Microbiomes a Versatile Tool for FSMA Validation and Verification
The use of genomics tools are valuable additions to companies seeking to meet and exceed validation and verification requirements for FSMA compliance (21 CFR 117.3). In this installment of Food Genomics, we present reasons why microbiome analyses are powerful tools for FSMA requirements currently and certainly in the future.
Recall in the first installment of Food Genomics we defined a microbiome as the community of microorganisms that inhabit a particular environment or sample. For example, a food plant’s microbiome includes all the microorganisms that colonize a plant’s surfaces and internal passages. This can be a targeted (amplicon sequencing-based) or a metagenome (whole shotgun metagenome-based) microbiome. Microbiome analysis can be carried out on processing plant environmental samples, raw ingredients, during shelf life or challenge studies, and in cases of overt spoilage.
As a refresher of FSMA requirements, here is a brief overview. Validation activities include obtaining and evaluating scientific and technical evidence that a control measure, combination of control measures, or the food safety plan as a whole, when properly implemented, is capable of effectively controlling the identified microbial hazards. In other words, can the food safety plan, when implemented, actually control the identified hazards? Verification activities include the application of methods, procedures, tests and other evaluations, in addition to monitoring, to determine whether a control measure or combination of control measures is or has been operating as intended, and to establish the validity of the food safety plan. Verification ensures that the controls in the food safety plan are actually being properly implemented in a way to control the hazards.
Validation establishes the scientific basis for food safety plan process preventive controls. Some examples include using scientific principles and data such as routine indicator microbiology, using expert opinions, conducting in-plant observations or tests, and challenging the process at the limits of its operating controls by conducting challenge studies. FSMA-required validation frequency first includes before the food safety plan is implemented (ideally), within the first 90 calendar days of production, or within a reasonable timeframe with written justification by the preventive controls qualified individual. Additional validation efforts must occur when a change in control measure(s) could impact efficacy or when reanalysis indicates the need.
FSMA requirements stipulate that validation is not required for food allergen preventive controls, sanitation preventive controls, supply-chain program, or recall plan effectiveness. Other preventive controls also may not require validation with written justification. Despite the lack of regulatory expectation, prudent processors may wish to validate these controls in the course of developing their food safety plan. For example, validating sanitation-related controls for pathogen and allergen controls of complex equipment and for how long a processing line can run between cleaning are obvious needs.
There are many routine verification activities expected of FSMA-compliant companies. For process verification, validation of effectiveness, checking equipment calibration, records review, and targeted sampling and testing are examples. Food allergen control verification includes label review and visual inspection of equipment; however, prudent manufacturers using equipment for both allergen-containing and allergen-free foods should consider targeted sampling and testing for allergens. Sanitation verification includes visual inspection of equipment, with environmental monitoring as needed for RTE foods exposed to the environment after processing and before packaging. Supply-chain verification should include second- and third-party audits and targeted sampling and testing. Additional verification activities include system verification, food safety plan reanalysis, third-party audits and internal audits.
Verification procedures should be designed to demonstrate that the food safety plan is consistently being implemented as written. Such procedures are required as appropriate to the food, facility and nature of the preventive control, and can include calibration of process monitoring and verification instruments, and targeted product and environmental monitoring testing.
Just how can genomics, specifically microbiomics, play a pivotal role in FSMA compliance?
Microbiomes may be particularly suited as a testing program for validation and verification of process controls, sanitation controls and supply-chain controls. Samples for microbiome analyses can include ingredients, in-process material, finished product and environmental testing. Because food safety systems change with time, knowing the impact of such changes on evolution of a facility microbiome can be a critical factor in ensuring the success of the food safety plan. This becomes increasingly important when a company changes suppliers, process or product. Such changes can alter hazards and associated risks by selecting for or against populations of desirable or undesirable microbes. Microbiomes also are helpful in defining risks when companies experience unanticipated problems, recurring deviations, or when a preventative control is known to be ineffective. Microbiomes may further shed light on the risks of distribution system abuses and new, unexpected or anticipated consumer use and misuse of a product. Should new scientific information be discovered that leads to doubts of the effectiveness of a preventative control measure, microbiomes can be used to both qualitatively and quantitatively reassess risk.
For companies with a well-established food safety plans, microbiomes are ideally suited to generate data that informs reanalysis of plan effectiveness. By coupling targeted pathogen testing with microbiomes, a full picture of the microbial community in a facility can be developed. To accomplish this task, we recommend an initial baseline microbiome screen of ingredients, products and sensitive areas in the processing environment. Both regular microbiome screens and microbiome screens following ingredient, process or product changes should be carried out. Particularly powerful is conducting a before and after intervention microbiome to compare intervention effectiveness on the total microbiota of the sample over the intended shelf life of the product. Coupling microbiome data with traditional indicator and pathogen testing provides knowledge of the behavior of microbial populations in a facility.
A reminder that microbiomes are not substitutes for targeted pathogen testing. If a food safety plan hazard analysis clearly identifies Salmonella, Listeria monocytogenes, or other pathogen as reasonably foreseeable then specific validation and verification testing for such hazards is essential to ensure that preventative controls are working. Also, microbiomes have little utility for allergens needing control.
In summary, validation demonstrates that the food safety plan will effectively control the identified hazards and verification demonstrates that the food safety plan is properly implemented by those involved. In future columns we will provide examples of the use of advances genomics to ensure FSMA compliance. Always fell free to write us with any questions or comments.
Next month’s installment: How is DNA Sequenced?
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