological Research (NCTR).

The success of FVM’s research microbiology program is predicated on improved integration and coordination of research activities, effective and efficient use of laboratory staff and resources and the development of a unified research vision that supports and aligns with the needs of the Agency’s regulatory mission. An integrated science/research program based on the principles of prevention and risk-based priority setting provides research solutions to support current and evolving FDA regulatory issues and science priorities.

To help achieve these goals, FVM program leadership initiated a review of its microbiology laboratory programs focusing on scientific capacity, efficiency, and the management of the program’s multiple elements across CFSAN and CVM. Specifically, the review was structured to take stock of FVM’s current microbiological capacity -- how that capacity is deployed and applied across the program; the efficiency of management practices that affect how well staff and other resources are used to oversee microbiology work; to determine if microbiology research is meeting program needs; to identify if there is unnecessary duplication; and to ensure that microbiological research yields mission-relevant outcomes. The review also examined how FVM’s microbiology laboratory programs interact with other U.S. government and state agencies, the external scientific community, and other external stakeholders.

The review is intended to identify opportunities for improvements that may exist across the FVM microbiology research program, and also highlight challenges that should be addressed to ensure that the FVM program maintains a strong laboratory infrastructure which can effectively and efficiently provide the science base necessary for FDA regulatory decisions and actions.

CFSAN and CVM Research Microbiology Programs

Within the FVM program, microbiology research is conducted across 5 divisions within CFSAN (across 3 offices) and 1 division within CVM. Scientists representing the following offices and divisions were included in this review:

Division of Molecular Biology (DMB)
Division of Virulence Assessment (DVA)
Division of Microbiology (DM)
CFSAN – Office of Food Safety (OFS)
Division of Seafood Science and Technology, Dauphin Island (DSST or OFS/DI)
Division of Food Processing Science and Technology, Moffett Center (DFPST or OFS/MC)
CVM – Office of Research (OR)
Division of Animal and Food Microbiology (DAFM)

Division Mission Statements  

Division of Molecular Biology

To conduct advanced molecular- and cell biology-based assay development to support the regulatory mission of the FDA and CFSAN, including forward-looking, proactive assessments of new technology and scientific disciplines for regulatory use.

Division of Virulence Assessment

DVA originates, plans, and conducts independent and collaborative research with other centers, agencies and entities on the adverse effects of microbes and their products on public health in support of the center’s food safety and food defense research goals. Develops and characterizes biomarkers associated with exposure and susceptibility to microbes and their products. Correlates research using in vitro systems for evaluating effects or presence of harmful microbial products with animal model data with the aim of replacing, where possible, the animal model with the in vitro system. Develops and applies appropriate biochemical and/or molecular biological methods and instrumentation to purify and/or clone the factor(s) from microbes (including microbial threat agents) that are responsible for causing human illness and uses the knowledge obtained to develop rapid detection methods for foodborne pathogens. Conducts research on the isolation and characterization of food allergens and gluten and optimizes methods for detection of food allergens and gluten. Coordinates all research activities with other center components to assure maximum productivity of division projects and programs and provides scientific and technical expertise to other center and Agency components on virulence aspects of microbiology.

Division of Microbiology

DM develops, optimizes and validates methods for recovery, detection, identification, and quantitation of pathogens and/or toxins from foods and cosmetics, and the processing environment. DM also maintains FDA's food-related gateway to the Centers for Disease Control and Prevention (CDC) PulseNet System. Develops and applies subtyping methods to further enhance data generated for PulseNet, strain identification and molecular epidemiological investigations.

Division of Seafood Science and Technology

DSST, in conjunction with federal, state, academic, and public partners is responsible for providing the scientific basis for Agency policy, regulation and compliance programs which promote and protect the public's health by ensuring that the nation's seafood supply is safe, sanitary and secure.

Division of Food Processing Science and Technology

DFPST conducts food safety, nutrition, and defense research in food processing, food packaging and food technology as it relates to food production and handling principles. DFPST also participates, in conjunction with the CFSAN Office of Analytics and Outreach and others, in educational and information programs on contemporary food safety and security issues. Evaluates and accredits Grade “A” Milk laboratories and certifies state laboratory evaluation officers. Conducts proficiency testing program for milk, shellfish, Food Emergency Response Network/Laboratory Response Network (FERN/LRN), and other food laboratories. Provides consultation to FDA, and outside organizations on laboratory equipment, apparatus, methods, and facilities problems associated with laboratory examination of foods.

Division of Animal and Food Microbiology

DAFM conducts basic and applied research to support regulatory decision-making by the CVM. This research involves the isolation, identification and characterization of microorganisms potentially harmful to animals and humans. In particular, DAFM's research explores the effects of antimicrobial drug use in animals on: 1) effectiveness against pathogens, 2) changes in the environmental microbial ecology, and 3) the development of antimicrobial resistance in pathogenic and commensal microorganisms.

It is also important to recognize that the FVM microbiology research programs not only support the regulatory and compliance activities of other CFSAN and CVM offices, but coordinate where appropriate with ORA, NCTR, other FDA centers, academia, and federal, state and international partners.

Methodology Used For The FVM Microbiology Program Review

The FVM microbiology program review was conducted with the assistance of a consulting firm (Versar) and focused on the laboratory capacity, efficiency and management of the program’s multiple elements across CFSAN and CVM. The review included:

  • Anonymous and confidential interviews of employees involved in all the elements of FVM’s research microbiology program
  • Independent review by three outside consultants, who met with FVM program senior leadership to brief and discuss the materials and provided separate recommendations

Interviews of CFSAN and CVM Scientists

As part of this review, FVM program leadership organized in-person interviews of personnel working in microbiology research within three offices in CFSAN and one office in CVM. Interviewees were asked a series of 26 open-ended questions in four major areas: 11 addressing science; 4 addressing organizational management; 6 addressing collaboration/communication, and 5 addressing expertise and training. The questions may be found in Appendix A of the Versar FDA Microbiology Program Review main report.

FDA identified 104 interviewees working in OARSA (32), OFS/DI (9), OFS/MC (12), ORS (34), and CVM (17) to participate in the interview process. All potential participants were contacted via email to schedule appointments for interviews, and 94 interviews were scheduled to be conducted in person in College Park and Laurel, MD, Dauphin Island, AL, and Moffett Center, IL with: 28 interviewees in OARSA, 9 interviewees in OFS/DI, 12 interviewees in OFS/MC, 30 interviewees in ORS, and 15 interviewees in CVM.

Interviewees included principal investigators, subject matter experts, support scientists and technicians, team and project leaders, and line managers, as well as others directly involved in facilitating/supporting microbiology research within the program. The Oak Ridge Institute for Science and Education (ORISE) fellows, contractors and staff fellows were not included in the interview process. In terms of experience, the durations interviewees had reportedly worked in their current positions ranged from <1 to 27 years and the number of years they had worked at FDA ranged from 1.5 to 53 years. The composition of the interviewee pool by office, division, and branch is presented in Appendix B of the Versar main report.

Interviews were conducted under conditions of anonymity and confidentiality by Versar during the months of February through April 2014. During the interviews, employees’ responses were written down by hand. In addition, the interviews were digitally recorded to improve accuracy of transcription. A written summary of each interview was prepared by Versar for use in writing the report, and relevant responses were extracted into the report by office/group, with no other identification, except where necessary to clarify the viewpoint of the interviewee responding (e.g., support scientist or team leader). Relevant observations, comments, and recommendations are presented intact or relatively intact in Appendix C of the Versar main report.

The first phase of the FDA Microbiology Program Review was completed by Versar and culminated in a report summarizing the results of the interviews. Written summaries and recordings of individual interviews were maintained by Versar, and were deleted upon delivery of the final report to FDA.

External Consultants Review

As part of the next phase of the FVM Microbiology Program Review, FDA sought the aid of three internationally-recognized and respected scientists and managers of large programs with relevant microbiology and laboratory experience to review the report and assist with recommendations to improve the program to better meet today’s and prepare for tomorrow’s microbiology challenges. The experts were provided a set of questions to consider and supporting background materials to facilitate their review. The three experts met with FVM program senior science leadership to discuss the results of the interviews and subsequently developed written recommendations for FDA to consider. The final report was completed December 31, 2014 (see Appendix B).

Formation of a FVM Program Microbiology Review Working Group

Following completion of the review and consultant recommendations, FVM program senior leadership formed an internal microbiology working group chaired by the OFVM Chief Science Officer / Research Director with representatives from all research divisions and offices that were included in the report. The working group was tasked with reviewing the documents and developing a report which not only identified the most significant challenges and opportunities for improvements, but also presented plausible recommendations for strengthening FVM’s research microbiology program. The working group divided into three subgroups to consider issues and recommendations that were raised in each of the following sections: science; communication/collaboration; and expertise/training. The entire working group reconvened to discuss the organizational management section. Expert panel recommendations have been included where appropriate and are separately distinguished from FVM program scientist comments.

It is important to note that since the completion of the review, several recommendations have already been considered and implemented and are having a positive effect on the FVM microbiology program. Additionally, some recommendations may be outside the scope of this review and the FVM program may not be in the position to address at this time. However, they are presented to ensure transparency, accountability and clarity.


Key Findings

Most of the individuals involved in microbiology research within the FVM program are dedicated and passionate about their work, enthusiastic about the science, and truly believe in the mission. Regardless of their level of satisfaction with the current status of the program, most interviewees had a lot to say during the interview process because they really care about what they do and want the program to succeed.

The top five program challenges identified across all offices were 1) staffing, 2) leadership and/or management issues, 3) lack of communication/transparency with upper management, 4) insufficient resources, and 5) insufficient communication and collaboration within and among groups. However, the offices differed substantially in the relative emphasis placed on these issues and the reasons they were felt to be weaknesses. Sciences issues, problems of coordination among offices, low morale, and professional development and travel problems were identified as weaknesses in select offices.

Outside reviewers and interviewees involved in microbiology research within the FVM program believe that maintaining in-house capabilities is essential to fulfilling FDA’s and the program’s mission and protecting public health, and that maintaining a current scientific knowledge base is required for writing regulations. There is support across groups for maintaining an appropriate level of basic research and traditional microbiology capabilities and concern that further narrowing the scope of research may negatively impact the program’s ability to protect public health.

The FVM research program however seems to be dispersed in a number of different offices which has resulted in some level of duplication, competition, and at times the appearance of inequitable funding and disparate resource practices. Despite some efforts to coordinate research, the current organizational structure appears to be inefficient with multiple administrative structures and distinct research silos situated across the program.

While interviewees in general acknowledged that the centers gave out many recognition awards and often did a good job with this process, there were numerous recommendations for improvement in this area, including: improving the awards/promotion system, increasing acknowledgement and appreciation of efforts; promoting/converting staff based on performance; giving cash, travel opportunities, or time off as awards; and investing in ongoing/new research projects. This was an area addressed by scientists at all levels, and was of particular interest among support scientists/technicians who generally tended to feel that they were overlooked in the awards process as compared to principal investigators.

Overall, there was generally little overt focus on FDA Food Safety Modernization Act (FSMA) and the challenges it will present the microbiology program except at OFS/MC, where research in food processing and preventive controls appeared more directly tied to FSMA objectives.



The need to improve the alignment between research offices and center/program priorities was a recurring theme. Interviewees felt strongly that to accomplish this, deficiencies in communication and transparency practices must first be addressed. In some cases, lack of communication/transparency with senior center management was attributed to respective groups’ remote location away from headquarters.

There is a general understanding among the interviewees that FVM’s program focus is on applied research that improves food and feed safety and allows FDA to provide scientifically informed regulatory decisions. However, it was felt that a certain degree of basic work is needed but must fit within the scope of FDA’s needs.

Interviewees mentioned the need to reduce duplicate research among researchers throughout the centers, but several pointed out that some apparent duplication may be useful, depending on whether the research was being used to address different issues or questions (e.g. rational overlap).

There were many complaints about the current Component Automated Research Tracking System (CARTS) process. Most reflected dissatisfaction with the project review and approval process. However the general opinion from those complainants was that CARTS must be flexible to meet current and future needs.

In general, those who are not directly involved in whole genome sequencing, regardless of their office or group affiliation, have questions concerning the ultimate value of the program to the Agency and its implications in protecting public health. Interviewees felt there was a challenge to achieve an effective balance in research efforts both between traditional and modern microbiology research and between basic and applied research.

Interviewees pointed out the need for further recognition to show appreciation for their scientific achievements. Although some interviewees felt that time off was an appropriate award, others questioned the value of 1 or 2 days off, especially in consideration of the accumulation of excess use-or-lose leave for senior staff members.
Interviewees felt that senior management should be focused on exploring options for direct hiring for certain scientific job series and developing programs to minimize gaps in scientific expertise caused by anticipated personnel changes (e.g., retirements and promotions), and unanticipated personnel changes (e.g., employee departures).

It is important to note that there appears to be both a lack of professional development and travel opportunities for support scientists and technicians due to budget constraints.


Recommendations to enhance communication and transparency as a means of improving the alignment between research offices and center/program priorities outweighed all other suggestions, which included maintaining the Agency’s research base, reorganizing microbiological research, evaluating the impact of research, conducting branch/program reviews to assess alignment, and aligning research and priorities based on the severity of the pathogen.

A recurring theme was the desire for senior center management to clearly and regularly communicate the organization goals and then follow up with clear expectations for collaboration and focus that enables the centers and the FVM program to successfully meet their public health objectives.

Specific recommendations included:

  • The FVM microbiology research program should maintain some appropriate level of basic microbiology research to maintain breadth of expertise to support newer technologies, to respond to outbreaks, for support in compliance and enforcement actions, and to be prepared to address emerging problems. Interviewees also recommended maintaining research efforts in genomics, including whole genome sequencing, advanced molecular methods, and meta-genomics.
  • The need to increase efforts in specific areas/fields other than genomics: in particular virology; food parasitology; physiology of pathogenesis; pathogen evolution; microbial ecology; environmental microbiology; virulence assessment; immunobiology; preventive controls; laboratory proficiency testing; produce and seafood safety; and antimicrobial resistance.
  • The need for a greater emphasis/expansion towards method development and method validation (i.e, the development of more sensitive detection methods, rapid detection methods, and methods for emerging pathogens); investigation of new technologies; research into emerging pathogens in food and feed; and, traditional/classic/basic and applied microbiological research to support FSMA.
  • Redirection in methods development and/or validation related to methods expected to be eclipsed by whole genome sequencing (e.g., microarray, mass spectrometry, some polymerase chain reaction methods, and work on pulse field gel electrophoresis) and to the number of new methods being developed without accompanying validation.
  • Enhancement of CARTS with particular emphasis on improving communication of the parameters for acceptable projects, improving feedback on project rejections, expediting turn-around time for the project approval process, improving transparency of the project review process and generally improving the CARTS system overall.
  • Greater acknowledgement/appreciation of scientific staff contributions from management (all levels) and co-workers by holding celebrations of awards/accomplishments at the division level; increasing recognition via the website and other means; and improving acknowledgement for Public Health Commission Corps Officers.
  • Reward scientific accomplishments/achievements via promotion/conversion, where appropriate. Interviewees suggested greater full time employee (FTE) conversion rates for outstanding Fellows, increasing opportunities for advancement (via e.g., creating group leader positions, leadership rotations); improving the promotion system; and changing the criteria for promotion of support scientists/technicians.
  • Include official travel as an incentive and reward to show appreciation for scientific achievement (would also help to offset some of the current budget restrictions for travel).
  • Greater investment of research funds in ongoing/new projects as a means of rewarding scientific accomplishment by allocating funds or support staff to a successful project, or allowing scientists to participate in projects outside their immediate position description.
  • The need for greater emphasis on succession planning. It is recognized that many FVM program scientists are nearing their eligibility to retire date in the immediate future.

Expert Panel Responses

The wealth of well recognized multi-disciplinary expertise currently supporting the microbiology program is a definite strength of FVM program. In-house research is an important capacity within FVM program, and should be maintained.

  • However, the research being done, some of which has been going on for years now, needs to be reviewed, evaluated and refocused to ensure mission relevance as well as synergy with the new direction FSMA is taking FDA (e.g. prevention versus detection).
  • To some extent, this also is tied to scientist development and promotion. It was stated by many that promotions required publications and that much of the microbiological research was applied and therefore not publishable. Thus, alternative goals linked to promotion and reward should be explored.

It is recommended that a new workgroup composed of scientific leaders from CFSAN, CVM, OFVM and ORA be created to align current research activities with the new FVM program strategic plan, to be released in fiscal year 2016.

  • The workgroup would be tasked with developing a FVM program annual performance plan which will clearly indicate the goals, objectives, and action items that are expected from each office which in turn has responsibility to communicate these to divisions and branches/teams and, very importantly, monitor progress towards achieving the goals.
  • This exercise should clearly expose areas of duplication or gaps that need to be identified. Research currently being conducted that does not address any current or future objectives must be looked at with care to assess its worth.

Management issues were also highlighted as key concerns with many interviewees. Some managers were perceived well while others were seen as ineffective, disengaged, and did not represent their units in an effective manner.

Organizational Management


There is a perceived lack of coordination among all groups in the microbiology program that may be hindering effective utilization of the manpower and expertise within the program.

  • Interviewees in different groups were often completely unaware that others in the Program were working in the same research area.
  • There is no resource designated for publicizing in-house research within the Agency to identify areas of shared interest, expertise, and availability.

Organizational challenges exist in several groups that are in need of direct action by senior leadership. These include:

  • Addressing the division structures within OARSA.
  • Addressing the partnership with IFSH at Moffett Center.
  • Addressing the relationship between the CVM National Antimicrobial Resistance Monitoring System (NARMS) program and research groups within DAFM.
  • Addressing competition for research areas and resources among CFSAN laboratories.

There appear to be issues with line management in several groups attributed to the lack of permanent, strong, and/or effective line management. Interviewees felt line management issues were affecting research in both OARSA and ORS, and collaboration between OARSA and ORS.

  • Although issues with line management were identified in the other groups, they were not felt to have an impact on research efforts.

Regarding information technology capabilities, interviewees identified two major areas of improvement.

  • Resolution of firewall and security issues for scientific computing.
  • Additional areas identified for information technology (IT) improvements were implementing use of E-notebooks, improving in-house IT support, implementing better information management systems, improving the IT infrastructure (e.g., bandwidth), and improving video conferencing support.

Interviewees across the FVM program also identified a clear need for hiring additional support staff: including administrative support; scientific writers, editors, and graphic artists for publications; culture coordinators; service contract support; and project managers to coordinate large, cross-cutting initiatives.


Recommendations ranged from unifying all or some of the microbiology groups under a single authority to being based upon expertise along functional lines (e.g., specialized area of research, commodity). Senior Leadership should address competition for research areas and resources issues by encouraging greater collaboration, grouping research along functional lines, and discouraging individual ownership of areas of expertise.

Specific recommendations included:

  • Develop a systematic approach for allocation of resources to include:
    • Re-allocation of knowledgeable staff as needed for short- or long-term projects; allowing more flexibility in the assignment of support scientists/ technicians.
    • Redistribution of staff between the NARMS program and DAFM within CVM; and cross-training support staff.
    • Establishment of a centralized system that would indicate which groups were in need of additional resources based on workload.
    • Establishment of a panel of scientists to participate in resource allocation; and applying a working group structure to the allocation of staff.
    • Expand the capabilities for process and storing large datasets to support Agency activities as well as establish a central bioinformatics group.
    • Initiate a comprehensive science review of microbiology projects across the FVM program.
  • Realign/reorganize microbiology programs or projects through:
    • Establishment of new vertical leadership structure(s) to improve alignment across the centers by consolidating some or all the microbiology research groups in CFSAN (ORS, OFS and OARSA) into one super office; or, placing all microbiology research under OFVM direction.
    • Creation of intramural Centers of Excellence (e.g., Escherichia coli research, antibiotic resistance).
    • Increase the use of integrated teams and matrix management to address specific issues and special projects.

Expert Panel Response

Structure should be defined by function. The CFSAN Science and Strategic Plan for 2011-2014 clearly listed five well defined strategic goals. However, it appears that there was limited strategic oversight provided to offices, divisions, branches, and teams to ensure research aligned with the five strategic goals. This has resulted in an apparent uncoordinated approach that favors competition and duplication of effort across the center that needs to be addressed. Whether or not a re-organization would effectively address these concerns is for FVM program leadership to decide.

Communication and Collaboration


Improved coordination between offices and divisions was of paramount concern to all interviewees and recommendations included scheduling regular meetings between science leaders of microbiology divisions across the FVM program and educating staff on how research priorities are established, delegated and tracked.

The effectiveness of current efforts in communication/transparency by upper management drops sharply for groups that are within CFSAN but outside College Park. This appears to be attributable to:

  • Physical separation: Interviewees in off-site locations commented that they rarely saw or spoke with members of senior management and felt that those within ORS had much more ready access to members of upper management.
  • Ineffectiveness of communicating through line management: interviewees in both OARSA and OFS/MC commented that information concerning changes in program priorities or processes is not always relayed in branch/division meetings.
  • There is also a lack of knowledge about areas of common interest across groups and a perceived reluctance to engage in future collaboration based on prior negative experiences.

There is a culture of competition between CFSAN ORS and OARSA that may be hindering microbiology research efforts.

  • Despite common areas of research between the two offices, interviewees felt there was little collaboration or willingness to share facilities, resulting in inefficiencies as well as duplication of research efforts at times.
  • The perception among OARSA interviewees that there is bias within upper management for ORS both in terms of resources and research areas which has contributed to low morale and perceived bias within OARSA that are counterproductive to program efforts.
  • The shift of some researchers and projects from OARSA to ORS has also contributed to the feeling of competition between the offices.

Coordination efforts with regulatory policy staff were reported to occur via direct interactions with the policy offices, via working groups, through the research prioritization process and CARTS, and in outbreak response and compliance activities. Interviewees noted that improvements were still needed in coordination, especially regarding general knowledge about the policy programs and how the microbiology research laboratories can align with their strategic needs.

  • Additionally, there is a real need to enhance coordination with the ORA field laboratories as many interviewees felt there was duplication of research efforts with the center laboratory programs in certain areas.

Regarding the CFSAN extramural Centers of Excellence(COE), the majority of interviewees indicated that they were unfamiliar with any coordination efforts between the centers’ microbiological research programs and any COE.

  • Though COE research projects may be in CARTS, center researchers do not typically peruse the ongoing activities to see if there is potential alignment with their projects.


Foster and increase interactions between science leadership and researchers across the microbiology groups housed in OARSA and ORS to develop a unified science strategy.

Establishment of standard operating procedures (SOP) for research collaborations between offices as well as subsequent training of researchers on SOP expectations would increase coordination.

Create greater in-house awareness of the microbiology research portfolio by publicizing abstracts or summaries (outside of CARTS) across the FVM program.

Specific recommendations included:

  • Consider building intramural interdisciplinary teams to address specific high priority projects that encompass both program and research office interests and planning activities.
  • Encourage increased interactions and communication between appropriate COE (e.g. the Joint Institute for Food Safety and Nutrition (JIFSAN), the Institute for Food Safety and Health (IFSH) and the Western Center for Food Safety) and CFSAN/CVM microbiology staff regarding scientific priorities and ongoing activities.
    • One particular recommendation of note was to request a new Memorandum of Understanding (MOU) to redefine the roles of FDA and Illinois Institute of Technology in the current COE partnership.
  • Increase collaborations with other federal agencies, academic institutions, and international partners to further leverage resources. In the past, disparate scientific approaches have been reported by researchers in areas where the CDC and FDA have overlapping investments (e.g., whole genome sequencing).
    • Develop a mechanism or structure by senior leadership that optimizes FDA, CDC and U.S. Department of Agriculture interactions and communications on a regular basis and disseminate that information to appropriate laboratory staff.
    • Formalize procedures (SOPs) for initiating and managing collaborations between FVM program offices and with external organizations (e.g., academia, other federal agencies, and COE).
    • Explore where MOU or other mechanisms can be implemented to facilitate collaborations with other federal agencies and international bodies.
    • Create a mechanism that is widely used and frequently updated to identify both internal and external expertise, as a means to identify possible collaborators.

Expert Panel Responses

The lack of communication and transparency have been identified, by almost all offices, as major impediments contributing to distrust, confusion, lack of direction, unclear objectives, ambiguous decision-making process, and perceived uneven handedness in treatment.

  • This absence of coordination causes duplication of effort, wastes time and money, and can create real problems in the function of the program.
  • Senior leadership should address this matter strategically and in a clear and transparent manner to reduce these concerns.

A science communications position/team is needed to not only develop best practices for corresponding and highlighting information across the FVM program, but to enhance the public health significance of FDA research with external stakeholders.

Training and Expertise


Across the different research groups, there were major differences in perceptions of their roles within and contributions to the program. However, across all groups, interviewees felt the greatest program strength was expertise.

  • The FVM program is home to world-renowned scientists in all offices.
  • Despite a shift in the program towards genomics methods, all groups reported expertise in both traditional and molecular microbiology, and diverse expertise within groups was cited as an overall strength.
  • The program possesses specialized microbiology expertise in seafood safety, food processing and technology, and antimicrobial resistance, as well as expertise in laboratory proficiency testing and preventive controls, which will have increasing value with the implementation of FSMA.
  • Bioinformatics was identified as the chief imbalance/gap across the FVM program, followed closely by an urgent need to increase our IT capabilities.

The top responses for improving recruitment, development, and retention of professional expertise were improving the hiring system, encouraging training and travel, and increasing opportunities for advancement. In particular, staff exchanges and sabbaticals across the FVM program were tools that were suggested to be further developed.

In terms of staffing, interviewees addressed the challenges of hiring qualified scientists and support scientists/technicians, retaining staff, succession planning to maintain institutional knowledge, achieving the proper balance of senior vs. junior staff, effective deployment of staff, and improving alignment of staff and their research with the FVM program regulatory mission.

  • It was noted that hiring tended to be based more on available funding than need; interviewees recommended a risk assessment/gap analysis for identification of priority areas for hiring/redistribution of scientists across the centers.

Although training and education and travel and attendance at meetings were mentioned in relation to both development and retention, they featured more prominently in development, where interviewees noted the importance of encouraging/requiring training and increasing opportunities for travel, along with addressing the accompanying budget limitations.

  • Support scientists in particular felt that additional opportunities were needed to attend technical training because on-line training was not effective for laboratory techniques, and noted that they had few opportunities to expand their skills vs. ORISE Fellows, for whom funding for training was built into their contracts.


Interviewees across all offices felt that opportunities for technical training should be increased via: providing on-site training; developing training programs between the microbiological research offices; partnering with other centers or groups within FDA or academic partners, such as JIFSAN; or offering off-site training especially for methods and techniques.

Regarding recruitment of top scientists, recommendations focused on improved outreach to industry and academia as well as greater use of professional organizations to solicit applications and get the message out to the scientific community rather than solely rely on USA jobs.

Specific recommendations included:

  • As a first step, have the two staff college’s directors work more closely together in developing professional training programs across the FVM program enterprise to address gaps and deficiencies.
  • Explore opportunities to receive training at other FDA center staff colleges (e.g., the Center for Drug Evaluation and Research, the Center for Devices and Radiological Health, ORA University) and academic institutions, such as through the JIFSAN partnership.
  • Develop a staff exchange program for shadowing/cross-training (cross pollination) of knowledge (e.g., ORA staff go to center laboratories and vice versa)
  • Partner with various professional societies (e.g. the American Society of Microbiology, the International Association of Food Protection) to bring training opportunities (seminars, workshops) to CFSAN and CVM.
  • It was important to note that scientists at OFS/DI and OFS/MC felt they were at a disadvantage at times as travel and continuing education funds are used to cover costs for their scientists to travel to CFSAN College Park or White Oak for required meetings, which reduces their allocation for professional development.

Expert Panel Responses

One consistent comment across programs seemed to be the disproportionate distribution and lack of FTEs, while at the same time there is an acknowledgement of duplication of research. It would appear that the solution is not to add FTEs, but rather combine or align expertise into better structured groups or establish clearly defined objectives so that work is not duplicated and is strategically aligned with the needs of the centers.

Next Step

In summary, the working group identified challenges and developed recommendations across four broad categories that align with how the microbiology review was constructed:  

  • Science;
  • Organizational Management;
  • Communication and Collaboration; and
  • Training and Expertise.

FVM’s microbiology laboratory program faces significant challenges arising from new technologies being developed and used in food and feed, new methods of identifying and assessing microbial hazards, resource constraints, increased need for coordination across the FVM program enterprise, and continued high public expectations concerning the rigor and effectiveness of FDA’s research programs.

  • Achieving FVM program public health goals depends not only on the quality of research, but also our organizational effectiveness.
  • Only a prepared, versatile and resourceful organization can efficiently coordinate and manage serious issues confronting our food supply in an increasingly complicated and global marketplace.

The FVM program is taking the necessary steps to ensure that its science/research program continues to provide national and international scientific leadership and makes best use of current Agency resources, while at the same time assessing where additional investments need to be made based on the principles of prevention and risk-based priority setting.

  • The working group believes that enactment of the recommendations contained in this report will significantly strengthen the FVM microbiology laboratory program and ensure that it continues to provide the foundation for sound regulatory policy, as well as compliance and enforcement actions.
  • It is recommended that a new implementation working group be chartered, comprised of FVM program senior science leaders, to further prioritize and determine feasibility and timelines of recommendations offered in this review.

The working group would like to recognize the efforts of the FVM program scientists who participated in the interview process and shared their thoughts and vision regarding the microbiology research program. Thanks are also extended to Versar for their contributions and to our external experts who provided timely and cognizant appraisals of the FVM microbiology program.


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