2007-2009 Subcommittee: Determination of the Most Appropriate Technologies for the FSIS to Adopt in Performing Routine and Baseline Microbiological Analyses
- Dr. Uday Dessai, Working Group Chair
- Dr. Peggy Cook
- Dr. Daniel Engeljohn
- Dr. Walt Hill
- Dr. Lee-Ann Jaykus
- Dr. Julie Ann Kase
- Dr. Stephen Knabel
- Ms. Barbara Kowalcyk
- Dr. Jianghong Meng
- Ms. Angela Ruple
- Dr. Robert Tauxe
- Dr. Sterling Thompson
- Dr. Irene Wesley
Microbiological analysis is central to the United States Department of Agriculture's Food Safety and Inspection
Service (FSIS) food safety mission. Because microbiological data are critical to developing data-driven
quantitative risk assessments and serve as a keystone in policy decisions and regulatory actions, the Agency
continually seeks improvement in laboratory and in-plant testing capabilities. First-generation microbiological
methods simply detected a given bacterial species in a food product, but FSIS now depends on a suite of analyses
for regulatory actions, monitoring, and risk assessments. Currently, antibiograms, pulsed-field gel electrophoresis
(PFGE), immunoassays, and serotype determinations are all important features of FSIS analyses. The Agency has
recently benefited from the addition of new technologies to its laboratory methodologies, such as polymerase
chain reaction (PCR) technology. While PCR is not a substitute for traditional microbiological methods, it has
proved to be a rapid, accurate screen that has improved the speed at which FSIS samples are processed while also
reducing the cost. The adoption of this and other technologies in routine analyses has enabled FSIS to accomplish
a marked increase in the sensitivity and specificity of their testing methods, which were also accompanied by a
decrease in the time needed to generate results.
A varied spectrum of methodologies and platforms are currently available for consideration by FSIS. Some of these
technologies have the potential to be used as add-ons to the Agency's current methods through minor modifications.
The others may need an entirely different platform. However, the use of new and improved technologies for FSIS'
microbiological analyses can provide more useful data to further strengthen risk-based initiatives and science-based
programs at reduced cost. For example, genomic assays can provide rapid detection of the complete set of DNA sequences
indicative of any known microbiological food safety hazard (to include antibiotic resistance, virulence factors,
markers, etc.), while the nanotechnology-based methods have the potential for developing real-time microbiological
detection systems for effective process control. Further, nanosensor-type technologies can be used to gain access
into pathogen harborage sites in the processing environment. Overall, with the adoption of newer technologies at
FSIS, the depth and spectrum of microbiological analyses could be enhanced substantially in addition to the potential
reductions in cost and in the time needed to generate results.
Charge to the Subcommittee
The National Advisory Committee on Microbiological Criteria for Foods (NACMCF) should provide guidance to assist with
the Agency's goal of moving into the next generation of microbiological testing methods. To do so, NACMCF should
review current platforms and methods, including molecular/genotyping assays, nanotechnology, and other available
or evolving technologies, for potential applicability to FSIS microbiological testing. NACMCF should explore the
suitability of selected technologies/methods for incorporation into FSIS microbiological testing programs
(laboratory and in-plant) as add-ons/modifications to the Agency's current methods or as entirely different
The Agency recognizes that this charge might best be approached by NACMCF in two stages. The first would focus on
laboratory methods for pathogen detection, and the second on in-plant testing to reliably assess process control.
Tests for use in FSIS laboratories versus those used in-plant are likely to require different technologies.
Analyses carried out in FSIS laboratories will be used for baseline monitoring of national microbial trends and
regulatory sampling. In-plant sampling may primarily help in assessing process control and real-time monitoring of
FSIS requests that NACMCF examine the merits of available technologies for application to FSIS microbiological
testing with a focus on:
- Specificity and sensitivity
- Adaptability to various matrices (including foods, the processing environment, and human clinical samples)
- Scope of analyses (including species identification, serotype equivalence, antibiotic resistance, PFGE equivalence, and additional indicators of microbial hazards, such as virulence factors)
- Data acquisition and transfer
- Ability to be effectively incorporated into FSIS methods
- Cost and resource efficiency
(Please consider both laboratory and in-plant uses for each of the following)
- What are the most appropriate technologies FSIS should consider for improved microbiological analyses? What are the most promising methods that could replace or complement those currently used at FSIS? What are the important parameters to be considered in determining the suitability of a method for a particular application (such as laboratory analyses for pathogens versus in-plant testing for process control, or routine versus baseline testing, and enumeration of pathogens and indicators)?
- What are the advantages and disadvantages of these newer technologies/methods? When selecting newer technologies/methods consider the FSIS approach of reliance on culture-confirmed positives for target organisms in the context of method correlation, substitution, and degree of confidence. For instance, if the technology does not measure or correlate with viable cell presence, can reasonable decisions be made about the safety of the product?
- When adopting new technologies and testing platforms, what considerations must be made regarding sampling protocols? How does sampling (size, site, rinse, excision) impact assay sensitivity, specificity, and limit of detection? Are there any practical ways (concentration technologies, etc.) that could be adopted to compensate for potential loss in specificity, sensitivity, and detection limit requirements for microbiological targets?
- Consider specifically the accuracy, applicability, and validation of an assay capable of detecting thousands of single-nucleotide polymorphisms (SNPs) in a single reaction. Would such an assay be timely, cost-effective, and capable of screening specimens to monitor process control? Would it be capable of differentiating multiple microbial species in a single sample? Could it have application for differentiating bacterial subspecies (particularly relevant for salmonellae, which are currently characterized by serotype), or detecting antibiotic resistance genes and virulence factors? Determine the suitability of incorporating SNPs in meeting the current and future testing needs of FSIS.
- When selecting a new technology, what factors should be considered, such that the data generated would be useful in an expanded manner to include attribution/risk profiles and models for human illnesses?
- What issues will need to be considered to make newer and promising technologies a reality in FSIS' future testing for pathogens and indicator organisms? For technologies that may be useful in the future, identify research gaps that need to be addressed prior to implementation.
Summary of Subcommittee Meeting, May 19-20, 2008
- The Subcommittee met from May 19-20, 2008 in Washington DC.
- This Subcommittee has developed a solid working draft document which provides background information
on microbiological testing at FSIS, why testing is done, resources for testing, public health implications
for testing, traditional and emerging testing methodologies.
- The Subcommittee is also drafting a process which can be used to evaluate emerging microbiological
methods for their adoption, with a focus on their use in meeting public health goals.
- Subcommittee members were engaged in discussions on how emerging technologies may be used by FSIS in the
future, including advantages and disadvantages of the different technologies and considerations for adoption.
- Members have been assigned to complete specific sections of the draft report, and are planning meeting
during the week of July 28, 2008 to continue work. The next draft will be circulated to Subcommittee members
prior to the July meeting.
Summary of Subcommittee Meeting, Jul 28-30, 2008
- The Subcommittee met from July 28-30, 2008 in Washington, DC.
- The Subcommittee refined the working draft document.
- The Subcommittee refined the draft process which can be used to evaluate emerging microbiological methods for their
adoption, with a focus on their use in meeting public health goals.
- The Subcommittee began deliberations on appropriate use of molecular sub-typing by FSIS.
- The Subcommittee also drafted preliminary conclusions and recommendations.
- Members have been assigned to complete specific sections of the draft report, and are planning a web meeting on
August 21, 2008, to continue work. The next draft will be circulated to Subcommittee members prior to the September meeting.
Summary of Subcommittee Meeting, Sep 24-25, 2008
- The Subcommittee met from September 24-25, 2008, in Washington, DC.
- The Subcommittee reorganized and further refined the working draft document including tables, appendices and references.
- The Subcommittee continued deliberations on appropriate use of molecular subtyping by FSIS.
- Members have been assigned to complete specific sections of the draft report, and are planning a web
meeting on November 12, 2008, to continue work. An updated draft will be circulated to Subcommittee members
prior to the November meeting.
October 2, 2008