The USDA Food Safety and Inspection Service (FSIS) collects samples of meat and poultry products to estimate the national prevalence and levels of bacteria of public health concern. Each report is a compilation of data obtained for a particular species or type of animal.
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For example, FSIS conducted the first Raw Chicken Parts Baseline Survey (RCPBS) from January to August 2012.
The RCPBS was designed to determine the presence and the levels of selected bacteria on raw chicken parts produced in federally inspected plants. In addition, FSIS wanted to determine the national prevalence of Salmonella and Campylobacter on raw chicken parts.
Additional goals for this survey were determining if there was a significant difference between production shifts as they related to bacterial levels, and comparing the bacterial presence and levels on raw parts with skin-on versus parts with skin-off.
Relative to qualitative microbiological results, the Salmonella percent positive rate for chicken parts was 26.3 percent and 21.4 percent for Campylobacter.
Using data from this study, FSIS calculated national prevalence estimates for Salmonella and Campylobacter; specifically they calculated the prevalence or weighted average of Salmonella and Campylobacter for all chicken parts. (These national prevalence estimates are different from the percent positives because they are weighted in relation to production volume.)
The estimated national prevalence of Salmonella in chicken parts is 24.02 percent with a 95 percent confidence interval between 19.24 percent and 28.79 percent. The estimated national prevalence of Campylobacter in chicken parts is 21.70 percent with a 95 percent confidence interval between 18.70 percent and 24.69 percent.
“Having a known baseline level is step one to improvement in any process,” Coleman points out. “Now the challenge is clear and industry is responding with ways to reduce levels over time.”
When environmental monitoring came in vogue, it was viewed as a tool to help reduce the prevalent risks that are an issue in nearly every type of food plant, Coleman mentions. “But after years of running these programs, there is a tendency to react less and less to a few isolated positive results,” she says. “So while many companies have embraced environmental monitoring over the past 15 years or so, which is evidenced by the number of environmental swabs we receive to test daily in our laboratories, as an industry we need to figure out better ways to extract actionable information from the sporadic positives that many plants experience.”
“To that end, we are working along with other industry stakeholders to elevate environmental monitoring to the next level through progressive solutions, such as EnviroMap, helping to track and map specific organisms,” Coleman relates.
Will metagenomics techniques impact environmental testing in the future? “Environmental testing will likely be improved by the application of metagenomics techniques,” Coleman predicts, “but I think we have a ways to go to get a good practical application.”
Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics, or community genomics.
There is more work to be done on tracking and investigating foodborne contamination with a focus on prevention of contamination and subsequent recalls, Coleman believes. “We recommend that companies use all of the available tools to uncover issues before a recall becomes necessary,” she notes. “If sporadic pathogen positives are found via an environmental monitoring plan, conducting selective finished product testing before shipping might be a good idea to verify the effectiveness of a specific remediation effort.”
What else will help any such efforts? “We need a way to look at all microorganisms in a sample and then use the information to track them,” Coleman says. “We need to be able to tell if this is the same system we saw last week or a new one. We need to determine how to get to the molecular level with bacterial diagnostics.”