Does USDA Prescribe a PCR Platform for Food Pathogen Testing?

When the U.S. Department of Agriculture Food Safety and Inspection Service (USDA/FSIS) changes the analytical methods used within its laboratory network, it can raise questions for laboratories and food manufacturers using other methods. Does a change in the FSIS Microbiology Laboratory Guidebook (MLG) affect the continued use of a method? And are laboratories expected to use the same analytical platform currently selected by FSIS? 

Recent FSIS communications provide important clarification on these questions, including the continued use of BAX® PCR methods for food pathogen detection. 

Do Food Laboratories Have to Use the Same PCR Method as USDA/FSIS? 

FSIS selects analytical platforms and methods for use within its own laboratory network and may change those methods as part of its routine laboratory operations. The selection of a platform for FSIS laboratories does not, in itself, determine the validity or suitability of independently validated alternative methods used by industry or commercial laboratories. 

This distinction is particularly relevant in the context of the evolution of the current FSIS MLG. Importantly, this update should be distinguished from the broader validation, performance, and suitability of BAX® methods for their intended applications. 

Indeed, the removal of any method from the current MLG does not invalidate the method or preclude its continued use by laboratories. FSIS also stated that the previous BAX® methods remain supportable and indicated that the revised MLG methods were not found to provide significantly greater sensitivity. 

The distinction is therefore important: the analytical platform selected by FSIS for its own laboratory activities should not be interpreted as determining which independently validated method a laboratory must use. 

What Does This Mean for BAX® Users? 

Laboratories may continue to use BAX® methods in accordance with the applicable analytical framework and validated scope for the specific assay and application. 

Depending on the assay and application, BAX® PCR methods are supported by independent validations, certifications and regulatory recognitions, including AOAC, AFNOR, Health Canada, NordVal and other applicable schemes. 

FSIS also refers laboratories to methods validated by recognized independent validation organizations when selecting analytical methods for FSIS-regulated products. For laboratories evaluating a method, it is therefore important to refer to the applicable validation certificate and understand the specific scope for which the method has been validated. 

This includes the applicable matrix, test portion size, enrichment protocol and analytical conditions. When a method is applied to matrices or applications outside its certified validation scope, laboratories should verify fitness for purpose in accordance with their laboratory quality management system and applicable regulatory or accreditation requirements. 

Why the Validated Scope Matters 

Independent validation provides laboratories with information about how an analytical method has been evaluated and the conditions under which its performance has been demonstrated. 

For BAX® users, detailed validation scopes are available for applicable assays and applications through independent validation organizations and regulatory resources. Laboratories should always refer to the relevant certificate and validated scope when determining whether a method is appropriate for a particular testing application. 

This is particularly important because pathogen testing requirements can vary by matrix, test portion, enrichment protocol and target organism. Method selection should therefore consider the complete validated application rather than the analytical platform alone. 

More Than 25 Years of BAX® PCR 

BAX® has more than 25 years of use in molecular food pathogen detection and is supported by multiple independent validation, certification and recognition schemes. Depending on the specific assay and application, these include AOAC INTERNATIONAL PTM and OMA, AFNOR Certification, Health Canada, NordVal, MAPA and historical adoption by USDA/FSIS within the MLG. 

Hygiena® also maintains a validation database covering a broad range of food, feed, pet food, environmental and other industrial matrices. Application guidance and scientific support are available to help laboratories understand the applicable validation scope and determine appropriate implementation for their testing needs. 

Additional FSIS Clarification for STEC Screening 

FSIS has also provided clarification regarding screening strategies for non-O157 STEC within establishment testing programs. Establishments may screen for STEC serogroups before screening for the stx and eae genes. 

According to FSIS, the order of screening is not determinative provided establishments establish appropriate decision criteria, corrective actions and product disposition procedures. This provides establishments with flexibility when implementing STEC screening strategies within their testing programs. 

What Laboratories Should Take Away 

The removal of any method from the current FSIS MLG does not invalidate the methods or prevent their continued use. 

FSIS's selection of analytical platforms for its own laboratory network is an operational laboratory decision. BAX® methods continue to be supported by independent validation evidence and may be used in accordance with their applicable validated claims, recognition status, laboratory quality systems and regulatory requirements. 

For laboratories using or evaluating a BAX® PCR method, the appropriate validation certificate and scope should be consulted to confirm the applicable matrix, test portion, enrichment protocol and analytical conditions. 

Learn More About BAX® Validations 

For additional information about the validation status or scope of a specific BAX® PCR method, explore the applicable validation resources or contact Hygiena® for technical and scientific support.